Daily Papers

Language Models (LMs) have demonstrated impressive molecule understanding ability on various 1D text-related tasks. However, they inherently lack 2D graph perception - a critical ability of human professionals in comprehending molecules' topological structures. To bridge this gap, we propose MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter. MolCA enables an LM (e.g., Galactica) to understand both text- and graph-based molecular contents via the cross-modal projector. Specifically, the cross-modal projector is implemented as a Q-Former to connect a graph encoder's representation space and an LM's text space. Further, MolCA employs a uni-modal adapter (i.e., LoRA) for the LM's efficient adaptation to downstream tasks. Unlike previous studies that couple an LM with a graph encoder via cross-modal contrastive learning, MolCA retains the LM's ability of open-ended text generation and augments it with 2D graph information. To showcase its effectiveness, we extensively benchmark MolCA on tasks of molecule captioning, IUPAC name prediction, and molecule-text retrieval, on which MolCA significantly outperforms the baselines. Our codes and checkpoints can be found at https://github.com/acharkq/MolCA.

Aligning molecular sequence representations (e.g., SMILES notations) with textual descriptions is critical for applications spanning drug discovery, materials design, and automated chemical literature analysis. Existing methodologies typically treat molecular captioning (molecule-to-text) and text-based molecular design (text-to-molecule) as separate tasks, relying on supervised fine-tuning or contrastive learning pipelines. These approaches face three key limitations: (i) conventional metrics like BLEU prioritize linguistic fluency over chemical accuracy, (ii) training datasets frequently contain chemically ambiguous narratives with incomplete specifications, and (iii) independent optimization of generation directions leads to bidirectional inconsistency. To address these issues, we propose RTMol, a bidirectional alignment framework that unifies molecular captioning and text-to-SMILES generation through self-supervised round-trip learning. The framework introduces novel round-trip evaluation metrics and enables unsupervised training for molecular captioning without requiring paired molecule-text corpora. Experiments demonstrate that RTMol enhances bidirectional alignment performance by up to 47% across various LLMs, establishing an effective paradigm for joint molecule-text understanding and generation.

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

Optical Chemical Structure Recognition (OCSR) is crucial for digitizing chemical knowledge by converting molecular images into machine-readable formats. While recent vision-language models (VLMs) have shown potential in this task, their image-captioning approach often struggles with complex molecular structures and inconsistent annotations. To overcome these challenges, we introduce GTR-Mol-VLM, a novel framework featuring two key innovations: (1) the Graph Traversal as Visual Chain of Thought mechanism that emulates human reasoning by incrementally parsing molecular graphs through sequential atom-bond predictions, and (2) the data-centric principle of Faithfully Recognize What You've Seen, which addresses the mismatch between abbreviated structures in images and their expanded annotations. To support model development, we constructed GTR-CoT-1.3M, a large-scale instruction-tuning dataset with meticulously corrected annotations, and introduced MolRec-Bench, the first benchmark designed for a fine-grained evaluation of graph-parsing accuracy in OCSR. Comprehensive experiments demonstrate that GTR-Mol-VLM achieves superior results compared to specialist models, chemistry-domain VLMs, and commercial general-purpose VLMs. Notably, in scenarios involving molecular images with functional group abbreviations, GTR-Mol-VLM outperforms the second-best baseline by approximately 14 percentage points, both in SMILES-based and graph-based metrics. We hope that this work will drive OCSR technology to more effectively meet real-world needs, thereby advancing the fields of cheminformatics and AI for Science. We will release GTR-CoT at https://github.com/opendatalab/GTR-CoT.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties.

PaliGemma 2 is an upgrade of the PaliGemma open Vision-Language Model (VLM) based on the Gemma 2 family of language models. We combine the SigLIP-So400m vision encoder that was also used by PaliGemma with the whole range of Gemma 2 models, from the 2B one all the way up to the 27B model. We train these models at three resolutions (224px, 448px, and 896px) in multiple stages to equip them with broad knowledge for transfer via fine-tuning. The resulting family of base models covering different model sizes and resolutions allows us to investigate factors impacting transfer performance (such as learning rate) and to analyze the interplay between the type of task, model size, and resolution. We further increase the number and breadth of transfer tasks beyond the scope of PaliGemma including different OCR-related tasks such as table structure recognition, molecular structure recognition, music score recognition, as well as long fine-grained captioning and radiography report generation, on which PaliGemma 2 obtains state-of-the-art results.

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

This work investigates descriptive captions as an additional source of supervision for biological multimodal foundation models. Images and captions can be viewed as complementary samples from the latent morphospace of a species, each capturing certain biological traits. Incorporating captions during training encourages alignment with this shared latent structure, emphasizing potentially diagnostic characters while suppressing spurious correlations. The main challenge, however, lies in obtaining faithful, instance-specific captions at scale. This requirement has limited the utilization of natural language supervision in organismal biology compared with many other scientific domains. We complement this gap by generating synthetic captions with multimodal large language models (MLLMs), guided by Wikipedia-derived visual information and taxon-tailored format examples. These domain-specific contexts help reduce hallucination and yield accurate, instance-based descriptive captions. Using these captions, we train BIOCAP (i.e., BIOCLIP with Captions), a biological foundation model that captures rich semantics and achieves strong performance in species classification and text-image retrieval. These results demonstrate the value of descriptive captions beyond labels in bridging biological images with multimodal foundation models.

Large Language Models (LLMs) have demonstrated exceptional performance in biochemical tasks, especially the molecule caption translation task, which aims to bridge the gap between molecules and natural language texts. However, previous methods in adapting LLMs to the molecule-caption translation task required extra domain-specific pre-training stages, suffered weak alignment between molecular and textual spaces, or imposed stringent demands on the scale of LLMs. To resolve the challenges, we propose In-Context Molecule Adaptation (ICMA), as a new paradigm allowing LLMs to learn the molecule-text alignment from context examples via In-Context Molecule Tuning. Specifically, ICMA incorporates the following three stages: Cross-modal Retrieval, Post-retrieval Re-ranking, and In-context Molecule Tuning. Initially, Cross-modal Retrieval utilizes BM25 Caption Retrieval and Molecule Graph Retrieval to retrieve informative context examples. Additionally, we also propose Post-retrieval Re-ranking with Sequence Reversal and Random Walk to further improve the quality of retrieval results. Finally, In-Context Molecule Tuning unlocks the in-context molecule learning capability of LLMs with retrieved examples and adapts the parameters of LLMs for the molecule-caption translation task. Experimental results demonstrate that ICMT can empower LLMs to achieve state-of-the-art or comparable performance without extra training corpora and intricate structures, showing that LLMs are inherently in-context molecule learners.

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 introduce a versatile flexible-captioning vision-language model (VLM) capable of generating region-specific descriptions of varying lengths. The model, FlexCap, is trained to produce length-conditioned captions for input bounding boxes, and this allows control over the information density of its output, with descriptions ranging from concise object labels to detailed captions. To achieve this we create large-scale training datasets of image region descriptions of varying length, starting from captioned images. This flexible-captioning capability has several valuable applications. First, FlexCap demonstrates superior performance in dense captioning tasks on the Visual Genome dataset. Second, a visual question answering (VQA) system can be built by employing FlexCap to generate localized descriptions as inputs to a large language model. The resulting system achieves state-of-the-art zero-shot performance on a number of VQA datasets. We also demonstrate a localize-then-describe approach with FlexCap can be better at open-ended object detection than a describe-then-localize approach with other VLMs. We highlight a novel characteristic of FlexCap, which is its ability to extract diverse visual information through prefix conditioning. Finally, we qualitatively demonstrate FlexCap's broad applicability in tasks such as image labeling, object attribute recognition, and visual dialog. Project webpage: https://flex-cap.github.io .

