Daily Papers

Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language foundation models, which thrive on substantially larger scales. Furthermore, genome understanding involves numerous downstream genome annotation tasks with inherent data heterogeneity, thereby necessitating more efficient and robust fine-tuning methods tailored for genomics. Here, we present Lingo: Language prefix fIne-tuning for GenOmes. Unlike DNA foundation models, Lingo strategically leverages natural language foundation models' contextual cues, recalibrating their linguistic knowledge to genomic sequences. Lingo further accommodates numerous, heterogeneous downstream fine-tune tasks by an adaptive rank sampling method that prunes and stochastically reintroduces pruned singular vectors within small computational budgets. Adaptive rank sampling outperformed existing fine-tuning methods on all benchmarked 14 genome understanding tasks, while requiring fewer than 2\% of trainable parameters as genomic-specific adapters. Impressively, applying these adapters on natural language foundation models matched or even exceeded the performance of DNA foundation models. Lingo presents a new paradigm of efficient and scalable genome understanding via genomic-specific adapters on language models.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

Understanding the performance of machine learning models across diverse data distributions is critically important for reliable applications. Motivated by this, there is a growing focus on curating benchmark datasets that capture distribution shifts. While valuable, the existing benchmarks are limited in that many of them only contain a small number of shifts and they lack systematic annotation about what is different across different shifts. We present MetaShift--a collection of 12,868 sets of natural images across 410 classes--to address this challenge. We leverage the natural heterogeneity of Visual Genome and its annotations to construct MetaShift. The key construction idea is to cluster images using its metadata, which provides context for each image (e.g. "cats with cars" or "cats in bathroom") that represent distinct data distributions. MetaShift has two important benefits: first, it contains orders of magnitude more natural data shifts than previously available. Second, it provides explicit explanations of what is unique about each of its data sets and a distance score that measures the amount of distribution shift between any two of its data sets. We demonstrate the utility of MetaShift in benchmarking several recent proposals for training models to be robust to data shifts. We find that the simple empirical risk minimization performs the best when shifts are moderate and no method had a systematic advantage for large shifts. We also show how MetaShift can help to visualize conflicts between data subsets during model training.

Despite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering. Cognition is core to tasks that involve not just recognizing, but reasoning about our visual world. However, models used to tackle the rich content in images for cognitive tasks are still being trained using the same datasets designed for perceptual tasks. To achieve success at cognitive tasks, models need to understand the interactions and relationships between objects in an image. When asked "What vehicle is the person riding?", computers will need to identify the objects in an image as well as the relationships riding(man, carriage) and pulling(horse, carriage) in order to answer correctly that "the person is riding a horse-drawn carriage". In this paper, we present the Visual Genome dataset to enable the modeling of such relationships. We collect dense annotations of objects, attributes, and relationships within each image to learn these models. Specifically, our dataset contains over 100K images where each image has an average of 21 objects, 18 attributes, and 18 pairwise relationships between objects. We canonicalize the objects, attributes, relationships, and noun phrases in region descriptions and questions answer pairs to WordNet synsets. Together, these annotations represent the densest and largest dataset of image descriptions, objects, attributes, relationships, and question answers.

Multimodal Large Language Models (MLLMs) have shown promise in a broad range of vision-language tasks with their strong reasoning and generalization capabilities. However, they heavily depend on high-quality data in the Supervised Fine-Tuning (SFT) phase. The existing approaches aim to curate high-quality data via GPT-4V, but they are not scalable due to the commercial nature of GPT-4V and the simplicity of the prompts used to instruct the model. To this end, we devised the FullAnno system, which is a data engine that can generate large-scale, high-quality, and fine-grained image annotations consisting of the category and position of objects, region descriptions, text information, as well as image dense captions. This engine is characterized by its cascade annotation process, which involves multiple expert models and employs rich prompts to instruct LLMs in generating dense image captions. We re-annotated the COCO and Visual Genome datasets using our FullAnno system, tripling the number of object annotations and increasing the length of the original image captions by a factor of 15. Experiments show that the regenerated annotation can significantly enhance the capabilities of LLaVA-v1.5 on several benchmarks. The re-annotated data are available at: https://arcana-project-page.github.io

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates 28 distinct datasets across 7 tasks, with input lengths ranging from 70 to 1000. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with 21 times fewer parameters and approximately 56 times less GPU time in pre-training.

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel with the urgent demand for robust algorithms, deep learning has succeeded in a variety of fields such as vision, speech, and text processing. Yet genomics entails unique challenges to deep learning since we are expecting from deep learning a superhuman intelligence that explores beyond our knowledge to interpret the genome. A powerful deep learning model should rely on insightful utilization of task-specific knowledge. In this paper, we briefly discuss the strengths of different deep learning models from a genomic perspective so as to fit each particular task with a proper deep architecture, and remark on practical considerations of developing modern deep learning architectures for genomics. We also provide a concise review of deep learning applications in various aspects of genomic research, as well as pointing out potential opportunities and obstacles for future genomics applications.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to reduce pesticide use, adaptation to climate change, resistance to heat and drought stresses, or low gluten content of grains. Wheat breeding experiments are documented by a large body of scientific literature and observational data obtained in-field and under controlled conditions. The cross-referencing of complementary information from the literature and observational data is essential to the study of the genotype-phenotype relationship and to the improvement of wheat selection. The scientific literature on genetic marker-assisted selection describes much information about the genotype-phenotype relationship. However, the variety of expressions used to refer to traits and phenotype values in scientific articles is a hinder to finding information and cross-referencing it. When trained adequately by annotated examples, recent text mining methods perform highly in named entity recognition and linking in the scientific domain. While several corpora contain annotations of human and animal phenotypes, currently, no corpus is available for training and evaluating named entity recognition and entity-linking methods in plant phenotype literature. The Triticum aestivum trait Corpus is a new gold standard for traits and phenotypes of wheat. It consists of 540 PubMed references fully annotated for trait, phenotype, and species named entities using the Wheat Trait and Phenotype Ontology and the species taxonomy of the National Center for Biotechnology Information. A study of the performance of tools trained on the Triticum aestivum trait Corpus shows that the corpus is suitable for the training and evaluation of named entity recognition and linking.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation, PAAG, a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a significant increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 22.0% in the immunoglobulin domain) in comparison to the existing model. We anticipate that PAAG will broaden the horizons of protein design by leveraging the knowledge from between textual annotation and proteins.

This paper presents NorNE, a manually annotated corpus of named entities which extends the annotation of the existing Norwegian Dependency Treebank. Comprising both of the official standards of written Norwegian (Bokm{\aa}l and Nynorsk), the corpus contains around 600,000 tokens and annotates a rich set of entity types including persons, organizations, locations, geo-political entities, products, and events, in addition to a class corresponding to nominals derived from names. We here present details on the annotation effort, guidelines, inter-annotator agreement and an experimental analysis of the corpus using a neural sequence labeling architecture.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our Species-Profile Adaptive Collaborative Experts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.

We investigate how to teach large language models (LLMs) to perform scientific reasoning by leveraging expert discussions as a learning signal. Focusing on the genomics domain, we develop an automated pipeline to extract trainable data and introduce Genome-Bench, a new benchmark constructed from over a decade of scientific forum discussions on genome engineering. Our pipeline transforms raw interactions into a reinforcement learning-friendly multiple-choice questions format, supported by 3000+ high-quality question-answer pairs spanning foundational biology, experimental troubleshooting, tool usage, and beyond. We fine-tune an LLM using RL with a rule-based reward signal derived from the synthetic MCQ dataset to enhance domain-specific reasoning. Our results show that reinforcement learning from scientific discussions improves model performance by over 15% compared to the base model on Genome-Bench, narrowing the gap between open-source LLMs and expert-level reasoning. To our knowledge, this is the first end-to-end pipeline for teaching LLMs to reason from scientific discussions, with promising potential for generalization across scientific domains beyond biology.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through continued pretraining and multi-modal alignment, enabling simultaneous comprehension of textual descriptions and protein sequences. Through a thorough analysis of existing model architectures and text-based protein understanding benchmarks, we identify significant data leakage issues present in current benchmarks. Moreover, conventional metrics derived from natural language processing fail to accurately assess the model's performance in this domain. To address these limitations, we reorganize existing datasets and introduce a novel evaluation framework based on biological entities. Motivated by our observation, we propose a retrieval-enhanced method, which significantly outperforms fine-tuned LLMs for protein-to-text generation and shows accuracy and efficiency in training-free scenarios. Our code and data can be seen at https://github.com/IDEA-XL/RAPM.

Data annotation is the labeling or tagging of raw data with relevant information, essential for improving the efficacy of machine learning models. The process, however, is labor-intensive and expensive. The emergence of advanced Large Language Models (LLMs), exemplified by GPT-4, presents an unprecedented opportunity to revolutionize and automate the intricate process of data annotation. While existing surveys have extensively covered LLM architecture, training, and general applications, this paper uniquely focuses on their specific utility for data annotation. This survey contributes to three core aspects: LLM-Based Data Annotation, Assessing LLM-generated Annotations, and Learning with LLM-generated annotations. Furthermore, the paper includes an in-depth taxonomy of methodologies employing LLMs for data annotation, a comprehensive review of learning strategies for models incorporating LLM-generated annotations, and a detailed discussion on primary challenges and limitations associated with using LLMs for data annotation. As a key guide, this survey aims to direct researchers and practitioners in exploring the potential of the latest LLMs for data annotation, fostering future advancements in this critical domain. We provide a comprehensive papers list at https://github.com/Zhen-Tan-dmml/LLM4Annotation.git.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

Data annotation is an essential step for constructing new datasets. However, the conventional approach of data annotation through crowdsourcing is both time-consuming and expensive. In addition, the complexity of this process increases when dealing with low-resource languages owing to the difference in the language pool of crowdworkers. To address these issues, this study proposes an autonomous annotation method by utilizing large language models, which have been recently demonstrated to exhibit remarkable performance. Through our experiments, we demonstrate that the proposed method is not just cost-efficient but also applicable for low-resource language annotation. Additionally, we constructed an image captioning dataset using our approach and are committed to open this dataset for future study. We have opened our source code for further study and reproducibility.