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

We present MolT5 - a self-supervised learning framework for pretraining models on a vast amount of unlabeled natural language text and molecule strings. MolT5 allows for new, useful, and challenging analogs of traditional vision-language tasks, such as molecule captioning and text-based de novo molecule generation (altogether: translation between molecules and language), which we explore for the first time. Since MolT5 pretrains models on single-modal data, it helps overcome the chemistry domain shortcoming of data scarcity. Furthermore, we consider several metrics, including a new cross-modal embedding-based metric, to evaluate the tasks of molecule captioning and text-based molecule generation. Our results show that MolT5-based models are able to generate outputs, both molecules and captions, which in many cases are high quality.

Image captioning is a fundamental task in vision-language understanding, where the model predicts a textual informative caption to a given input image. In this paper, we present a simple approach to address this task. We use CLIP encoding as a prefix to the caption, by employing a simple mapping network, and then fine-tunes a language model to generate the image captions. The recently proposed CLIP model contains rich semantic features which were trained with textual context, making it best for vision-language perception. Our key idea is that together with a pre-trained language model (GPT2), we obtain a wide understanding of both visual and textual data. Hence, our approach only requires rather quick training to produce a competent captioning model. Without additional annotations or pre-training, it efficiently generates meaningful captions for large-scale and diverse datasets. Surprisingly, our method works well even when only the mapping network is trained, while both CLIP and the language model remain frozen, allowing a lighter architecture with less trainable parameters. Through quantitative evaluation, we demonstrate our model achieves comparable results to state-of-the-art methods on the challenging Conceptual Captions and nocaps datasets, while it is simpler, faster, and lighter. Our code is available in https://github.com/rmokady/CLIP_prefix_caption.

Image captioning is a central task in computer vision which has experienced substantial progress following the advent of vision-language pre-training techniques. In this paper, we highlight a frequently overlooked limitation of captioning models that often fail to capture semantically significant elements. This drawback can be traced back to the text-image datasets; while their captions typically offer a general depiction of image content, they frequently omit salient details. To mitigate this limitation, we propose FuseCap - a novel method for enriching captions with additional visual information, obtained from vision experts, such as object detectors, attribute recognizers, and Optical Character Recognizers (OCR). Our approach fuses the outputs of such vision experts with the original caption using a large language model (LLM), yielding enriched captions that present a comprehensive image description. We validate the effectiveness of the proposed caption enrichment method through both quantitative and qualitative analysis. Our method is then used to curate the training set of a captioning model based BLIP which surpasses current state-of-the-art approaches in generating accurate and detailed captions while using significantly fewer parameters and training data. As additional contributions, we provide a dataset comprising of 12M image-enriched caption pairs and show that the proposed method largely improves image-text retrieval.

Image captioning is one of the straightforward tasks that can take advantage of large-scale web-crawled data which provides rich knowledge about the visual world for a captioning model. However, since web-crawled data contains image-text pairs that are aligned at different levels, the inherent noises (e.g., misaligned pairs) make it difficult to learn a precise captioning model. While the filtering strategy can effectively remove noisy data, however, it leads to a decrease in learnable knowledge and sometimes brings about a new problem of data deficiency. To take the best of both worlds, we propose a noise-aware learning framework, which learns rich knowledge from the whole web-crawled data while being less affected by the noises. This is achieved by the proposed quality controllable model, which is learned using alignment levels of the image-text pairs as an additional control signal during training. The alignment-conditioned training allows the model to generate high-quality captions of well-aligned by simply setting the control signal to desired alignment level at inference time. Through in-depth analysis, we show that our controllable captioning model is effective in handling noise. In addition, with two tasks of zero-shot captioning and text-to-image retrieval using generated captions (i.e., self-retrieval), we also demonstrate our model can produce high-quality captions in terms of descriptiveness and distinctiveness. Code is available at https://github.com/kakaobrain/noc.

Large language models are playing an increasingly significant role in molecular research, yet existing models often generate erroneous information, posing challenges to accurate molecular comprehension. Traditional evaluation metrics for generated content fail to assess a model's accuracy in molecular understanding. To rectify the absence of factual evaluation, we present MoleculeQA, a novel question answering (QA) dataset which possesses 62K QA pairs over 23K molecules. Each QA pair, composed of a manual question, a positive option and three negative options, has consistent semantics with a molecular description from authoritative molecular corpus. MoleculeQA is not only the first benchmark for molecular factual bias evaluation but also the largest QA dataset for molecular research. A comprehensive evaluation on MoleculeQA for existing molecular LLMs exposes their deficiencies in specific areas and pinpoints several particularly crucial factors for molecular understanding.

Supervised visual captioning models typically require a large scale of images or videos paired with descriptions in a specific language (i.e., the vision-caption pairs) for training. However, collecting and labeling large-scale datasets is time-consuming and expensive for many scenarios and languages. Therefore, sufficient labeled pairs are usually not available. To deal with the label shortage problem, we present a simple yet effective zero-shot approach MultiCapCLIP that can generate visual captions for different scenarios and languages without any labeled vision-caption pairs of downstream datasets. In the training stage, MultiCapCLIP only requires text data for input. Then it conducts two main steps: 1) retrieving concept prompts that preserve the corresponding domain knowledge of new scenarios; 2) auto-encoding the prompts to learn writing styles to output captions in a desired language. In the testing stage, MultiCapCLIP instead takes visual data as input directly to retrieve the concept prompts to generate the final visual descriptions. The extensive experiments on image and video captioning across four benchmarks and four languages (i.e., English, Chinese, German, and French) confirm the effectiveness of our approach. Compared with state-of-the-art zero-shot and weakly-supervised methods, our method achieves 4.8% and 21.5% absolute improvements in terms of BLEU@4 and CIDEr metrics. Our code is available at https://github.com/yangbang18/MultiCapCLIP.

Scientific figure captioning is a complex task that requires generating contextually appropriate descriptions of visual content. However, existing methods often fall short by utilizing incomplete information, treating the task solely as either an image-to-text or text summarization problem. This limitation hinders the generation of high-quality captions that fully capture the necessary details. Moreover, existing data sourced from arXiv papers contain low-quality captions, posing significant challenges for training large language models (LLMs). In this paper, we introduce a framework called Multi-LLM Collaborative Figure Caption Generation (MLBCAP) to address these challenges by leveraging specialized LLMs for distinct sub-tasks. Our approach unfolds in three key modules: (Quality Assessment) We utilize multimodal LLMs to assess the quality of training data, enabling the filtration of low-quality captions. (Diverse Caption Generation) We then employ a strategy of fine-tuning/prompting multiple LLMs on the captioning task to generate candidate captions. (Judgment) Lastly, we prompt a prominent LLM to select the highest quality caption from the candidates, followed by refining any remaining inaccuracies. Human evaluations demonstrate that informative captions produced by our approach rank better than human-written captions, highlighting its effectiveness. Our code is available at https://github.com/teamreboott/MLBCAP

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in interpreting molecular structures, their instruction datasets are limited to the specific knowledge from task-oriented datasets and do not fully cover the fundamental characteristics of molecules, hindering their abilities as general-purpose molecular assistants. To address this issue, we propose Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules via multi-modal instruction tuning. To this end, we design key data types that encompass the fundamental features of molecules, incorporating essential knowledge from molecular structures. In addition, to improve understanding of molecular features, we introduce a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of different molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and generating relevant responses to users' queries with detailed explanations, implying its potential as a general-purpose assistant for molecular analysis.

Weakly-Supervised Scene Graph Generation (WSSGG) research has recently emerged as an alternative to the fully-supervised approach that heavily relies on costly annotations. In this regard, studies on WSSGG have utilized image captions to obtain unlocalized triplets while primarily focusing on grounding the unlocalized triplets over image regions. However, they have overlooked the two issues involved in the triplet formation process from the captions: 1) Semantic over-simplification issue arises when extracting triplets from captions, where fine-grained predicates in captions are undesirably converted into coarse-grained predicates, resulting in a long-tailed predicate distribution, and 2) Low-density scene graph issue arises when aligning the triplets in the caption with entity/predicate classes of interest, where many triplets are discarded and not used in training, leading to insufficient supervision. To tackle the two issues, we propose a new approach, i.e., Large Language Model for weakly-supervised SGG (LLM4SGG), where we mitigate the two issues by leveraging the LLM's in-depth understanding of language and reasoning ability during the extraction of triplets from captions and alignment of entity/predicate classes with target data. To further engage the LLM in these processes, we adopt the idea of Chain-of-Thought and the in-context few-shot learning strategy. To validate the effectiveness of LLM4SGG, we conduct extensive experiments on Visual Genome and GQA datasets, showing significant improvements in both Recall@K and mean Recall@K compared to the state-of-the-art WSSGG methods. A further appeal is that LLM4SGG is data-efficient, enabling effective model training with a small amount of training images.

Image captioning aims to describe visual content in natural language. As 'a picture is worth a thousand words', there could be various correct descriptions for an image. However, with maximum likelihood estimation as the training objective, the captioning model is penalized whenever its prediction mismatches with the label. For instance, when the model predicts a word expressing richer semantics than the label, it will be penalized and optimized to prefer more concise expressions, referred to as conciseness optimization. In contrast, predictions that are more concise than labels lead to richness optimization. Such conflicting optimization directions could eventually result in the model generating general descriptions. In this work, we introduce Semipermeable MaxImum Likelihood Estimation (SMILE), which allows richness optimization while blocking conciseness optimization, thus encouraging the model to generate longer captions with more details. Extensive experiments on two mainstream image captioning datasets MSCOCO and Flickr30K demonstrate that SMILE significantly enhances the descriptiveness of generated captions. We further provide in-depth investigations to facilitate a better understanding of how SMILE works.

Humans describe complex scenes with compositionality, using simple text descriptions enriched with links and relationships. While vision-language research has aimed to develop models with compositional understanding capabilities, this is not reflected yet in existing datasets which, for the most part, still use plain text to describe images. In this work, we propose a new annotation strategy, graph-based captioning (GBC) that describes an image using a labelled graph structure, with nodes of various types. The nodes in GBC are created using, in a first stage, object detection and dense captioning tools nested recursively to uncover and describe entity nodes, further linked together in a second stage by highlighting, using new types of nodes, compositions and relations among entities. Since all GBC nodes hold plain text descriptions, GBC retains the flexibility found in natural language, but can also encode hierarchical information in its edges. We demonstrate that GBC can be produced automatically, using off-the-shelf multimodal LLMs and open-vocabulary detection models, by building a new dataset, GBC10M, gathering GBC annotations for about 10M images of the CC12M dataset. We use GBC10M to showcase the wealth of node captions uncovered by GBC, as measured with CLIP training. We show that using GBC nodes' annotations -- notably those stored in composition and relation nodes -- results in significant performance boost on downstream models when compared to other dataset formats. To further explore the opportunities provided by GBC, we also propose a new attention mechanism that can leverage the entire GBC graph, with encouraging experimental results that show the extra benefits of incorporating the graph structure. Our datasets are released at https://huggingface.co/graph-based-captions.

We present the first approach to automated audio captioning. We employ an encoder-decoder scheme with an alignment model in between. The input to the encoder is a sequence of log mel-band energies calculated from an audio file, while the output is a sequence of words, i.e. a caption. The encoder is a multi-layered, bi-directional gated recurrent unit (GRU) and the decoder a multi-layered GRU with a classification layer connected to the last GRU of the decoder. The classification layer and the alignment model are fully connected layers with shared weights between timesteps. The proposed method is evaluated using data drawn from a commercial sound effects library, ProSound Effects. The resulting captions were rated through metrics utilized in machine translation and image captioning fields. Results from metrics show that the proposed method can predict words appearing in the original caption, but not always correctly ordered.

Novel object captioning (NOC) aims to describe images containing objects without observing their ground truth captions during training. Due to the absence of caption annotation, captioning models cannot be directly optimized via sequence-to-sequence training or CIDEr optimization. As a result, we present Paraphrasing-to-Captioning (P2C), a two-stage learning framework for NOC, which would heuristically optimize the output captions via paraphrasing. With P2C, the captioning model first learns paraphrasing from a language model pre-trained on text-only corpus, allowing expansion of the word bank for improving linguistic fluency. To further enforce the output caption sufficiently describing the visual content of the input image, we perform self-paraphrasing for the captioning model with fidelity and adequacy objectives introduced. Since no ground truth captions are available for novel object images during training, our P2C leverages cross-modality (image-text) association modules to ensure the above caption characteristics can be properly preserved. In the experiments, we not only show that our P2C achieves state-of-the-art performances on nocaps and COCO Caption datasets, we also verify the effectiveness and flexibility of our learning framework by replacing language and cross-modality association models for NOC. Implementation details and code are available in the supplementary materials.

Understanding the chemical structure from a graphical representation of a molecule is a challenging image caption task that would greatly benefit molecule-centric scientific discovery. Variations in molecular images and caption subtasks pose a significant challenge in both image representation learning and task modeling. Yet, existing methods only focus on a specific caption task that translates a molecular image into its graph structure, i.e., OCSR. In this paper, we propose the Optical Chemical Structure Understanding (OCSU) task, which extends OCSR to molecular image caption from motif level to molecule level and abstract level. We present two approaches for that, including an OCSR-based method and an end-to-end OCSR-free method. The proposed Double-Check achieves SOTA OCSR performance on real-world patent and journal article scenarios via attentive feature enhancement for local ambiguous atoms. Cascading with SMILES-based molecule understanding methods, it can leverage the power of existing task-specific models for OCSU. While Mol-VL is an end-to-end optimized VLM-based model. An OCSU dataset, Vis-CheBI20, is built based on the widely used CheBI20 dataset for training and evaluation. Extensive experimental results on Vis-CheBI20 demonstrate the effectiveness of the proposed approaches. Improving OCSR capability can lead to a better OCSU performance for OCSR-based approach, and the SOTA performance of Mol-VL demonstrates the great potential of end-to-end approach.

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text. Briefly, we detect the molecule names in each sequence and replace them to the corresponding SMILES. In this way, the SMILES could leverage the information from surrounding text, and vice versa. The above wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem are all fed into a language model for pre-training. Experimental results demonstrate that MolXPT outperforms strong baselines of molecular property prediction on MoleculeNet, performs comparably to the best model in text-molecule translation while using less than half of its parameters, and enables zero-shot molecular generation without finetuning.

Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the inherent hierarchical structures in molecules. Notably, higher-order molecular structures contain rich semantics of functional groups, which encode crucial biochemical functionalities of the molecules. We show that neglecting the hierarchical information in tokenization will lead to subpar molecule-language alignment and severe hallucination. To address this limitation, we propose HIerarchical GrapH Tokenization (HIGHT). HIGHT employs a hierarchical graph tokenizer that encodes the hierarchy of atom, motif, and molecular levels of informative tokens to improve the molecular perception of LLMs. HIGHT also adopts an augmented instruction tuning dataset, enriched with the hierarchical graph information, to further enhance the molecule-language alignment. Extensive experiments on 14 real-world benchmarks verify the effectiveness of HIGHT in reducing hallucination by 40%, and significant improvements in various molecule-language downstream tasks. The project is available at https: //higraphllm.github.io/.