With the advent of artificial intelligence (AI), many researchers are attempting to extract structured information from document-level biomedical literature by fine-tuning large language models (LLMs). However, they face significant challenges such as the need for expensive hardware, like high-performance GPUs and the high labor costs associated with annotating training datasets, especially in biomedical realm. Recent research on LLMs, such as GPT-4 and Llama3, has shown promising performance in zero-shot settings, inspiring us to explore a novel approach to achieve the same results from unannotated full documents using general LLMs with lower hardware and labor costs. Our approach combines two major stages: named entity recognition (NER) and relation extraction (RE). NER identifies chemical, disease and gene entities from the document with synonym and hypernym extraction using an LLM with a crafted prompt. RE extracts relations between entities based on predefined relation schemas and prompts. To enhance the effectiveness of prompt, we propose a five-part template structure and a scenario-based prompt design principles, along with evaluation method to systematically assess the prompts. Finally, we evaluated our approach against fine-tuning and pre-trained models on two biomedical datasets: ChemDisGene and CDR. The experimental results indicate that our proposed method can achieve comparable accuracy levels to fine-tuning and pre-trained models but with reduced human and hardware expenses.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

In this paper, we present a simple and efficient GEC sequence tagger using a Transformer encoder. Our system is pre-trained on synthetic data and then fine-tuned in two stages: first on errorful corpora, and second on a combination of errorful and error-free parallel corpora. We design custom token-level transformations to map input tokens to target corrections. Our best single-model/ensemble GEC tagger achieves an F_{0.5} of 65.3/66.5 on CoNLL-2014 (test) and F_{0.5} of 72.4/73.6 on BEA-2019 (test). Its inference speed is up to 10 times as fast as a Transformer-based seq2seq GEC system. The code and trained models are publicly available.

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127

The NLP pipeline has evolved dramatically in the last few years. The first step in the pipeline is to find suitable annotated datasets to evaluate the tasks we are trying to solve. Unfortunately, most of the published datasets lack metadata annotations that describe their attributes. Not to mention, the absence of a public catalogue that indexes all the publicly available datasets related to specific regions or languages. When we consider low-resource dialectical languages, for example, this issue becomes more prominent. In this paper we create Masader, the largest public catalogue for Arabic NLP datasets, which consists of 200 datasets annotated with 25 attributes. Furthermore, We develop a metadata annotation strategy that could be extended to other languages. We also make remarks and highlight some issues about the current status of Arabic NLP datasets and suggest recommendations to address them.

Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over 10 years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved F_1 scores of 88.6, 95.0, and 55.8 per cent in the mention extraction of procedures, drugs, and diseases, respectively.

Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at https://github.com/gersteinlab/biocoder.

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.

Recent advancements in machine learning have significantly improved the identification of disease-associated genes from gene expression datasets. However, these processes often require extensive expertise and manual effort, limiting their scalability. Large Language Model (LLM)-based agents have shown promise in automating these tasks due to their increasing problem-solving abilities. To support the evaluation and development of such methods, we introduce GenoTEX, a benchmark dataset for the automated analysis of gene expression data. GenoTEX provides annotated code and results for solving a wide range of gene identification problems, encompassing dataset selection, preprocessing, and statistical analysis, in a pipeline that follows computational genomics standards. The benchmark includes expert-curated annotations from bioinformaticians to ensure accuracy and reliability. To provide baselines for these tasks, we present GenoAgent, a team of LLM-based agents that adopt a multi-step programming workflow with flexible self-correction, to collaboratively analyze gene expression datasets. Our experiments demonstrate the potential of LLM-based methods in analyzing genomic data, while error analysis highlights the challenges and areas for future improvement. We propose GenoTEX as a promising resource for benchmarking and enhancing automated methods for gene expression data analysis. The benchmark is available at https://github.com/Liu-Hy/GenoTex.

The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach to decoding the genome. As GFMs scale up and reshape the landscape of AI-driven genomics, the field faces an urgent need for rigorous and reproducible evaluation. We present OmniGenBench, a modular benchmarking platform designed to unify the data, model, benchmarking, and interpretability layers across GFMs. OmniGenBench enables standardized, one-command evaluation of any GFM across five benchmark suites, with seamless integration of over 31 open-source models. Through automated pipelines and community-extensible features, the platform addresses critical reproducibility challenges, including data transparency, model interoperability, benchmark fragmentation, and black-box interpretability. OmniGenBench aims to serve as foundational infrastructure for reproducible genomic AI research, accelerating trustworthy discovery and collaborative innovation in the era of genome-scale modeling.

This paper explores the use of open generative Large Language Models (LLMs) for annotation tasks in the social sciences. The study highlights the challenges associated with proprietary models, such as limited reproducibility and privacy concerns, and advocates for the adoption of open (source) models that can be operated on independent devices. Two examples of annotation tasks, sentiment analysis in tweets and identification of leisure activities in childhood aspirational essays are provided. The study evaluates the performance of different prompting strategies and models (neural-chat-7b-v3-2, Starling-LM-7B-alpha, openchat_3.5, zephyr-7b-alpha and zephyr-7b-beta). The results indicate the need for careful validation and tailored prompt engineering. The study highlights the advantages of open models for data privacy and reproducibility.

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Diderot's Encyclop\'edie is a reference work from XVIIIth century in Europe that aimed at collecting the knowledge of its era. Wikipedia has the same ambition with a much greater scope. However, the lack of digital connection between the two encyclopedias may hinder their comparison and the study of how knowledge has evolved. A key element of Wikipedia is Wikidata that backs the articles with a graph of structured data. In this paper, we describe the annotation of more than 10,300 of the Encyclop\'edie entries with Wikidata identifiers enabling us to connect these entries to the graph. We considered geographic and human entities. The Encyclop\'edie does not contain biographic entries as they mostly appear as subentries of locations. We extracted all the geographic entries and we completely annotated all the entries containing a description of human entities. This represents more than 2,600 links referring to locations or human entities. In addition, we annotated more than 9,500 entries having a geographic content only. We describe the annotation process as well as application examples. This resource is available at https://github.com/pnugues/encyclopedie_1751

Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

Domain-specific named entity recognition (NER) on Computer Science (CS) scholarly articles is an information extraction task that is arguably more challenging for the various annotation aims that can beset the task and has been less studied than NER in the general domain. Given that significant progress has been made on NER, we believe that scholarly domain-specific NER will receive increasing attention in the years to come. Currently, progress on CS NER -- the focus of this work -- is hampered in part by its recency and the lack of a standardized annotation aim for scientific entities/terms. This work proposes a standardized task by defining a set of seven contribution-centric scholarly entities for CS NER viz., research problem, solution, resource, language, tool, method, and dataset. Following which, its main contributions are: combines existing CS NER resources that maintain their annotation focus on the set or subset of contribution-centric scholarly entities we consider; further, noting the need for big data to train neural NER models, this work additionally supplies thousands of contribution-centric entity annotations from article titles and abstracts, thus releasing a cumulative large novel resource for CS NER; and, finally, trains a sequence labeling CS NER model inspired after state-of-the-art neural architectures from the general domain NER task. Throughout the work, several practical considerations are made which can be useful to information technology designers of the digital libraries.

This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts and over 350,000 linked mentions), as well as the size of the concept ontology (over 3 million concepts from UMLS 2017) and its broad coverage of biomedical disciplines. In addition to the full corpus, a sub-corpus of MedMentions is also presented, comprising annotations for a subset of UMLS 2017 targeted towards document retrieval. To encourage research in Biomedical Named Entity Recognition and Linking, data splits for training and testing are included in the release, and a baseline model and its metrics for entity linking are also described.

The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

News headline generation is a crucial task in increasing productivity for both the readers and producers of news. This task can easily be aided by automated News headline-generation models. However, the presence of irrelevant headlines in scraped news articles results in sub-optimal performance of generation models. We propose that relevance-based headline classification can greatly aid the task of generating relevant headlines. Relevance-based headline classification involves categorizing news headlines based on their relevance to the corresponding news articles. While this task is well-established in English, it remains under-explored in low-resource languages like Telugu due to a lack of annotated data. To address this gap, we present TeClass, the first-ever human-annotated Telugu news headline classification dataset, containing 78,534 annotations across 26,178 article-headline pairs. We experiment with various baseline models and provide a comprehensive analysis of their results. We further demonstrate the impact of this work by fine-tuning various headline generation models using TeClass dataset. The headlines generated by the models fine-tuned on highly relevant article-headline pairs, showed about a 5 point increment in the ROUGE-L scores. To encourage future research, the annotated dataset as well as the annotation guidelines will be made publicly available.

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for their type (review, study, clinical case, other), domain (clinical, biomedical, other), and educational quality. The educational quality score (rated 1 to 5) estimates how useful a paragraph is for college-level learning. These annotations are then used to fine-tune a small language model, which propagates the labels across the full PMC-OA corpus. The resulting metadata allows us to extract refined subsets, including 2M clinical case paragraphs with over 450K high-quality ones from articles with commercial-use licenses, and to construct several variants via quality filtering and domain upsampling. Clinical text is typically difficult to access due to privacy constraints, as hospital records cannot be publicly shared. Hence, our dataset provides an alternative large-scale, openly available collection of clinical cases from PubMed, making it a valuable resource for biomedical and clinical NLP. Preliminary continual-pretraining experiments with OLMo2 suggest these curated subsets enable targeted improvements, with clinical upsampling boosting performance by ~5% on MMLU ProfMed and educational quality filtering improving MedQA and MedMCQA by ~1%. Combinations of these techniques led to faster convergence, reaching same performance with a third of training tokens, indicating potential for more efficient and effective biomedical pretraining strategies.

Long-range dependencies are critical for understanding genomic structure and function, yet most conventional methods struggle with them. Widely adopted transformer-based models, while excelling at short-context tasks, are limited by the attention module's quadratic computational complexity and inability to extrapolate to sequences longer than those seen in training. In this work, we explore State Space Models (SSMs) as a promising alternative by benchmarking two SSM-inspired architectures, Caduceus and Hawk, on long-range genomics modeling tasks under conditions parallel to a 50M parameter transformer baseline. We discover that SSMs match transformer performance and exhibit impressive zero-shot extrapolation across multiple tasks, handling contexts 10 to 100 times longer than those seen during training, indicating more generalizable representations better suited for modeling the long and complex human genome. Moreover, we demonstrate that these models can efficiently process sequences of 1M tokens on a single GPU, allowing for modeling entire genomic regions at once, even in labs with limited compute. Our findings establish SSMs as efficient and scalable for long-context genomic analysis.

Recent approaches to large language model (LLM) alignment typically require millions of human annotations or rely on external aligned models for synthetic data generation. This paper introduces ALMA: Alignment with Minimal Annotation, demonstrating that effective alignment can be achieved using only 9,000 labeled examples -- less than 1% of conventional approaches. ALMA generates large amounts of high-quality synthetic alignment data through new techniques: diverse prompt synthesis via few-shot learning, diverse response generation with multiple model checkpoints, and judge (reward model) enhancement through score aggregation and self-distillation. Using only a pretrained Llama3 base model, 5,000 SFT examples, and 4,000 judge annotations, ALMA achieves performance close to Llama3-Instruct across diverse alignment benchmarks (e.g., 0.1% difference on AlpacaEval 2.0 score). These results are achieved with a multi-round, self-bootstrapped data synthesis and training recipe that continues to improve for 10 rounds, surpassing the typical 3-round ceiling of previous methods. These results suggest that base models already possess sufficient knowledge for effective alignment, and that synthetic data generation methods can expose it.

Scientific documents record research findings and valuable human knowledge, comprising a vast corpus of high-quality data. Leveraging multi-modality data extracted from these documents and assessing large models' abilities to handle scientific document-oriented tasks is therefore meaningful. Despite promising advancements, large models still perform poorly on multi-page scientific document extraction and understanding tasks, and their capacity to process within-document data formats such as charts and equations remains under-explored. To address these issues, we present DocGenome, a structured document benchmark constructed by annotating 500K scientific documents from 153 disciplines in the arXiv open-access community, using our custom auto-labeling pipeline. DocGenome features four key characteristics: 1) Completeness: It is the first dataset to structure data from all modalities including 13 layout attributes along with their LaTeX source codes. 2) Logicality: It provides 6 logical relationships between different entities within each scientific document. 3) Diversity: It covers various document-oriented tasks, including document classification, visual grounding, document layout detection, document transformation, open-ended single-page QA and multi-page QA. 4) Correctness: It undergoes rigorous quality control checks conducted by a specialized team. We conduct extensive experiments to demonstrate the advantages of DocGenome and objectively evaluate the performance of large models on our benchmark.

In this paper we address the scarcity of annotated data for NArabizi, a Romanized form of North African Arabic used mostly on social media, which poses challenges for Natural Language Processing (NLP). We introduce an enriched version of NArabizi Treebank (Seddah et al., 2020) with three main contributions: the addition of two novel annotation layers (named entity recognition and offensive language detection) and a re-annotation of the tokenization, morpho-syntactic and syntactic layers that ensure annotation consistency. Our experimental results, using different tokenization schemes, showcase the value of our contributions and highlight the impact of working with non-gold tokenization for NER and dependency parsing. To facilitate future research, we make these annotations publicly available. Our enhanced NArabizi Treebank paves the way for creating sophisticated language models and NLP tools for this under-represented language.

Pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art performance in natural language processing (NLP) tasks. Recently, BERT has been adapted to the biomedical domain. Despite the effectiveness, these models have hundreds of millions of parameters and are computationally expensive when applied to large-scale NLP applications. We hypothesized that the number of parameters of the original BERT can be dramatically reduced with minor impact on performance. In this study, we present Bioformer, a compact BERT model for biomedical text mining. We pretrained two Bioformer models (named Bioformer8L and Bioformer16L) which reduced the model size by 60% compared to BERTBase. Bioformer uses a biomedical vocabulary and was pre-trained from scratch on PubMed abstracts and PubMed Central full-text articles. We thoroughly evaluated the performance of Bioformer as well as existing biomedical BERT models including BioBERT and PubMedBERT on 15 benchmark datasets of four different biomedical NLP tasks: named entity recognition, relation extraction, question answering and document classification. The results show that with 60% fewer parameters, Bioformer16L is only 0.1% less accurate than PubMedBERT while Bioformer8L is 0.9% less accurate than PubMedBERT. Both Bioformer16L and Bioformer8L outperformed BioBERTBase-v1.1. In addition, Bioformer16L and Bioformer8L are 2-3 fold as fast as PubMedBERT/BioBERTBase-v1.1. Bioformer has been successfully deployed to PubTator Central providing gene annotations over 35 million PubMed abstracts and 5 million PubMed Central full-text articles. We make Bioformer publicly available via https://github.com/WGLab/bioformer, including pre-trained models, datasets, and instructions for downstream use.

The task of annotating data into concise summaries poses a significant challenge across various domains, frequently requiring the allocation of significant time and specialized knowledge by human experts. Despite existing efforts to use large language models for annotation tasks, significant problems such as limited applicability to unlabeled data, the absence of self-supervised methods, and the lack of focus on complex structured data still persist. In this work, we propose a GPT self-supervision annotation method, which embodies a generating-recovering paradigm that leverages the one-shot learning capabilities of the Generative Pretrained Transformer (GPT). The proposed approach comprises a one-shot tuning phase followed by a generation phase. In the one-shot tuning phase, we sample a data from the support set as part of the prompt for GPT to generate a textual summary, which is then used to recover the original data. The alignment score between the recovered and original data serves as a self-supervision navigator to refine the process. In the generation stage, the optimally selected one-shot sample serves as a template in the prompt and is applied to generating summaries from challenging datasets. The annotation performance is evaluated by tuning several human feedback reward networks and by calculating alignment scores between original and recovered data at both sentence and structure levels. Our self-supervised annotation method consistently achieves competitive scores, convincingly demonstrating its robust strength in various data-to-summary annotation tasks.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

Training and evaluating language models increasingly requires the construction of meta-datasets --diverse collections of curated data with clear provenance. Natural language prompting has recently lead to improved zero-shot generalization by transforming existing, supervised datasets into a diversity of novel pretraining tasks, highlighting the benefits of meta-dataset curation. While successful in general-domain text, translating these data-centric approaches to biomedical language modeling remains challenging, as labeled biomedical datasets are significantly underrepresented in popular data hubs. To address this challenge, we introduce BigBIO a community library of 126+ biomedical NLP datasets, currently covering 12 task categories and 10+ languages. BigBIO facilitates reproducible meta-dataset curation via programmatic access to datasets and their metadata, and is compatible with current platforms for prompt engineering and end-to-end few/zero shot language model evaluation. We discuss our process for task schema harmonization, data auditing, contribution guidelines, and outline two illustrative use cases: zero-shot evaluation of biomedical prompts and large-scale, multi-task learning. BigBIO is an ongoing community effort and is available at https://github.com/bigscience-workshop/biomedical

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., increases, improves) capturing diet-microbiome associations. We also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating 40+ protein-related datasets and 40+ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.

Motivation: Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters, limited flexibility of classification-based methods, and the lack of systematic evaluation metrics for protein Q&A systems. To tackle these issues, we propose the Prot2Chat framework. Results: We modified ProteinMPNN to encode protein sequence and structural information in a unified way. We used a large language model (LLM) to encode questions into vectors and developed a protein-text adapter to compress protein information into virtual tokens based on these vectors, achieving the early fusion of text and protein information. Finally, the same LLM reads the virtual tokens and the questions to generate answers. To optimize training efficiency, we froze the encoder and employed Low-Rank Adaptation (LoRA) techniques for the LLM. Experiments on two datasets show that both automated metrics and expert evaluations demonstrate the superior performance of our model, and zero-shot prediction results highlight its generalization ability. The models and codes are available at https://github.com/ wangzc1233/Prot2Chat. Contact: [email protected] or [email protected] Key words: Protein Q&A, Early-Fusion, LLM

Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments (reads) of the individual microbes can be obtained, which through assembly graphs can be combined into long contiguous DNA sequences (contigs). Given the complexity of microbial communities, single contig microbial genomes are rarely obtained. Instead, contigs are eventually clustered into bins, with each bin ideally making up a full genome. This process is referred to as metagenomic binning. Current state-of-the-art techniques for metagenomic binning rely only on the local features for the individual contigs. These techniques therefore fail to exploit the similarities between contigs as encoded by the assembly graph, in which the contigs are organized. In this paper, we propose to use Graph Neural Networks (GNNs) to leverage the assembly graph when learning contig representations for metagenomic binning. Our method, VaeG-Bin, combines variational autoencoders for learning latent representations of the individual contigs, with GNNs for refining these representations by taking into account the neighborhood structure of the contigs in the assembly graph. We explore several types of GNNs and demonstrate that VaeG-Bin recovers more high-quality genomes than other state-of-the-art binners on both simulated and real-world datasets.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models nucleotide evolution on phylogenetic trees using multispecies whole-genome alignments. Our approach integrates an alignment into the loss function during training but does not require it for making predictions, thereby enhancing the model's applicability. We applied this framework to train PhyloGPN, a model that excels at predicting functionally disruptive variants from a single sequence alone and demonstrates strong transfer learning capabilities.

Relevant information in documents is often summarized in tables, helping the reader to identify useful facts. Most benchmark datasets support either document layout analysis or table understanding, but lack in providing data to apply both tasks in a unified way. We define the task of Contextualized Table Extraction (CTE), which aims to extract and define the structure of tables considering the textual context of the document. The dataset comprises 75k fully annotated pages of scientific papers, including more than 35k tables. Data are gathered from PubMed Central, merging the information provided by annotations in the PubTables-1M and PubLayNet datasets. The dataset can support CTE and adds new classes to the original ones. The generated annotations can be used to develop end-to-end pipelines for various tasks, including document layout analysis, table detection, structure recognition, and functional analysis. We formally define CTE and evaluation metrics, showing which subtasks can be tackled, describing advantages, limitations, and future works of this collection of data. Annotations and code will be accessible a https://github.com/AILab-UniFI/cte-dataset.

In the absence of readily available labeled data for a given sequence labeling task and language, annotation projection has been proposed as one of the possible strategies to automatically generate annotated data. Annotation projection has often been formulated as the task of transporting, on parallel corpora, the labels pertaining to a given span in the source language into its corresponding span in the target language. In this paper we present T-Projection, a novel approach for annotation projection that leverages large pretrained text-to-text language models and state-of-the-art machine translation technology. T-Projection decomposes the label projection task into two subtasks: (i) A candidate generation step, in which a set of projection candidates using a multilingual T5 model is generated and, (ii) a candidate selection step, in which the generated candidates are ranked based on translation probabilities. We conducted experiments on intrinsic and extrinsic tasks in 5 Indo-European and 8 low-resource African languages. We demostrate that T-projection outperforms previous annotation projection methods by a wide margin. We believe that T-Projection can help to automatically alleviate the lack of high-quality training data for sequence labeling tasks. Code and data are publicly available.