Image captioning is a multimodal problem that has drawn extensive attention in both the natural language processing and computer vision community. In this paper, we present a novel image captioning architecture to better explore semantics available in captions and leverage that to enhance both image representation and caption generation. Our models first construct caption-guided visual relationship graphs that introduce beneficial inductive bias using weakly supervised multi-instance learning. The representation is then enhanced with neighbouring and contextual nodes with their textual and visual features. During generation, the model further incorporates visual relationships using multi-task learning for jointly predicting word and object/predicate tag sequences. We perform extensive experiments on the MSCOCO dataset, showing that the proposed framework significantly outperforms the baselines, resulting in the state-of-the-art performance under a wide range of evaluation metrics.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Image captioning is conventionally formulated as the task of generating captions for images that match the distribution of reference image-caption pairs. However, reference captions in standard captioning datasets are short and may not uniquely identify the images they describe. These problems are further exacerbated when models are trained directly on image-alt text pairs collected from the internet. In this work, we show that it is possible to generate more specific captions with minimal changes to the training process. We implement classifier-free guidance for an autoregressive captioning model by fine-tuning it to estimate both conditional and unconditional distributions over captions. The guidance scale applied at decoding controls a trade-off between maximizing p(caption|image) and p(image|caption). Compared to standard greedy decoding, decoding with a guidance scale of 2 substantially improves reference-free metrics such as CLIPScore (0.808 vs. 0.775) and captiontoimage retrieval performance in the CLIP embedding space (recall@1 44.6% vs. 26.5%), but worsens standard reference-based captioning metrics (e.g., CIDEr 78.6 vs 126.1). We further explore the use of language models to guide the decoding process, obtaining small improvements over the Pareto frontier of reference-free vs. reference-based captioning metrics that arises from classifier-free guidance, and substantially improving the quality of captions generated from a model trained only on minimally curated web data.

Image Captioning for state-of-the-art VLMs has significantly improved over time; however, this comes at the cost of increased computational complexity, making them less accessible for resource-constrained applications such as mobile devices and assistive technologies. Alternatively, smaller VLMs prioritize high-level scene descriptions, overlooking finer details that contribute to a richer understanding of an image. In this paper, we introduce a training-free framework that enhances caption diversity and informativeness by explicitly attending to distinct image regions using a comparably small VLM, BLIP, as the backbone. Our approach leverages structured segmentation to produce hierarchical representations that capture both global and localized semantics. Without requiring additional model training, we demonstrate that our method allows smaller VLMs to achieve performance comparable to larger models in terms of image-caption alignment, semantic integrity, and diversity. We evaluate our framework on MSCOCO, Flickr30k, and Nocaps test datasets, achieving a Div-2 score of 0.735, 0.750, and 0.748 for each dataset respectively, while maintaining strong image-caption relevancy and semantic integrity with the human-annotated captions.

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Zero-shot captioners are recently proposed models that utilize common-space vision-language representations to caption images without relying on paired image-text data. To caption an image, they proceed by textually decoding a text-aligned image feature, but they limit their scope to global representations and whole-image captions. We present , a unified framework for zero-shot captioning that shifts from an image-centric to a patch-centric paradigm, enabling the captioning of arbitrary regions without the need of region-level supervision. Instead of relying on global image representations, we treat individual patches as atomic captioning units and aggregate them to describe arbitrary regions, from single patches to non-contiguous areas and entire images. We analyze the key ingredients that enable current latent captioners to work in our novel proposed framework. Experiments demonstrate that backbones producing meaningful, dense visual features, such as DINO, are key to achieving state-of-the-art performance in multiple region-based captioning tasks. Compared to other baselines and state-of-the-art competitors, our models achieve better performance on zero-shot dense, region-set, and a newly introduced trace captioning task, highlighting the effectiveness of patch-wise semantic representations for scalable caption generation. Project page at https://paciosoft.com/Patch-ioner/ .

Embedding vision-language models (VLMs) are typically pretrained with short text windows (<77 tokens), which forces the truncation of long-format captions. Yet, the distribution of biomedical captions from large-scale open source literature reveals that a huge portion of captions far exceed 77 tokens. To this end, we investigate the impact of pretraining on long-format biomedical captions by extending the context length of text encoders in VLMs. We find that longer context (thus, enabling additional supervision provided in long-format captions) correlates with better retrieval and classification performance. Given this finding, we introduce BIOMEDICA-LongCAP, a dataset of 1M image-caption pairs enriched with context-aware descriptions from full-text articles, providing longer and additional textual supervision. Using BIOMEDICA-LongCAP, we train BMC-LongCLIP, a long-context biomedical VLM with a text encoder supporting windows of up to 512 tokens. Our model extends context capacity by 6.6x, reducing token waste from 55% to just 2.2%. On long-caption retrieval benchmarks, BMC-LongCLIP achieves up to +30% absolute gains in Recall@1 and +2% average improvements in classification, while also converging faster than short-context. Our results demonstrate that long-context modeling is a promising direction for advancing biomedical VLMs.

Modern image captioning models are usually trained with text similarity objectives. However, since reference captions in public datasets often describe the most salient common objects, models trained with text similarity objectives tend to ignore specific and detailed aspects of an image that distinguish it from others. Toward more descriptive and distinctive caption generation, we propose using CLIP, a multimodal encoder trained on huge image-text pairs from web, to calculate multimodal similarity and use it as a reward function. We also propose a simple finetuning strategy of the CLIP text encoder to improve grammar that does not require extra text annotation. This completely eliminates the need for reference captions during the reward computation. To comprehensively evaluate descriptive captions, we introduce FineCapEval, a new dataset for caption evaluation with fine-grained criteria: overall, background, object, relations. In our experiments on text-to-image retrieval and FineCapEval, the proposed CLIP-guided model generates more distinctive captions than the CIDEr-optimized model. We also show that our unsupervised grammar finetuning of the CLIP text encoder alleviates the degeneration problem of the naive CLIP reward. Lastly, we show human analysis where the annotators strongly prefer the CLIP reward to the CIDEr and MLE objectives according to various criteria. Code and Data: https://github.com/j-min/CLIP-Caption-Reward

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures, commonly encoded in the SMILES representation. However, current LLMs struggle to interpret SMILES, even failing to carry out basic tasks such as counting molecular rings. To address this limitation, we introduce CLEANMOL, a novel framework that formulates SMILES parsing into a suite of clean and deterministic tasks explicitly designed to promote graph-level molecular comprehension. These tasks span from subgraph matching to global graph matching, providing structured supervision aligned with molecular structural properties. We construct a molecular pretraining dataset with adaptive difficulty scoring and pre-train open-source LLMs on these tasks. Our results show that CLEANMOL not only enhances structural comprehension but also achieves the best or competes with the baseline on the Mol-Instructions benchmark.

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

Video Captioning (VC) is a challenging multi-modal task since it requires describing the scene in language by understanding various and complex videos. For machines, the traditional VC follows the "imaging-compression-decoding-and-then-captioning" pipeline, where compression is pivot for storage and transmission. However, in such a pipeline, some potential shortcomings are inevitable, i.e., information redundancy resulting in low efficiency and information loss during the sampling process for captioning. To address these problems, in this paper, we propose a novel VC pipeline to generate captions directly from the compressed measurement, which can be captured by a snapshot compressive sensing camera and we dub our model SnapCap. To be more specific, benefiting from the signal simulation, we have access to obtain abundant measurement-video-annotation data pairs for our model. Besides, to better extract language-related visual representations from the compressed measurement, we propose to distill the knowledge from videos via a pre-trained CLIP with plentiful language-vision associations to guide the learning of our SnapCap. To demonstrate the effectiveness of SnapCap, we conduct experiments on two widely-used VC datasets. Both the qualitative and quantitative results verify the superiority of our pipeline over conventional VC pipelines. In particular, compared to the "caption-after-reconstruction" methods, our SnapCap can run at least 3times faster, and achieve better caption results.