We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the https://baskargroup.github.io/Arboretum/{project website} for links to our data, models, and code.

We describe a dataset developed for Named Entity Recognition in German federal court decisions. It consists of approx. 67,000 sentences with over 2 million tokens. The resource contains 54,000 manually annotated entities, mapped to 19 fine-grained semantic classes: person, judge, lawyer, country, city, street, landscape, organization, company, institution, court, brand, law, ordinance, European legal norm, regulation, contract, court decision, and legal literature. The legal documents were, furthermore, automatically annotated with more than 35,000 TimeML-based time expressions. The dataset, which is available under a CC-BY 4.0 license in the CoNNL-2002 format, was developed for training an NER service for German legal documents in the EU project Lynx.

This paper presents a new challenging information extraction task in the domain of materials science. We develop an annotation scheme for marking information on experiments related to solid oxide fuel cells in scientific publications, such as involved materials and measurement conditions. With this paper, we publish our annotation guidelines, as well as our SOFC-Exp corpus consisting of 45 open-access scholarly articles annotated by domain experts. A corpus and an inter-annotator agreement study demonstrate the complexity of the suggested named entity recognition and slot filling tasks as well as high annotation quality. We also present strong neural-network based models for a variety of tasks that can be addressed on the basis of our new data set. On all tasks, using BERT embeddings leads to large performance gains, but with increasing task complexity, adding a recurrent neural network on top seems beneficial. Our models will serve as competitive baselines in future work, and analysis of their performance highlights difficult cases when modeling the data and suggests promising research directions.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

We release the Nemotron-4 340B model family, including Nemotron-4-340B-Base, Nemotron-4-340B-Instruct, and Nemotron-4-340B-Reward. Our models are open access under the NVIDIA Open Model License Agreement, a permissive model license that allows distribution, modification, and use of the models and its outputs. These models perform competitively to open access models on a wide range of evaluation benchmarks, and were sized to fit on a single DGX H100 with 8 GPUs when deployed in FP8 precision. We believe that the community can benefit from these models in various research studies and commercial applications, especially for generating synthetic data to train smaller language models. Notably, over 98% of data used in our model alignment process is synthetically generated, showcasing the effectiveness of these models in generating synthetic data. To further support open research and facilitate model development, we are also open-sourcing the synthetic data generation pipeline used in our model alignment process.

A hallmark of human innovation is the process of recombination -- creating original ideas by integrating elements of existing mechanisms and concepts. In this work, we automatically mine the scientific literature and build CHIMERA: a large-scale knowledge base (KB) of recombination examples. CHIMERA can be used to empirically explore at scale how scientists recombine concepts and take inspiration from different areas, or to train supervised machine learning models that learn to predict new creative cross-domain directions. To build this KB, we present a novel information extraction task of extracting recombination from scientific paper abstracts, collect a high-quality corpus of hundreds of manually annotated abstracts, and use it to train an LLM-based extraction model. The model is applied to a large corpus of papers in the AI domain, yielding a KB of over 28K recombination examples. We analyze CHIMERA to explore the properties of recombination in different subareas of AI. Finally, we train a scientific hypothesis generation model using the KB, which predicts new recombination directions that real-world researchers find inspiring. Our data and code are available at https://github.cs.huji.ac.il/tomhope-lab/CHIMERA

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Understanding causal narratives communicated in clinical notes can help make strides towards personalized healthcare. Extracted causal information from clinical notes can be combined with structured EHR data such as patients' demographics, diagnoses, and medications. This will enhance healthcare providers' ability to identify aspects of a patient's story communicated in the clinical notes and help make more informed decisions. In this work, we propose annotation guidelines, develop an annotated corpus and provide baseline scores to identify types and direction of causal relations between a pair of biomedical concepts in clinical notes; communicated implicitly or explicitly, identified either in a single sentence or across multiple sentences. We annotate a total of 2714 de-identified examples sampled from the 2018 n2c2 shared task dataset and train four different language model based architectures. Annotation based on our guidelines achieved a high inter-annotator agreement i.e. Fleiss' kappa (kappa) score of 0.72, and our model for identification of causal relations achieved a macro F1 score of 0.56 on the test data. The high inter-annotator agreement for clinical text shows the quality of our annotation guidelines while the provided baseline F1 score sets the direction for future research towards understanding narratives in clinical texts.

Proteins are essential to life's processes, underpinning evolution and diversity. Advances in sequencing technology have revealed millions of proteins, underscoring the need for sophisticated pre-trained protein models for biological analysis and AI development. Facebook's ESM2, the most advanced protein language model to date, leverages a masked prediction task for unsupervised learning, crafting amino acid representations with notable biochemical accuracy. Yet, it lacks in delivering functional protein insights, signaling an opportunity for enhancing representation quality.Our study addresses this gap by incorporating protein family classification into ESM2's training.This approach, augmented with Community Propagation-Based Clustering Algorithm, improves global protein representations, while a contextual prediction task fine-tunes local amino acid accuracy. Significantly, our model achieved state-of-the-art results in several downstream experiments, demonstrating the power of combining global and local methodologies to substantially boost protein representation quality.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

Scientific article summarization is challenging: large, annotated corpora are not available, and the summary should ideally include the article's impacts on research community. This paper provides novel solutions to these two challenges. We 1) develop and release the first large-scale manually-annotated corpus for scientific papers (on computational linguistics) by enabling faster annotation, and 2) propose summarization methods that integrate the authors' original highlights (abstract) and the article's actual impacts on the community (citations), to create comprehensive, hybrid summaries. We conduct experiments to demonstrate the efficacy of our corpus in training data-driven models for scientific paper summarization and the advantage of our hybrid summaries over abstracts and traditional citation-based summaries. Our large annotated corpus and hybrid methods provide a new framework for scientific paper summarization research.

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how very large-scale models and data play a role in effective protein model development. We introduce a suite of protein language models, named ProGen2, that are scaled up to 6.4B parameters and trained on different sequence datasets drawn from over a billion proteins from genomic, metagenomic, and immune repertoire databases. ProGen2 models show state-of-the-art performance in capturing the distribution of observed evolutionary sequences, generating novel viable sequences, and predicting protein fitness without additional finetuning. As large model sizes and raw numbers of protein sequences continue to become more widely accessible, our results suggest that a growing emphasis needs to be placed on the data distribution provided to a protein sequence model. We release the ProGen2 models and code at https://github.com/salesforce/progen.

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

We introduce S2ORC, a large corpus of 81.1M English-language academic papers spanning many academic disciplines. The corpus consists of rich metadata, paper abstracts, resolved bibliographic references, as well as structured full text for 8.1M open access papers. Full text is annotated with automatically-detected inline mentions of citations, figures, and tables, each linked to their corresponding paper objects. In S2ORC, we aggregate papers from hundreds of academic publishers and digital archives into a unified source, and create the largest publicly-available collection of machine-readable academic text to date. We hope this resource will facilitate research and development of tools and tasks for text mining over academic text.

The vast majority of existing datasets for Named Entity Recognition (NER) are built primarily on news, research papers and Wikipedia with a few exceptions, created from historical and literary texts. What is more, English is the main source for data for further labelling. This paper aims to fill in multiple gaps by creating a novel dataset "Razmecheno", gathered from the diary texts of the project "Prozhito" in Russian. Our dataset is of interest for multiple research lines: literary studies of diary texts, transfer learning from other domains, low-resource or cross-lingual named entity recognition. Razmecheno comprises 1331 sentences and 14119 tokens, sampled from diaries, written during the Perestroika. The annotation schema consists of five commonly used entity tags: person, characteristics, location, organisation, and facility. The labelling is carried out on the crowdsourcing platfrom Yandex.Toloka in two stages. First, workers selected sentences, which contain an entity of particular type. Second, they marked up entity spans. As a result 1113 entities were obtained. Empirical evaluation of Razmecheno is carried out with off-the-shelf NER tools and by fine-tuning pre-trained contextualized encoders. We release the annotated dataset for open access.

We present the development of a dataset for Kazakh named entity recognition. The dataset was built as there is a clear need for publicly available annotated corpora in Kazakh, as well as annotation guidelines containing straightforward--but rigorous--rules and examples. The dataset annotation, based on the IOB2 scheme, was carried out on television news text by two native Kazakh speakers under the supervision of the first author. The resulting dataset contains 112,702 sentences and 136,333 annotations for 25 entity classes. State-of-the-art machine learning models to automatise Kazakh named entity recognition were also built, with the best-performing model achieving an exact match F1-score of 97.22% on the test set. The annotated dataset, guidelines, and codes used to train the models are freely available for download under the CC BY 4.0 licence from https://github.com/IS2AI/KazNERD.

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.

With the release of ever more capable large language models (LLMs), researchers in NLP and related disciplines have started to explore the usability of LLMs for a wide variety of different annotation tasks. Very recently, a lot of this attention has shifted to tasks that are subjective in nature. Given that the latest generations of LLMs have digested and encoded extensive knowledge about different human subpopulations and individuals, the hope is that these models can be trained, tuned or prompted to align with a wide range of different human perspectives. While researchers already evaluate the success of this alignment via surveys and tests, there is a lack of resources to evaluate the alignment on what oftentimes matters the most in NLP; the actual downstream tasks. To fill this gap we present SubData, a Python library that offers researchers working on topics related to subjectivity in annotation tasks a convenient way of collecting, combining and using a range of suitable datasets.

Inspired by the great success of Masked Language Modeling (MLM) in the natural language domain, the paradigm of self-supervised pre-training and fine-tuning has also achieved remarkable progress in the field of DNA sequence modeling. However, previous methods often relied on massive pre-training data or large-scale base models with huge parameters, imposing a significant computational burden. To address this, many works attempted to use more compact models to achieve similar outcomes but still fell short by a considerable margin. In this work, we propose a Hybrid Architecture Distillation (HAD) approach, leveraging both distillation and reconstruction tasks for more efficient and effective pre-training. Specifically, we employ the NTv2-500M as the teacher model and devise a grouping masking strategy to align the feature embeddings of visible tokens while concurrently reconstructing the invisible tokens during MLM pre-training. To validate the effectiveness of our proposed method, we conducted comprehensive experiments on the Nucleotide Transformer Benchmark and Genomic Benchmark. Compared to models with similar parameters, our model achieved excellent performance. More surprisingly, it even surpassed the distillation ceiling-teacher model on some sub-tasks, which is more than 500 times larger. Lastly, we utilize t-SNE for more intuitive visualization, which shows that our model can gain a sophisticated understanding of the intrinsic representation pattern in genomic sequences.

A database of images of approximately 960 unique plants belonging to 12 species at several growth stages is made publicly available. It comprises annotated RGB images with a physical resolution of roughly 10 pixels per mm. To standardise the evaluation of classification results obtained with the database, a benchmark based on f_{1} scores is proposed. The dataset is available at https://vision.eng.au.dk/plant-seedlings-dataset

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

Named Entity Recognition (NER) is a foundational NLP task that aims to provide class labels like Person, Location, Organisation, Time, and Number to words in free text. Named Entities can also be multi-word expressions where the additional I-O-B annotation information helps label them during the NER annotation process. While English and European languages have considerable annotated data for the NER task, Indian languages lack on that front -- both in terms of quantity and following annotation standards. This paper releases a significantly sized standard-abiding Hindi NER dataset containing 109,146 sentences and 2,220,856 tokens, annotated with 11 tags. We discuss the dataset statistics in all their essential detail and provide an in-depth analysis of the NER tag-set used with our data. The statistics of tag-set in our dataset show a healthy per-tag distribution, especially for prominent classes like Person, Location and Organisation. Since the proof of resource-effectiveness is in building models with the resource and testing the model on benchmark data and against the leader-board entries in shared tasks, we do the same with the aforesaid data. We use different language models to perform the sequence labelling task for NER and show the efficacy of our data by performing a comparative evaluation with models trained on another dataset available for the Hindi NER task. Our dataset helps achieve a weighted F1 score of 88.78 with all the tags and 92.22 when we collapse the tag-set, as discussed in the paper. To the best of our knowledge, no available dataset meets the standards of volume (amount) and variability (diversity), as far as Hindi NER is concerned. We fill this gap through this work, which we hope will significantly help NLP for Hindi. We release this dataset with our code and models at https://github.com/cfiltnlp/HiNER

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and reasoning on textbook-style science questions, but few if any benchmarks are designed to evaluate language model performance on practical tasks required for scientific research, such as literature search, protocol planning, and data analysis. As a step toward building such benchmarks, we introduce the Language Agent Biology Benchmark (LAB-Bench), a broad dataset of over 2,400 multiple choice questions for evaluating AI systems on a range of practical biology research capabilities, including recall and reasoning over literature, interpretation of figures, access and navigation of databases, and comprehension and manipulation of DNA and protein sequences. Importantly, in contrast to previous scientific benchmarks, we expect that an AI system that can achieve consistently high scores on the more difficult LAB-Bench tasks would serve as a useful assistant for researchers in areas such as literature search and molecular cloning. As an initial assessment of the emergent scientific task capabilities of frontier language models, we measure performance of several against our benchmark and report results compared to human expert biology researchers. We will continue to update and expand LAB-Bench over time, and expect it to serve as a useful tool in the development of automated research systems going forward. A public subset of LAB-Bench is available for use at the following URL: https://huggingface.co/datasets/futurehouse/lab-bench

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

We present HaPy-Bug, a curated dataset of 793 Python source code commits associated with bug fixes, with each line of code annotated by three domain experts. The annotations offer insights into the purpose of modified files, changes at the line level, and reviewers' confidence levels. We analyze HaPy-Bug to examine the distribution of file purposes, types of modifications, and tangled changes. Additionally, we explore its potential applications in bug tracking, the analysis of bug-fixing practices, and the development of repository analysis tools. HaPy-Bug serves as a valuable resource for advancing research in software maintenance and security.

Biological protocols are fundamental to reproducible and safe life science research. While LLMs excel on general tasks, their systematic evaluation on these highly specialized, accuracy-critical, and inherently procedural texts remains limited. In this work, we present BioProBench, the first large-scale, integrated multi-task benchmark for biological protocol understanding and reasoning. While limited benchmarks have touched upon specific aspects like protocol QA, BioProBench provides a comprehensive suite of five core tasks: Protocol Question Answering, Step Ordering, Error Correction, Protocol Generation, and Protocol Reasoning, enabling a holistic evaluation of LLMs on procedural biological texts. Built upon 27K original protocols, it yields nearly 556K high-quality structured instances. We evaluate 12 mainstream open/closed-source LLMs on BioProBench. Experimental results reveal that while top models preform well on surface understanding tasks, struggle significantly with deep reasoning and structured generation tasks like ordering and generation. Furthermore, model comparisons reveal diverse performance: certain open-source models approach closed-source levels on some tasks, yet bio-specific small models lag behind general LLMs, indicating limitations on complex procedural content. Overall, our findings underscore that procedural reasoning within biological protocols represents a significant challenge for current LLMs. BioProBench serves as a standardized framework to diagnose these specific limitations and guide the development of AI systems better equipped for safely automating complex scientific procedures. The code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/GreatCaptainNemo/BioProBench.

The process of annotating data within the legal sector is filled with distinct challenges that differ from other fields, primarily due to the inherent complexities of legal language and documentation. The initial task usually involves selecting an appropriate raw dataset that captures the intricate aspects of legal texts. Following this, extracting text becomes a complicated task, as legal documents often have complex structures, footnotes, references, and unique terminology. The importance of data cleaning is magnified in this context, ensuring that redundant information is eliminated while maintaining crucial legal details and context. Creating comprehensive yet straightforward annotation guidelines is imperative, as these guidelines serve as the road map for maintaining uniformity and addressing the subtle nuances of legal terminology. Another critical aspect is the involvement of legal professionals in the annotation process. Their expertise is valuable in ensuring that the data not only remains contextually accurate but also adheres to prevailing legal standards and interpretations. This paper provides an expanded view of these challenges and aims to offer a foundational understanding and guidance for researchers and professionals engaged in legal data annotation projects. In addition, we provide links to our created and fine-tuned datasets and language models. These resources are outcomes of our discussed projects and solutions to challenges faced while working on them.

Named entity recognition is one of the cornerstones of Danish NLP, essential for language technology applications within both industry and research. However, Danish NER is inhibited by a lack of available datasets. As a consequence, no current models are capable of fine-grained named entity recognition, nor have they been evaluated for potential generalizability issues across datasets and domains. To alleviate these limitations, this paper introduces: 1) DANSK: a named entity dataset providing for high-granularity tagging as well as within-domain evaluation of models across a diverse set of domains; 2) DaCy 2.6.0 that includes three generalizable models with fine-grained annotation; and 3) an evaluation of current state-of-the-art models' ability to generalize across domains. The evaluation of existing and new models revealed notable performance discrepancies across domains, which should be addressed within the field. Shortcomings of the annotation quality of the dataset and its impact on model training and evaluation are also discussed. Despite these limitations, we advocate for the use of the new dataset DANSK alongside further work on the generalizability within Danish NER.

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks, and find that BioCLIP consistently and substantially outperforms existing baselines (by 17% to 20% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. Our code, models and data will be made available at https://github.com/Imageomics/bioclip.

Recently, Stitchable Neural Networks (SN-Net) is proposed to stitch some pre-trained networks for quickly building numerous networks with different complexity and performance trade-offs. In this way, the burdens of designing or training the variable-sized networks, which can be used in application scenarios with diverse resource constraints, are alleviated. However, SN-Net still faces a few challenges. 1) Stitching from multiple independently pre-trained anchors introduces high storage resource consumption. 2) SN-Net faces challenges to build smaller models for low resource constraints. 3). SN-Net uses an unlearned initialization method for stitch layers, limiting the final performance. To overcome these challenges, motivated by the recently proposed Learngene framework, we propose a novel method called Learngene Pool. Briefly, Learngene distills the critical knowledge from a large pre-trained model into a small part (termed as learngene) and then expands this small part into a few variable-sized models. In our proposed method, we distill one pretrained large model into multiple small models whose network blocks are used as learngene instances to construct the learngene pool. Since only one large model is used, we do not need to store more large models as SN-Net and after distilling, smaller learngene instances can be created to build small models to satisfy low resource constraints. We also insert learnable transformation matrices between the instances to stitch them into variable-sized models to improve the performance of these models. Exhaustive experiments have been implemented and the results validate the effectiveness of the proposed Learngene Pool compared with SN-Net.

In-context learning (ICL) -- the capacity of a model to infer and apply abstract patterns from examples provided within its input -- has been extensively studied in large language models trained for next-token prediction on human text. In fact, prior work often attributes this emergent behavior to distinctive statistical properties in human language. This raises a fundamental question: can ICL arise organically in other sequence domains purely through large-scale predictive training? To explore this, we turn to genomic sequences, an alternative symbolic domain rich in statistical structure. Specifically, we study the Evo2 genomic model, trained predominantly on next-nucleotide (A/T/C/G) prediction, at a scale comparable to mid-sized LLMs. We develop a controlled experimental framework comprising symbolic reasoning tasks instantiated in both linguistic and genomic forms, enabling direct comparison of ICL across genomic and linguistic models. Our results show that genomic models, like their linguistic counterparts, exhibit log-linear gains in pattern induction as the number of in-context demonstrations increases. To the best of our knowledge, this is the first evidence of organically emergent ICL in genomic sequences, supporting the hypothesis that ICL arises as a consequence of large-scale predictive modeling over rich data. These findings extend emergent meta-learning beyond language, pointing toward a unified, modality-agnostic view of in-context learning.

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

In this white paper we introduce Helix, an AI based solution for missense pathogenicity prediction. With recent advances in the sequencing of human genomes, massive amounts of genetic data have become available. This has shifted the burden of labor for genetic diagnostics and research from the gathering of data to its interpretation. Helix presents a state of the art platform for the prediction of pathogenicity in human missense variants. In addition to offering best-in-class predictive performance, Helix offers a platform that allows researchers to analyze and interpret variants in depth that can be accessed at helixlabs.ai.

We present the system description for our submission towards the Key Point Analysis Shared Task at ArgMining 2021. Track 1 of the shared task requires participants to develop methods to predict the match score between each pair of arguments and keypoints, provided they belong to the same topic under the same stance. We leveraged existing state of the art pre-trained language models along with incorporating additional data and features extracted from the inputs (topics, key points, and arguments) to improve performance. We were able to achieve mAP strict and mAP relaxed score of 0.872 and 0.966 respectively in the evaluation phase, securing 5th place on the leaderboard. In the post evaluation phase, we achieved a mAP strict and mAP relaxed score of 0.921 and 0.982 respectively. All the codes to generate reproducible results on our models are available on Github.