Zero-shot Image Captioning (ZIC) increasingly utilizes synthetic datasets generated by text-to-image (T2I) models to mitigate the need for costly manual annotation. However, these T2I models often produce images that exhibit semantic misalignments with their corresponding input captions (e.g., missing objects, incorrect attributes), resulting in noisy synthetic image-caption pairs that can hinder model training. Existing dataset pruning techniques are largely designed for removing noisy text in web-crawled data. However, these methods are ill-suited for the distinct challenges of synthetic data, where captions are typically well-formed, but images may be inaccurate representations. To address this gap, we introduce SynC, a novel framework specifically designed to refine synthetic image-caption datasets for ZIC. Instead of conventional filtering or regeneration, SynC focuses on reassigning captions to the most semantically aligned images already present within the synthetic image pool. Our approach employs a one-to-many mapping strategy by initially retrieving multiple relevant candidate images for each caption. We then apply a cycle-consistency-inspired alignment scorer that selects the best image by verifying its ability to retrieve the original caption via image-to-text retrieval. Extensive evaluations demonstrate that SynC consistently and significantly improves performance across various ZIC models on standard benchmarks (MS-COCO, Flickr30k, NoCaps), achieving state-of-the-art results in several scenarios. SynC offers an effective strategy for curating refined synthetic data to enhance ZIC.

Researchers use figures to communicate rich, complex information in scientific papers. The captions of these figures are critical to conveying effective messages. However, low-quality figure captions commonly occur in scientific articles and may decrease understanding. In this paper, we propose an end-to-end neural framework to automatically generate informative, high-quality captions for scientific figures. To this end, we introduce SCICAP, a large-scale figure-caption dataset based on computer science arXiv papers published between 2010 and 2020. After pre-processing - including figure-type classification, sub-figure identification, text normalization, and caption text selection - SCICAP contained more than two million figures extracted from over 290,000 papers. We then established baseline models that caption graph plots, the dominant (19.2%) figure type. The experimental results showed both opportunities and steep challenges of generating captions for scientific figures.

Image descriptions can help visually impaired people to quickly understand the image content. While we made significant progress in automatically describing images and optical character recognition, current approaches are unable to include written text in their descriptions, although text is omnipresent in human environments and frequently critical to understand our surroundings. To study how to comprehend text in the context of an image we collect a novel dataset, TextCaps, with 145k captions for 28k images. Our dataset challenges a model to recognize text, relate it to its visual context, and decide what part of the text to copy or paraphrase, requiring spatial, semantic, and visual reasoning between multiple text tokens and visual entities, such as objects. We study baselines and adapt existing approaches to this new task, which we refer to as image captioning with reading comprehension. Our analysis with automatic and human studies shows that our new TextCaps dataset provides many new technical challenges over previous datasets.

We present a self-supervised method to improve an agent's abilities in describing arbitrary objects while actively exploring a generic environment. This is a challenging problem, as current models struggle to obtain coherent image captions due to different camera viewpoints and clutter. We propose a three-phase framework to fine-tune existing captioning models that enhances caption accuracy and consistency across views via a consensus mechanism. First, an agent explores the environment, collecting noisy image-caption pairs. Then, a consistent pseudo-caption for each object instance is distilled via consensus using a large language model. Finally, these pseudo-captions are used to fine-tune an off-the-shelf captioning model, with the addition of contrastive learning. We analyse the performance of the combination of captioning models, exploration policies, pseudo-labeling methods, and fine-tuning strategies, on our manually labeled test set. Results show that a policy can be trained to mine samples with higher disagreement compared to classical baselines. Our pseudo-captioning method, in combination with all policies, has a higher semantic similarity compared to other existing methods, and fine-tuning improves caption accuracy and consistency by a significant margin. Code and test set annotations available at https://hsp-iit.github.io/embodied-captioning/

The task of image captioning demands an algorithm to generate natural language descriptions of visual inputs. Recent advancements have seen a convergence between image captioning research and the development of Large Language Models (LLMs) and Multimodal LLMs -- like GPT-4V and Gemini -- which extend the capabilities of text-only LLMs to multiple modalities. This paper investigates whether Multimodal LLMs can supplant traditional image captioning networks by evaluating their performance on various image description benchmarks. We explore both the zero-shot capabilities of these models and their adaptability to different semantic domains through fine-tuning methods, including prompt learning, prefix tuning, and low-rank adaptation. Our results demonstrate that while Multimodal LLMs achieve impressive zero-shot performance, fine-tuning for specific domains while maintaining their generalization capabilities intact remains challenging. We discuss the implications of these findings for future research in image captioning and the development of more adaptable Multimodal LLMs.

Molecule and text representation learning has gained increasing interest due to its potential for enhancing the understanding of chemical information. However, existing models often struggle to capture subtle differences between molecules and their descriptions, as they lack the ability to learn fine-grained alignments between molecular substructures and chemical phrases. To address this limitation, we introduce MolBridge, a novel molecule-text learning framework based on substructure-aware alignments. Specifically, we augment the original molecule-description pairs with additional alignment signals derived from molecular substructures and chemical phrases. To effectively learn from these enriched alignments, MolBridge employs substructure-aware contrastive learning, coupled with a self-refinement mechanism that filters out noisy alignment signals. Experimental results show that MolBridge effectively captures fine-grained correspondences and outperforms state-of-the-art baselines on a wide range of molecular benchmarks, highlighting the significance of substructure-aware alignment in molecule-text learning.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Image captioning systems are unable to generate fine-grained captions as they are trained on data that is either noisy (alt-text) or generic (human annotations). This is further exacerbated by maximum likelihood training that encourages generation of frequently occurring phrases. Previous works have tried to address this limitation by fine-tuning captioners with a self-retrieval (SR) reward. However, we find that SR fine-tuning has a tendency to reduce caption faithfulness and even hallucinate. In this work, we circumvent this bottleneck by improving the MLE initialization of the captioning system and designing a curriculum for the SR fine-tuning process. To this extent, we present (1) Visual Caption Boosting, a novel framework to instill fine-grainedness in generic image captioning datasets while remaining anchored in human annotations; and (2) BagCurri, a carefully designed training curriculum that more optimally leverages the contrastive nature of the self-retrieval reward. Jointly, they enable the captioner to describe fine-grained aspects in the image while preserving faithfulness to ground-truth captions. Our approach outperforms previous work by +8.9% on SR against 99 random distractors (RD100) (Dessi et al., 2023); and +7.6% on ImageCoDe. Additionally, existing metrics to evaluate captioning systems fail to reward diversity or evaluate a model's fine-grained understanding ability. Our third contribution addresses this by proposing self-retrieval from the lens of evaluation. We introduce TrueMatch, a benchmark comprising bags of highly similar images that uses SR to assess the captioner's ability to capture subtle visual distinctions. We evaluate and compare several state-of-the-art open-source MLLMs on TrueMatch, and find that our SR approach outperforms them all by a significant margin (e.g. +4.8% - 7.1% over Cambrian) while having 1-2 orders of magnitude fewer parameters.

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.

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance the new field of LLM for molecular discovery, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. Based on our proposed taxonomy for both problems, we analyze representative techniques in each category, highlighting how LLM capabilities are leveraged across different learning settings. In addition, we include the commonly used datasets and evaluation protocols. We conclude by discussing key challenges and future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as biomolecular studies remains limited. To address this challenge, we introduce Mol-Instructions, a meticulously curated, comprehensive instruction dataset expressly designed for the biomolecular realm. Mol-Instructions is composed of three pivotal components: molecule-oriented instructions, protein-oriented instructions, and biomolecular text instructions, each curated to enhance the understanding and prediction capabilities of LLMs concerning biomolecular features and behaviors. Through extensive instruction tuning experiments on the representative LLM, we underscore the potency of Mol-Instructions to enhance the adaptability and cognitive acuity of large models within the complex sphere of biomolecular studies, thereby promoting advancements in the biomolecular research community. Mol-Instructions is made publicly accessible for future research endeavors and will be subjected to continual updates for enhanced applicability.