The Novelties corpus is a collection of novels (and parts of novels) annotated for Alias Resolution, among other tasks. This document describes the guidelines applied during the annotation process. It contains the instructions used by the annotators, as well as a number of examples retrieved from the annotated novels, and illustrating how canonical names should be defined, and which names should be considered as referring to the same entity.

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making them unable to benefit from transfer learning across families. To address this, we propose Protein Evolutionary Transformer (PoET), an autoregressive generative model of whole protein families that learns to generate sets of related proteins as sequences-of-sequences across tens of millions of natural protein sequence clusters. PoET can be used as a retrieval-augmented language model to generate and score arbitrary modifications conditioned on any protein family of interest, and can extrapolate from short context lengths to generalize well even for small families. This is enabled by a unique Transformer layer; we model tokens sequentially within sequences while attending between sequences order invariantly, allowing PoET to scale to context lengths beyond those used during training. In extensive experiments on deep mutational scanning datasets, we show that PoET outperforms existing protein language models and evolutionary sequence models for variant function prediction across proteins of all MSA depths. We also demonstrate PoET's ability to controllably generate new protein sequences.

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Despite much progress in recent years, the vast majority of work in natural language processing (NLP) is on standard languages with many speakers. In this work, we instead focus on low-resource languages and in particular non-standardized low-resource languages. Even within branches of major language families, often considered well-researched, little is known about the extent and type of available resources and what the major NLP challenges are for these language varieties. The first step to address this situation is a systematic survey of available corpora (most importantly, annotated corpora, which are particularly valuable for NLP research). Focusing on Germanic low-resource language varieties, we provide such a survey in this paper. Except for geolocation (origin of speaker or document), we find that manually annotated linguistic resources are sparse and, if they exist, mostly cover morphosyntax. Despite this lack of resources, we observe that interest in this area is increasing: there is active development and a growing research community. To facilitate research, we make our overview of over 80 corpora publicly available. We share a companion website of this overview at https://github.com/mainlp/germanic-lrl-corpora .

We introduce a new -- currently 42 gigabyte -- ``living'' dataset of phone images of dog feces, annotated with manually drawn or AI-assisted polygon labels. There are 6k full resolution images and 4k detailed polygon annotations. The collection and annotation of images started in late 2020 and the dataset grows by roughly 1GB a month. We train VIT and MaskRCNN baseline models to explore the difficulty of the dataset. The best model achieves a pixelwise average precision of 0.858 on a 691-image validation set and 0.847 on a small independently captured 30-image contributor test set. The most recent snapshot of dataset is made publicly available through three different distribution methods: one centralized (Girder) and two decentralized (IPFS and BitTorrent). We study of the trade-offs between distribution methods and discuss the feasibility of each with respect to reliably sharing open scientific data. The code to reproduce the experiments is hosted on GitHub, and the data is published under the Creative Commons Attribution 4.0 International license. Model weights are made publicly available with the dataset. Experimental hardware, time, energy, and emissions are quantified.

Extracting key information from scientific papers has the potential to help researchers work more efficiently and accelerate the pace of scientific progress. Over the last few years, research on Scientific Information Extraction (SciIE) witnessed the release of several new systems and benchmarks. However, existing paper-focused datasets mostly focus only on specific parts of a manuscript (e.g., abstracts) and are single-modality (i.e., text- or table-only), due to complex processing and expensive annotations. Moreover, core information can be present in either text or tables or across both. To close this gap in data availability and enable cross-modality IE, while alleviating labeling costs, we propose a semi-supervised pipeline for annotating entities in text, as well as entities and relations in tables, in an iterative procedure. Based on this pipeline, we release novel resources for the scientific community, including a high-quality benchmark, a large-scale corpus, and a semi-supervised annotation pipeline. We further report the performance of state-of-the-art IE models on the proposed benchmark dataset, as a baseline. Lastly, we explore the potential capability of large language models such as ChatGPT for the current task. Our new dataset, results, and analysis validate the effectiveness and efficiency of our semi-supervised pipeline, and we discuss its remaining limitations.

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multimodal data integration. However, progress remains fragmented across data modalities, architectures, and evaluation standards. LLM4Cell presents the first unified survey of 58 foundation and agentic models developed for single-cell research, spanning RNA, ATAC, multi-omic, and spatial modalities. We categorize these methods into five families-foundation, text-bridge, spatial, multimodal, epigenomic, and agentic-and map them to eight key analytical tasks including annotation, trajectory and perturbation modeling, and drug-response prediction. Drawing on over 40 public datasets, we analyze benchmark suitability, data diversity, and ethical or scalability constraints, and evaluate models across 10 domain dimensions covering biological grounding, multi-omics alignment, fairness, privacy, and explainability. By linking datasets, models, and evaluation domains, LLM4Cell provides the first integrated view of language-driven single-cell intelligence and outlines open challenges in interpretability, standardization, and trustworthy model development.

Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4 have demonstrated exceptional capabilities in processing, translating, and generating human languages. These breakthroughs have also been reflected in protein research, leading to the rapid development of numerous new methods in a short time, with unprecedented performance. Language models, in particular, have seen widespread use in protein research, as they have been utilized to embed proteins, generate novel ones, and predict tertiary structures. In this book chapter, we provide an overview of the use of protein generative models, reviewing 1) language models for the design of novel artificial proteins, 2) works that use non-Transformer architectures, and 3) applications in directed evolution approaches.

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniques, while promising, require large annotated datasets and extensive feature engineering and are prone to overfitting. Addressing these challenges, we introduce PathoLM, a cutting-edge pathogen language model optimized for the identification of pathogenicity in bacterial and viral sequences. Leveraging the strengths of pre-trained DNA models such as the Nucleotide Transformer, PathoLM requires minimal data for fine-tuning, thereby enhancing pathogen detection capabilities. It effectively captures a broader genomic context, significantly improving the identification of novel and divergent pathogens. We developed a comprehensive data set comprising approximately 30 species of viruses and bacteria, including ESKAPEE pathogens, seven notably virulent bacterial strains resistant to antibiotics. Additionally, we curated a species classification dataset centered specifically on the ESKAPEE group. In comparative assessments, PathoLM dramatically outperforms existing models like DciPatho, demonstrating robust zero-shot and few-shot capabilities. Furthermore, we expanded PathoLM-Sp for ESKAPEE species classification, where it showed superior performance compared to other advanced deep learning methods, despite the complexities of the task.

Planktonic organisms are of fundamental importance to marine ecosystems: they form the basis of the food web, provide the link between the atmosphere and the deep ocean, and influence global-scale biogeochemical cycles. Scientists are increasingly using imaging-based technologies to study these creatures in their natural habit. Images from such systems provide an unique opportunity to model and understand plankton ecosystems, but the collected datasets can be enormous. The Imaging FlowCytobot (IFCB) at Woods Hole Oceanographic Institution, for example, is an in situ system that has been continuously imaging plankton since 2006. To date, it has generated more than 700 million samples. Manual classification of such a vast image collection is impractical due to the size of the data set. In addition, the annotation task is challenging due to the large space of relevant classes, intra-class variability, and inter-class similarity. Methods for automated classification exist, but the accuracy is often below that of human experts. Here we introduce WHOI-Plankton: a large scale, fine-grained visual recognition dataset for plankton classification, which comprises over 3.4 million expert-labeled images across 70 classes. The labeled image set is complied from over 8 years of near continuous data collection with the IFCB at the Martha's Vineyard Coastal Observatory (MVCO). We discuss relevant metrics for evaluation of classification performance and provide results for a traditional method based on hand-engineered features and two methods based on convolutional neural networks.

Keyphrase generation is the task consisting in generating a set of words or phrases that highlight the main topics of a document. There are few datasets for keyphrase generation in the biomedical domain and they do not meet the expectations in terms of size for training generative models. In this paper, we introduce kp-biomed, the first large-scale biomedical keyphrase generation dataset with more than 5M documents collected from PubMed abstracts. We train and release several generative models and conduct a series of experiments showing that using large scale datasets improves significantly the performances for present and absent keyphrase generation. The dataset is available under CC-BY-NC v4.0 license at https://huggingface.co/ datasets/taln-ls2n/kpbiomed.

Keyphrase generation is the task of predicting a set of lexical units that conveys the main content of a source text. Existing datasets for keyphrase generation are only readily available for the scholarly domain and include non-expert annotations. In this paper we present KPTimes, a large-scale dataset of news texts paired with editor-curated keyphrases. Exploring the dataset, we show how editors tag documents, and how their annotations differ from those found in existing datasets. We also train and evaluate state-of-the-art neural keyphrase generation models on KPTimes to gain insights on how well they perform on the news domain. The dataset is available online at https://github.com/ygorg/KPTimes .

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the continual influx of domain-specific terminologies in scholarly literature. Current research in Biomedical Method (BioMethod) NER suffers from a scarcity of resources, primarily attributed to the intricate nature of methodological concepts, which necessitate a profound understanding for precise delineation. In this study, we propose a novel dataset for biomedical method entity recognition, employing an automated BioMethod entity recognition and information retrieval system to assist human annotation. Furthermore, we comprehensively explore a range of conventional and contemporary open-domain NER methodologies, including the utilization of cutting-edge large-scale language models (LLMs) customised to our dataset. Our empirical findings reveal that the large parameter counts of language models surprisingly inhibit the effective assimilation of entity extraction patterns pertaining to biomedical methods. Remarkably, the approach, leveraging the modestly sized ALBERT model (only 11MB), in conjunction with conditional random fields (CRF), achieves state-of-the-art (SOTA) performance.

Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high precision but suffer from lower recall. Recently, machine learning-based methods have been proposed to identify biomedical concepts, which can recognize more unseen concept synonyms by automatic feature learning. However, most methods require large corpora of manually annotated data for model training, which is difficult to obtain due to the high cost of human annotation. In this paper, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. We first use all concepts and synonyms in HPO to construct a dictionary, which is then used to automatically build a distantly supervised training dataset for machine learning. Next, a cutting-edge deep learning model is trained to classify each candidate phrase (n-gram from input sentence) into a corresponding concept label. Finally, the dictionary and machine learning-based prediction results are combined for improved performance. Our method is validated with two HPO corpora, and the results show that PhenoTagger compares favorably to previous methods. In addition, to demonstrate the generalizability of our method, we retrained PhenoTagger using the disease ontology MEDIC for disease concept recognition to investigate the effect of training on different ontologies. Experimental results on the NCBI disease corpus show that PhenoTagger without requiring manually annotated training data achieves competitive performance as compared with state-of-the-art supervised methods.

Passage ranking involves two stages: passage retrieval and passage re-ranking, which are important and challenging topics for both academics and industries in the area of Information Retrieval (IR). However, the commonly-used datasets for passage ranking usually focus on the English language. For non-English scenarios, such as Chinese, the existing datasets are limited in terms of data scale, fine-grained relevance annotation and false negative issues. To address this problem, we introduce T2Ranking, a large-scale Chinese benchmark for passage ranking. T2Ranking comprises more than 300K queries and over 2M unique passages from real-world search engines. Expert annotators are recruited to provide 4-level graded relevance scores (fine-grained) for query-passage pairs instead of binary relevance judgments (coarse-grained). To ease the false negative issues, more passages with higher diversities are considered when performing relevance annotations, especially in the test set, to ensure a more accurate evaluation. Apart from the textual query and passage data, other auxiliary resources are also provided, such as query types and XML files of documents which passages are generated from, to facilitate further studies. To evaluate the dataset, commonly used ranking models are implemented and tested on T2Ranking as baselines. The experimental results show that T2Ranking is challenging and there is still scope for improvement. The full data and all codes are available at https://github.com/THUIR/T2Ranking/

The challenge of replicating research results has posed a significant impediment to the field of molecular biology. The advent of modern intelligent systems has led to notable progress in various domains. Consequently, we embarked on an investigation of intelligent monitoring systems as a means of tackling the issue of the reproducibility crisis. Specifically, we first curate a comprehensive multimodal dataset, named ProBio, as an initial step towards this objective. This dataset comprises fine-grained hierarchical annotations intended for the purpose of studying activity understanding in BioLab. Next, we devise two challenging benchmarks, transparent solution tracking and multimodal action recognition, to emphasize the unique characteristics and difficulties associated with activity understanding in BioLab settings. Finally, we provide a thorough experimental evaluation of contemporary video understanding models and highlight their limitations in this specialized domain to identify potential avenues for future research. We hope ProBio with associated benchmarks may garner increased focus on modern AI techniques in the realm of molecular biology.

We introduce FindingEmo, a new image dataset containing annotations for 25k images, specifically tailored to Emotion Recognition. Contrary to existing datasets, it focuses on complex scenes depicting multiple people in various naturalistic, social settings, with images being annotated as a whole, thereby going beyond the traditional focus on faces or single individuals. Annotated dimensions include Valence, Arousal and Emotion label, with annotations gathered using Prolific. Together with the annotations, we release the list of URLs pointing to the original images, as well as all associated source code.

Software that contains machine learning algorithms is an integral part of automotive perception, for example, in driving automation systems. The development of such software, specifically the training and validation of the machine learning components, require large annotated datasets. An industry of data and annotation services has emerged to serve the development of such data-intensive automotive software components. Wide-spread difficulties to specify data and annotation needs challenge collaborations between OEMs (Original Equipment Manufacturers) and their suppliers of software components, data, and annotations. This paper investigates the reasons for these difficulties for practitioners in the Swedish automotive industry to arrive at clear specifications for data and annotations. The results from an interview study show that a lack of effective metrics for data quality aspects, ambiguities in the way of working, unclear definitions of annotation quality, and deficits in the business ecosystems are causes for the difficulty in deriving the specifications. We provide a list of recommendations that can mitigate challenges when deriving specifications and we propose future research opportunities to overcome these challenges. Our work contributes towards the on-going research on accountability of machine learning as applied to complex software systems, especially for high-stake applications such as automated driving.

Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit. Relying on either four primitive bases or independently designed DNA tokenizers, existing approaches with naive masked language modeling pre-training often fail to adapt to the varying complexities of genomic sequences. Leveraging Token Merging techniques, this paper introduces a hierarchical architecture that jointly optimizes a dynamic genomic tokenizer and latent Transformers with context-aware pre-training tasks. As for network structures, the tokenization module automatically chunks adjacent bases into words by stacking multiple layers of the differentiable token merging blocks with local-window constraints, then a Latent Encoder captures the global context of these merged words by full-attention blocks. Symmetrically employing a Latent Decoder and a Local Decoder, MergeDNA learns with two pre-training tasks: Merged Token Reconstruction simultaneously trains the dynamic tokenization module and adaptively filters important tokens, while Adaptive Masked Token Modeling learns to predict these filtered tokens to capture informative contents. Extensive experiments show that MergeDNA achieves superior performance on three popular DNA benchmarks and several multi-omics tasks with fine-tuning or zero-shot evaluation, outperforming typical tokenization methods and large-scale DNA foundation models.

The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. Almost all research on large-scale biosequence transformers has focused on one domain at a time (single-omic), usually nucleotides or peptides. These models have seen incredible success in downstream tasks in each domain and have achieved particularly noteworthy breakthroughs in sequences of peptides and structural modeling. However, these single-omic models are naturally incapable of modeling multi-omic tasks, one of the most biologically critical being nucleotide-peptide interactions. We present our work training the first multi-omic nucleotide-peptide foundation models. We show that these multi-omic models (MOMs) can learn joint representations between various single-omic distributions that are emergently consistent with the Central Dogma of molecular biology, despite only being trained on unlabeled biosequences. We further demonstrate that MOMs can be fine-tuned to achieve state-of-the-art results on peptide-nucleotide interaction tasks, namely predicting the change in Gibbs free energy ({\Delta}G) of the binding interaction between a given oligonucleotide and peptide, as well as the effect on this binding interaction due to mutations in the oligonucleotide sequence ({\Delta}{\Delta}G). Remarkably, we show that multi-omic biosequence transformers emergently learn useful structural information without any prior structural training, allowing us to predict which peptide residues are most involved in the peptide-nucleotide binding interaction. Lastly, we provide evidence that multi-omic biosequence models are non-inferior to foundation models trained on single-omics distributions, suggesting a more generalized or foundational approach to building these models.

This paper presents a comprehensive study on resume classification to reduce the time and labor needed to screen an overwhelming number of applications significantly, while improving the selection of suitable candidates. A total of 6,492 resumes are extracted from 24,933 job applications for 252 positions designated into four levels of experience for Clinical Research Coordinators (CRC). Each resume is manually annotated to its most appropriate CRC position by experts through several rounds of triple annotation to establish guidelines. As a result, a high Kappa score of 61% is achieved for inter-annotator agreement. Given this dataset, novel transformer-based classification models are developed for two tasks: the first task takes a resume and classifies it to a CRC level (T1), and the second task takes both a resume and a job description to apply and predicts if the application is suited to the job T2. Our best models using section encoding and multi-head attention decoding give results of 73.3% to T1 and 79.2% to T2. Our analysis shows that the prediction errors are mostly made among adjacent CRC levels, which are hard for even experts to distinguish, implying the practical value of our models in real HR platforms.

The research described in this paper concerns automatic cyberbullying detection in social media. There are two goals to achieve: building a gold standard cyberbullying detection dataset and measuring the performance of the Samurai cyberbullying detection system. The Formspring dataset provided in a Kaggle competition was re-annotated as a part of the research. The annotation procedure is described in detail and, unlike many other recent data annotation initiatives, does not use Mechanical Turk for finding people willing to perform the annotation. The new annotation compared to the old one seems to be more coherent since all tested cyberbullying detection system performed better on the former. The performance of the Samurai system is compared with 5 commercial systems and one well-known machine learning algorithm, used for classifying textual content, namely Fasttext. It turns out that Samurai scores the best in all measures (accuracy, precision and recall), while Fasttext is the second-best performing algorithm.

We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have achieved remarkable success in natural language generation, their application to DNA sequence generation remains largely underexplored. In this work, we introduce ATGC-Gen, an Automated Transformer Generator for Controllable Generation, which leverages cross-modal encoding to integrate diverse biological signals. ATGC-Gen is instantiated with both decoder-only and encoder-only transformer architectures, allowing flexible training and generation under either autoregressive or masked recovery objectives. We evaluate ATGC-Gen on representative tasks including promoter and enhancer sequence design, and further introduce a new dataset based on ChIP-Seq experiments for modeling protein binding specificity. Our experiments demonstrate that ATGC-Gen can generate fluent, diverse, and biologically relevant sequences aligned with the desired properties. Compared to prior methods, our model achieves notable improvements in controllability and functional relevance, highlighting the potential of language models in advancing programmable genomic design. The source code is released at (https://github.com/divelab/AIRS/blob/main/OpenBio/ATGC_Gen).

This work introduces Salamandra, a suite of open-source decoder-only large language models available in three different sizes: 2, 7, and 40 billion parameters. The models were trained from scratch on highly multilingual data that comprises text in 35 European languages and code. Our carefully curated corpus is made exclusively from open-access data compiled from a wide variety of sources. Along with the base models, supplementary checkpoints that were fine-tuned on public-domain instruction data are also released for chat applications. Additionally, we also share our preliminary experiments on multimodality, which serve as proof-of-concept to showcase potential applications for the Salamandra family. Our extensive evaluations on multilingual benchmarks reveal that Salamandra has strong capabilities, achieving competitive performance when compared to similarly sized open-source models. We provide comprehensive evaluation results both on standard downstream tasks as well as key aspects related to bias and safety.With this technical report, we intend to promote open science by sharing all the details behind our design choices, data curation strategy and evaluation methodology. In addition to that, we deviate from the usual practice by making our training and evaluation scripts publicly accessible. We release all models under a permissive Apache 2.0 license in order to foster future research and facilitate commercial use, thereby contributing to the open-source ecosystem of large language models.

Recently, open-domain question answering systems have begun to rely heavily on annotated datasets to train neural passage retrievers. However, manually annotating such datasets is both difficult and time-consuming, which limits their availability for less popular languages. In this work, we experiment with several methods for automatically collecting weakly labeled datasets and show how they affect the performance of the neural passage retrieval models. As a result of our work, we publish the MAUPQA dataset, consisting of nearly 400,000 question-passage pairs for Polish, as well as the HerBERT-QA neural retriever.