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount significance in facilitating biomedical research. However, existing multimodal molecular foundation models exhibit limitations in capturing intricate connections between molecular structures and texts, and more importantly, none of them attempt to leverage a wealth of molecular expertise derived from knowledge graphs. In this study, we introduce MolFM, a multimodal molecular foundation model designed to facilitate joint representation learning from molecular structures, biomedical texts, and knowledge graphs. We propose cross-modal attention between atoms of molecular structures, neighbors of molecule entities and semantically related texts to facilitate cross-modal comprehension. We provide theoretical analysis that our cross-modal pre-training captures local and global molecular knowledge by minimizing the distance in the feature space between different modalities of the same molecule, as well as molecules sharing similar structures or functions. MolFM achieves state-of-the-art performance on various downstream tasks. On cross-modal retrieval, MolFM outperforms existing models with 12.13% and 5.04% absolute gains under the zero-shot and fine-tuning settings, respectively. Furthermore, qualitative analysis showcases MolFM's implicit ability to provide grounding from molecular substructures and knowledge graphs. Code and models are available on https://github.com/BioFM/OpenBioMed.

In this work, we aim to analyze and optimize the EnCLAP framework, a state-of-the-art model in automated audio captioning. We investigate the impact of modifying the acoustic encoder components, explore pretraining with different dataset scales, and study the effectiveness of a reranking scheme. Through extensive experimentation and quantitative analysis of generated captions, we develop EnCLAP++, an enhanced version that significantly surpasses the original.

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at https://github.com/ChnQ/LLM4Mol.

Contrastive language-image pre-training (CLIP) models have demonstrated considerable success across various vision-language tasks, such as text-to-image retrieval, where the model is required to effectively process natural language input to produce an accurate visual output. However, current models still face limitations in dealing with linguistic variations in input queries, such as paraphrases, making it challenging to handle a broad range of user queries in real-world applications. In this study, we introduce a straightforward fine-tuning approach to enhance the representations of CLIP models for paraphrases. Our approach involves a two-step paraphrase generation process, where we automatically create two categories of paraphrases from web-scale image captions by leveraging large language models. Subsequently, we fine-tune the CLIP text encoder using these generated paraphrases while freezing the image encoder. Our resulting model, which we call ParaCLIP, exhibits significant improvements over baseline CLIP models across various tasks, including paraphrased retrieval (with rank similarity scores improved by up to 2.0% and 5.6%), Visual Genome Relation and Attribution, as well as seven semantic textual similarity tasks.

Phrase localization is a task that studies the mapping from textual phrases to regions of an image. Given difficulties in annotating phrase-to-object datasets at scale, we develop a Multimodal Alignment Framework (MAF) to leverage more widely-available caption-image datasets, which can then be used as a form of weak supervision. We first present algorithms to model phrase-object relevance by leveraging fine-grained visual representations and visually-aware language representations. By adopting a contrastive objective, our method uses information in caption-image pairs to boost the performance in weakly-supervised scenarios. Experiments conducted on the widely-adopted Flickr30k dataset show a significant improvement over existing weakly-supervised methods. With the help of the visually-aware language representations, we can also improve the previous best unsupervised result by 5.56%. We conduct ablation studies to show that both our novel model and our weakly-supervised strategies significantly contribute to our strong results.

Generating a description of an image is called image captioning. Image captioning requires to recognize the important objects, their attributes and their relationships in an image. It also needs to generate syntactically and semantically correct sentences. Deep learning-based techniques are capable of handling the complexities and challenges of image captioning. In this survey paper, we aim to present a comprehensive review of existing deep learning-based image captioning techniques. We discuss the foundation of the techniques to analyze their performances, strengths and limitations. We also discuss the datasets and the evaluation metrics popularly used in deep learning based automatic image captioning.

The task of describing video content in natural language is commonly referred to as video captioning. Unlike conventional video captions, which are typically brief and widely available, long-form paragraph descriptions in natural language are scarce. This limitation of current datasets is due to the expensive human manual annotation required and to the highly challenging task of explaining the language formation process from the perspective of the underlying story, as a complex system of interconnected events in space and time. Through a thorough analysis of recently published methods and available datasets, we identify a general lack of published resources dedicated to the problem of describing videos in complex language, beyond the level of descriptions in the form of enumerations of simple captions. Furthermore, while state-of-the-art methods produce impressive results on the task of generating shorter captions from videos by direct end-to-end learning between the videos and text, the problem of explaining the relationship between vision and language is still beyond our reach. In this work, we propose a shared representation between vision and language, based on graphs of events in space and time, which can be obtained in an explainable and analytical way, to integrate and connect multiple vision tasks to produce the final natural language description. Moreover, we also demonstrate how our automated and explainable video description generation process can function as a fully automatic teacher to effectively train direct, end-to-end neural student pathways, within a self-supervised neuro-analytical system. We validate that our explainable neuro-analytical approach generates coherent, rich and relevant textual descriptions on videos collected from multiple varied datasets, using both standard evaluation metrics, human annotations and consensus from ensembles of state-of-the-art VLMs.

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.

Deep learning in computational biochemistry has traditionally focused on molecular graphs neural representations; however, recent advances in language models highlight how much scientific knowledge is encoded in text. To bridge these two modalities, we investigate how molecular property information can be transferred from natural language to graph representations. We study property prediction performance gains after using contrastive learning to align neural graph representations with representations of textual descriptions of their characteristics. We implement neural relevance scoring strategies to improve text retrieval, introduce a novel chemically-valid molecular graph augmentation strategy inspired by organic reactions, and demonstrate improved performance on downstream MoleculeNet property classification tasks. We achieve a +4.26% AUROC gain versus models pre-trained on the graph modality alone, and a +1.54% gain compared to recently proposed molecular graph/text contrastively trained MoMu model (Su et al. 2022).

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled sequence-only (e.g., SMILES or SELFIES) generalist molecular LLMs, and researchers are now exploring multimodal approaches that incorporate molecular structural information for further gains. However, a genuinely multimodal, generalist LLM that covers a broad spectrum of molecular tasks has yet to be fully investigated. We observe that naive next token prediction training ignores graph-structural information, limiting an LLM's ability to exploit molecular graphs. To address this, we propose (i) Molecular structure Preference Optimization (MolPO), which facilitates graph usage by optimizing preferences between pairs of correct and perturbed molecular structures, and (ii) an advanced graph encoder with a tailored pre-training strategy to improve the effect of graph utilization by MolPO. Building on these contributions, we introduce Mol-LLM, the first multimodal generalist model that (a) handles a broad spectrum of molecular tasks among molecular LLMs, (b) explicitly leverages molecular-structure information, and (c) takes advantage of extensive instruction tuning. Mol-LLM attains state-of-the-art or comparable results across the most comprehensive molecular-LLM benchmark-even on out-of-distribution datasets for reaction and property prediction, where it surpasses prior generalist molecular LLMs by a large margin.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

The massive growth of image-text data through web crawling inherently presents the challenge of variability in data quality. This paper introduces a novel algorithm, rooted in human knowledge, to compress this vast corpus of web-crawled image-text datasets to a compact and high-quality form. Our method unfolds in three major steps. First, we collect an image-text dataset, wherein each image is associated with multiple captions sourced from diverse origins. Then, to systemically capture human preferences regarding the best caption paired with each image, we establish a comprehensive set of both subjective and objective criteria for critically guiding the alignment assessment from labelers. Lastly, we train a reward model on the annotated dataset to internalize the nuanced human understanding of image-text alignment. The resulting reward model thus can act as a human-like referee to filter misaligned/low-quality image-text pairs. Extensive experiments demonstrate that we are able to secure (or even improve) model performance by compressing the image-text datasets up to ~90%. An impressive example is that, by aggressively reducing the total training sample from 130M to 15.5M (e.g., ~9x smaller), our BLIP-B/16 models still consistently show superior performance compared with the full-size-dataset counterpart on image-text retrieval (Flickr30K, COCO) by ~2.5% in Recall@1, and on image-captioning (Nocaps, COCO) by ~10.0% in CIDEr and ~2.7% in SPICE.

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream tasks: molecular property prediction against up to 19 baseline methods across four datasets, plus zero-shot molecule-morphology matching.

Recent advancements in multimodal models highlight the value of rewritten captions for improving performance, yet key challenges remain. For example, while synthetic captions often provide superior quality and image-text alignment, it is not clear whether they can fully replace AltTexts: the role of synthetic captions and their interaction with original web-crawled AltTexts in pre-training is still not well understood. Moreover, different multimodal foundation models may have unique preferences for specific caption formats, but efforts to identify the optimal captions for each model remain limited. In this work, we propose a novel, controllable, and scalable captioning pipeline designed to generate diverse caption formats tailored to various multimodal models. By examining Short Synthetic Captions (SSC) towards Dense Synthetic Captions (DSC+) as case studies, we systematically explore their effects and interactions with AltTexts across models such as CLIP, multimodal LLMs, and diffusion models. Our findings reveal that a hybrid approach that keeps both synthetic captions and AltTexts can outperform the use of synthetic captions alone, improving both alignment and performance, with each model demonstrating preferences for particular caption formats. This comprehensive analysis provides valuable insights into optimizing captioning strategies, thereby advancing the pre-training of multimodal foundation models.

Recent text-to-image matching models apply contrastive learning to large corpora of uncurated pairs of images and sentences. While such models can provide a powerful score for matching and subsequent zero-shot tasks, they are not capable of generating caption given an image. In this work, we repurpose such models to generate a descriptive text given an image at inference time, without any further training or tuning steps. This is done by combining the visual-semantic model with a large language model, benefiting from the knowledge in both web-scale models. The resulting captions are much less restrictive than those obtained by supervised captioning methods. Moreover, as a zero-shot learning method, it is extremely flexible and we demonstrate its ability to perform image arithmetic in which the inputs can be either images or text, and the output is a sentence. This enables novel high-level vision capabilities such as comparing two images or solving visual analogy tests. Our code is available at: https://github.com/YoadTew/zero-shot-image-to-text.

Accurate and automated captioning of aerial imagery is crucial for applications like environmental monitoring, urban planning, and disaster management. However, this task remains challenging due to complex spatial semantics and domain variability. To address these issues, we introduce AeroLite, a lightweight, tag-guided captioning framework designed to equip small-scale language models (1--3B parameters) with robust and interpretable captioning capabilities specifically for remote sensing images. AeroLite leverages GPT-4o to generate a large-scale, semantically rich pseudo-caption dataset by integrating multiple remote sensing benchmarks, including DLRSD, iSAID, LoveDA, WHU, and RSSCN7. To explicitly capture key semantic elements such as orientation and land-use types, AeroLite employs natural language processing techniques to extract relevant semantic tags. These tags are then learned by a dedicated multi-label CLIP encoder, ensuring precise semantic predictions. To effectively fuse visual and semantic information, we propose a novel bridging multilayer perceptron (MLP) architecture, aligning semantic tags with visual embeddings while maintaining minimal computational overhead. AeroLite's flexible design also enables seamless integration with various pretrained large language models. We adopt a two-stage LoRA-based training approach: the initial stage leverages our pseudo-caption dataset to capture broad remote sensing semantics, followed by fine-tuning on smaller, curated datasets like UCM and Sydney Captions to refine domain-specific alignment. Experimental evaluations demonstrate that AeroLite surpasses significantly larger models (e.g., 13B parameters) in standard captioning metrics, including BLEU and METEOR, while maintaining substantially lower computational costs.

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

Zero-shot video captioning requires that a model generate high-quality captions without human-annotated video-text pairs for training. State-of-the-art approaches to the problem leverage CLIP to extract visual-relevant textual prompts to guide language models in generating captions. These methods tend to focus on one key aspect of the scene and build a caption that ignores the rest of the visual input. To address this issue, and generate more accurate and complete captions, we propose a novel progressive multi-granularity textual prompting strategy for zero-shot video captioning. Our approach constructs three distinct memory banks, encompassing noun phrases, scene graphs of noun phrases, and entire sentences. Moreover, we introduce a category-aware retrieval mechanism that models the distribution of natural language surrounding the specific topics in question. Extensive experiments demonstrate the effectiveness of our method with 5.7%, 16.2%, and 3.4% improvements in terms of the main metric CIDEr on MSR-VTT, MSVD, and VATEX benchmarks compared to existing state-of-the-art.

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.

Image captioning has been a longstanding challenge in vision-language research. With the rise of LLMs, modern Vision-Language Models (VLMs) generate detailed and comprehensive image descriptions. However, benchmarking the quality of such captions remains unresolved. This paper addresses two key questions: (1) How well do current VLMs actually perform on image captioning, particularly compared to humans? We built CapArena, a platform with over 6000 pairwise caption battles and high-quality human preference votes. Our arena-style evaluation marks a milestone, showing that leading models like GPT-4o achieve or even surpass human performance, while most open-source models lag behind. (2) Can automated metrics reliably assess detailed caption quality? Using human annotations from CapArena, we evaluate traditional and recent captioning metrics, as well as VLM-as-a-Judge. Our analysis reveals that while some metrics (e.g., METEOR) show decent caption-level agreement with humans, their systematic biases lead to inconsistencies in model ranking. In contrast, VLM-as-a-Judge demonstrates robust discernment at both the caption and model levels. Building on these insights, we release CapArena-Auto, an accurate and efficient automated benchmark for detailed captioning, achieving 94.3% correlation with human rankings at just $4 per test. Data and resources will be open-sourced at https://caparena.github.io.

Image captioning aims at generating descriptive and meaningful textual descriptions of images, enabling a broad range of vision-language applications. Prior works have demonstrated that harnessing the power of Contrastive Image Language Pre-training (CLIP) offers a promising approach to achieving zero-shot captioning, eliminating the need for expensive caption annotations. However, the widely observed modality gap in the latent space of CLIP harms the performance of zero-shot captioning by breaking the alignment between paired image-text features. To address this issue, we conduct an analysis on the CLIP latent space which leads to two findings. Firstly, we observe that the CLIP's visual feature of image subregions can achieve closer proximity to the paired caption due to the inherent information loss in text descriptions. In addition, we show that the modality gap between a paired image-text can be empirically modeled as a zero-mean Gaussian distribution. Motivated by the findings, we propose a novel zero-shot image captioning framework with text-only training to reduce the modality gap. In particular, we introduce a subregion feature aggregation to leverage local region information, which produces a compact visual representation for matching text representation. Moreover, we incorporate a noise injection and CLIP reranking strategy to boost captioning performance. We also extend our framework to build a zero-shot VQA pipeline, demonstrating its generality. Through extensive experiments on common captioning and VQA datasets such as MSCOCO, Flickr30k and VQAV2, we show that our method achieves remarkable performance improvements. Code is available at https://github.com/Artanic30/MacCap.

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

Recent advancements in large language models have opened new possibilities for generative molecular drug design. We present Chemlactica and Chemma, two language models fine-tuned on a novel corpus of 110M molecules with computed properties, totaling 40B tokens. These models demonstrate strong performance in generating molecules with specified properties and predicting new molecular characteristics from limited samples. We introduce a novel optimization algorithm that leverages our language models to optimize molecules for arbitrary properties given limited access to a black box oracle. Our approach combines ideas from genetic algorithms, rejection sampling, and prompt optimization. It achieves state-of-the-art performance on multiple molecular optimization benchmarks, including an 8% improvement on Practical Molecular Optimization compared to previous methods. We publicly release the training corpus, the language models and the optimization algorithm.