Large language models (LLMs) with billions of parameters have demonstrated outstanding performance on various natural language processing tasks. This report presents OpenBA, an open-sourced 15B bilingual asymmetric seq2seq model, to contribute an LLM variant to the Chinese-oriented open-source model community. We enhance OpenBA with effective and efficient techniques as well as adopt a three-stage training strategy to train the model from scratch. Our solution can also achieve very competitive performance with only 380B tokens, which is better than LLaMA-70B on the BELEBELE benchmark, BLOOM-176B on the MMLU benchmark, GLM-130B on the C-Eval (hard) benchmark. This report provides the main details to pre-train an analogous model, including pre-training data processing, Bilingual Flan data collection, the empirical observations that inspire our model architecture design, training objectives of different stages, and other enhancement techniques. We have refactored our code to follow the design principles of the Huggingface Transformers Library, making it more convenient for developers to use, and released checkpoints of different training stages at https://huggingface.co/openBA. More details of our project are available at https://github.com/OpenNLG/openBA.git.

Recently proposed systems for open-domain question answering (OpenQA) require large amounts of training data to achieve state-of-the-art performance. However, data annotation is known to be time-consuming and therefore expensive to acquire. As a result, the appropriate datasets are available only for a handful of languages (mainly English and Chinese). In this work, we introduce and publicly release PolQA, the first Polish dataset for OpenQA. It consists of 7,000 questions, 87,525 manually labeled evidence passages, and a corpus of over 7,097,322 candidate passages. Each question is classified according to its formulation, type, as well as entity type of the answer. This resource allows us to evaluate the impact of different annotation choices on the performance of the QA system and propose an efficient annotation strategy that increases the passage retrieval performance by 10.55 p.p. while reducing the annotation cost by 82%.

We present a corpus of Finnish news articles with a manually prepared named entity annotation. The corpus consists of 953 articles (193,742 word tokens) with six named entity classes (organization, location, person, product, event, and date). The articles are extracted from the archives of Digitoday, a Finnish online technology news source. The corpus is available for research purposes. We present baseline experiments on the corpus using a rule-based and two deep learning systems on two, in-domain and out-of-domain, test sets.

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

In this paper we address issues with image retrieval benchmarking on standard and popular Oxford 5k and Paris 6k datasets. In particular, annotation errors, the size of the dataset, and the level of challenge are addressed: new annotation for both datasets is created with an extra attention to the reliability of the ground truth. Three new protocols of varying difficulty are introduced. The protocols allow fair comparison between different methods, including those using a dataset pre-processing stage. For each dataset, 15 new challenging queries are introduced. Finally, a new set of 1M hard, semi-automatically cleaned distractors is selected. An extensive comparison of the state-of-the-art methods is performed on the new benchmark. Different types of methods are evaluated, ranging from local-feature-based to modern CNN based methods. The best results are achieved by taking the best of the two worlds. Most importantly, image retrieval appears far from being solved.

We present a statistical model for German medical natural language processing trained for named entity recognition (NER) as an open, publicly available model. The work serves as a refined successor to our first GERNERMED model which is substantially outperformed by our work. We demonstrate the effectiveness of combining multiple techniques in order to achieve strong results in entity recognition performance by the means of transfer-learning on pretrained deep language models (LM), word-alignment and neural machine translation. Due to the sparse situation on open, public medical entity recognition models for German texts, this work offers benefits to the German research community on medical NLP as a baseline model. Since our model is based on public English data, its weights are provided without legal restrictions on usage and distribution. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED-pp

We present EMMa, an Extensible, Multimodal dataset of Amazon product listings that contains rich Material annotations. It contains more than 2.8 million objects, each with image(s), listing text, mass, price, product ratings, and position in Amazon's product-category taxonomy. We also design a comprehensive taxonomy of 182 physical materials (e.g., Plastic rightarrow Thermoplastic rightarrow Acrylic). Objects are annotated with one or more materials from this taxonomy. With the numerous attributes available for each object, we develop a Smart Labeling framework to quickly add new binary labels to all objects with very little manual labeling effort, making the dataset extensible. Each object attribute in our dataset can be included in either the model inputs or outputs, leading to combinatorial possibilities in task configurations. For example, we can train a model to predict the object category from the listing text, or the mass and price from the product listing image. EMMa offers a new benchmark for multi-task learning in computer vision and NLP, and allows practitioners to efficiently add new tasks and object attributes at scale.

Recently, there has been a significant upsurge of interest in leveraging large language models (LLMs) to assist scientific discovery. However, most LLMs only focus on general science, while they lack domain-specific knowledge, such as chemical molecules and amino acid sequences. To bridge these gaps, we introduce SciDFM, a mixture-of-experts LLM, which is trained from scratch and is able to conduct college-level scientific reasoning and understand molecules and amino acid sequences. We collect a large-scale training corpus containing numerous scientific papers and books from different disciplines as well as data from domain-specific databases. We further fine-tune the pre-trained model on lots of instruction data to improve performances on downstream benchmarks. From experiment results, we show that SciDFM achieves strong performance on general scientific benchmarks such as SciEval and SciQ, and it reaches a SOTA performance on domain-specific benchmarks among models of similar size. We further analyze the expert layers and show that the results of expert selection vary with data from different disciplines. To benefit the broader research community, we open-source SciDFM at https://huggingface.co/OpenDFM/SciDFM-MoE-A5.6B-v1.0.

This handbook is a hands-on guide on how to approach text annotation tasks. It provides a gentle introduction to the topic, an overview of theoretical concepts as well as practical advice. The topics covered are mostly technical, but business, ethical and regulatory issues are also touched upon. The focus lies on readability and conciseness rather than completeness and scientific rigor. Experience with annotation and knowledge of machine learning are useful but not required. The document may serve as a primer or reference book for a wide range of professions such as team leaders, project managers, IT architects, software developers and machine learning engineers.

Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C^2LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.

How to evaluate Large Language Models (LLMs) in code generation is an open question. Existing benchmarks demonstrate poor alignment with real-world code repositories and are insufficient to evaluate the coding abilities of LLMs. This paper proposes a new benchmark - EvoCodeBench to address the preceding problems, which has three primary advances. (1) EvoCodeBench aligns with real-world repositories in multiple dimensions, e.g., code distributions and dependency distributions. (2) EvoCodeBench offers comprehensive annotations (e.g., requirements, reference code, and reference dependencies), and robust evaluation metrics (e.g., Pass@k and Recall@k). (3) EvoCodeBench is an evolving benchmark to avoid data leakage. We build an automatic pipeline to update EvoCodeBench from the latest repositories. We release the first version - EvoCodeBench-2403, containing 275 samples from 25 real-world repositories. Based on EvoCodeBench, we propose repository-level code generation and evaluate 10 popular LLMs (e.g., gpt-4, gpt-3.5, DeepSeek Coder, StarCoder 2, CodeLLaMa, Gemma, and Qwen 1.5). Our experiments reveal the coding abilities of these LLMs in real-world repositories. For example, the highest Pass@1 of gpt-4 only is 20.73% in our experiments. We also analyze failed cases and summarize the shortcomings of existing LLMs in EvoCodeBench. We release EvoCodeBench, all prompts, and LLMs' completions for further community analysis.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Large language models, particularly GPT-3, are able to produce high quality summaries of general domain news articles in few- and zero-shot settings. However, it is unclear if such models are similarly capable in more specialized, high-stakes domains such as biomedicine. In this paper, we enlist domain experts (individuals with medical training) to evaluate summaries of biomedical articles generated by GPT-3, given zero supervision. We consider both single- and multi-document settings. In the former, GPT-3 is tasked with generating regular and plain-language summaries of articles describing randomized controlled trials; in the latter, we assess the degree to which GPT-3 is able to synthesize evidence reported across a collection of articles. We design an annotation scheme for evaluating model outputs, with an emphasis on assessing the factual accuracy of generated summaries. We find that while GPT-3 is able to summarize and simplify single biomedical articles faithfully, it struggles to provide accurate aggregations of findings over multiple documents. We release all data and annotations used in this work.

We introduce Korean Language Understanding Evaluation (KLUE) benchmark. KLUE is a collection of 8 Korean natural language understanding (NLU) tasks, including Topic Classification, SemanticTextual Similarity, Natural Language Inference, Named Entity Recognition, Relation Extraction, Dependency Parsing, Machine Reading Comprehension, and Dialogue State Tracking. We build all of the tasks from scratch from diverse source corpora while respecting copyrights, to ensure accessibility for anyone without any restrictions. With ethical considerations in mind, we carefully design annotation protocols. Along with the benchmark tasks and data, we provide suitable evaluation metrics and fine-tuning recipes for pretrained language models for each task. We furthermore release the pretrained language models (PLM), KLUE-BERT and KLUE-RoBERTa, to help reproducing baseline models on KLUE and thereby facilitate future research. We make a few interesting observations from the preliminary experiments using the proposed KLUE benchmark suite, already demonstrating the usefulness of this new benchmark suite. First, we find KLUE-RoBERTa-large outperforms other baselines, including multilingual PLMs and existing open-source Korean PLMs. Second, we see minimal degradation in performance even when we replace personally identifiable information from the pretraining corpus, suggesting that privacy and NLU capability are not at odds with each other. Lastly, we find that using BPE tokenization in combination with morpheme-level pre-tokenization is effective in tasks involving morpheme-level tagging, detection and generation. In addition to accelerating Korean NLP research, our comprehensive documentation on creating KLUE will facilitate creating similar resources for other languages in the future. KLUE is available at https://klue-benchmark.com.

The HuggingFace Datasets Hub hosts thousands of datasets. This provides exciting opportunities for language model training and evaluation. However, the datasets for a given type of task are stored with different schemas, and harmonization is harder than it seems (https://xkcd.com/927/). Multi-task training or evaluation requires manual work to fit data into task templates. Various initiatives independently address this problem by releasing the harmonized datasets or harmonization codes to preprocess datasets to the same format. We identify patterns across previous preprocessings, e.g. mapping of column names, and extraction of a specific sub-field from structured data in a column, and propose a structured annotation framework that makes our annotations fully exposed and not buried in unstructured code. We release a dataset annotation framework and dataset annotations for more than 400 English tasks (https://github.com/sileod/tasksource). These annotations provide metadata, like the name of the columns that should be used as input or labels for all datasets, and can save time for future dataset preprocessings, even if they do not use our framework. We fine-tune a multi-task text encoder on all tasksource tasks, outperforming every publicly available text encoder of comparable size on an external evaluation https://hf.co/sileod/deberta-v3-base-tasksource-nli.