This report introduces a solution to the Topic 1 Zero-shot Image Captioning of 2024 NICE : New frontiers for zero-shot Image Captioning Evaluation. In contrast to NICE 2023 datasets, this challenge involves new annotations by humans with significant differences in caption style and content. Therefore, we enhance image captions effectively through retrieval augmentation and caption grading methods. At the data level, we utilize high-quality captions generated by image caption models as training data to address the gap in text styles. At the model level, we employ OFA (a large-scale visual-language pre-training model based on handcrafted templates) to perform the image captioning task. Subsequently, we propose caption-level strategy for the high-quality caption data generated by the image caption models and integrate them with retrieval augmentation strategy into the template to compel the model to generate higher quality, more matching, and semantically enriched captions based on the retrieval augmentation prompts. Our approach achieves a CIDEr score of 234.11.

Neural captioners are typically trained to mimic human-generated references without optimizing for any specific communication goal, leading to problems such as the generation of vague captions. In this paper, we show that fine-tuning an out-of-the-box neural captioner with a self-supervised discriminative communication objective helps to recover a plain, visually descriptive language that is more informative about image contents. Given a target image, the system must learn to produce a description that enables an out-of-the-box text-conditioned image retriever to identify such image among a set of candidates. We experiment with the popular ClipCap captioner, also replicating the main results with BLIP. In terms of similarity to ground-truth human descriptions, the captions emerging from discriminative finetuning lag slightly behind those generated by the non-finetuned model, when the latter is trained and tested on the same caption dataset. However, when the model is used without further tuning to generate captions for out-of-domain datasets, our discriminatively-finetuned captioner generates descriptions that resemble human references more than those produced by the same captioner without finetuning. We further show that, on the Conceptual Captions dataset, discriminatively finetuned captions are more helpful than either vanilla ClipCap captions or ground-truth captions for human annotators tasked with an image discrimination task.

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.

Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent development of protein language models (pLMs) with supervised fine tuning provides a promising solution to this problem. However, the fine-tuned model is tailored for particular downstream prediction task, and achieving general-purpose protein understanding remains a challenge. In this paper, we introduce Structure-Enhanced Protein Instruction Tuning (SEPIT) framework to bridge this gap. Our approach integrates a noval structure-aware module into pLMs to inform them with structural knowledge, and then connects these enhanced pLMs to large language models (LLMs) to generate understanding of proteins. In this framework, we propose a novel two-stage instruction tuning pipeline that first establishes a basic understanding of proteins through caption-based instructions and then refines this understanding using a mixture of experts (MoEs) to learn more complex properties and functional information with the same amount of activated parameters. Moreover, we construct the largest and most comprehensive protein instruction dataset to date, which allows us to train and evaluate the general-purpose protein understanding model. Extensive experimental results on open-ended generation and closed-set answer tasks demonstrate the superior performance of SEPIT over both closed-source general LLMs and open-source LLMs trained with protein knowledge.

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/.

Identifying the chemical structure from a graphical representation, or image, of a molecule is a challenging pattern recognition task that would greatly benefit drug development. Yet, existing methods for chemical structure recognition do not typically generalize well, and show diminished effectiveness when confronted with domains where data is sparse, or costly to generate, such as hand-drawn molecule images. To address this limitation, we propose a new chemical structure recognition tool that delivers state-of-the-art performance and can adapt to new domains with a limited number of data samples and supervision. Unlike previous approaches, our method provides atom-level localization, and can therefore segment the image into the different atoms and bonds. Our model is the first model to perform OCSR with atom-level entity detection with only SMILES supervision. Through rigorous and extensive benchmarking, we demonstrate the preeminence of our chemical structure recognition approach in terms of data efficiency, accuracy, and atom-level entity prediction.

Image captioning has long been a pivotal task in visual understanding, with recent advancements in vision-language models (VLMs) significantly enhancing the ability to generate detailed image captions. However, the evaluation of detailed image captioning remains underexplored due to outdated evaluation metrics and coarse annotations. In this paper, we introduce DeCapBench along with a novel metric, DCScore, specifically designed for detailed captioning tasks. DCScore evaluates hallucinations and fine-grained comprehensiveness by deconstructing responses into the smallest self-sufficient units, termed primitive information units, and assessing them individually. Our evaluation shows that DCScore aligns more closely with human judgment than other rule-based or model-based metrics. Concurrently, DeCapBench exhibits a high correlation with VLM arena results on descriptive tasks, surpassing existing benchmarks for vision-language models. Additionally, we present an automatic fine-grained feedback collection method, FeedQuill, for preference optimization based on our advanced metric, showing robust generalization capabilities across auto-generated preference data. Extensive experiments on multiple VLMs demonstrate that our method not only significantly reduces hallucinations but also enhances performance across various benchmarks, achieving superior detail captioning performance while surpassing GPT-4o.

High-quality image captions play a crucial role in improving the performance of cross-modal applications such as text-to-image generation, text-to-video generation, and text-image retrieval. To generate long-form, high-quality captions, many recent studies have employed multimodal large language models (MLLMs). However, current MLLMs often produce captions that lack fine-grained details or suffer from hallucinations, a challenge that persists in both open-source and closed-source models. Inspired by Feature-Integration theory, which suggests that attention must focus on specific regions to integrate visual information effectively, we propose a divide-then-aggregate strategy. Our method first divides the image into semantic and spatial patches to extract fine-grained details, enhancing the model's local perception of the image. These local details are then hierarchically aggregated to generate a comprehensive global description. To address hallucinations and inconsistencies in the generated captions, we apply a semantic-level filtering process during hierarchical aggregation. This training-free pipeline can be applied to both open-source models (LLaVA-1.5, LLaVA-1.6, Mini-Gemini) and closed-source models (Claude-3.5-Sonnet, GPT-4o, GLM-4V-Plus). Extensive experiments demonstrate that our method generates more detailed, reliable captions, advancing multimodal description generation without requiring model retraining. The source code are available at https://github.com/GeWu-Lab/Patch-Matters

Recent advances in visual language models (VLMs) have significantly improved image captioning, but extending these gains to video understanding remains challenging due to the scarcity of fine-grained video captioning datasets. To bridge this gap, we propose a novel zero-shot video captioning approach that combines frame-level scene graphs from a video to obtain intermediate representations for caption generation. Our method first generates frame-level captions using an image VLM, converts them into scene graphs, and consolidates these graphs to produce comprehensive video-level descriptions. To achieve this, we leverage a lightweight graph-to-text model trained solely on text corpora, eliminating the need for video captioning annotations. Experiments on the MSR-VTT and ActivityNet Captions datasets show that our approach outperforms zero-shot video captioning baselines, demonstrating that aggregating frame-level scene graphs yields rich video understanding without requiring large-scale paired data or high inference cost.

This paper examines the problems of severe image-text misalignment and high redundancy in the widely-used large-scale Vision-Language Pre-Training (VLP) datasets. To address these issues, we propose an efficient and straightforward Vision-Language learning algorithm called TL;DR, which aims to compress the existing large VLP data into a small, high-quality set. Our approach consists of two major steps. First, a codebook-based encoder-decoder captioner is developed to select representative samples. Second, a new caption is generated to complement the original captions for selected samples, mitigating the text-image misalignment problem while maintaining uniqueness. As the result, TL;DR enables us to reduce the large dataset into a small set of high-quality data, which can serve as an alternative pre-training dataset. This algorithm significantly speeds up the time-consuming pretraining process. Specifically, TL;DR can compress the mainstream VLP datasets at a high ratio, e.g., reduce well-cleaned CC3M dataset from 2.82M to 0.67M (sim24\%) and noisy YFCC15M from 15M to 2.5M (sim16.7\%). Extensive experiments with three popular VLP models over seven downstream tasks show that VLP model trained on the compressed dataset provided by TL;DR can perform similar or even better results compared with training on the full-scale dataset. The code will be made available at https://github.com/showlab/datacentric.vlp.

Language-image pre-training largely relies on how precisely and thoroughly a text describes its paired image. In practice, however, the contents of an image can be so rich that well describing them requires lengthy captions (e.g., with 10 sentences), which are usually missing in existing datasets. Consequently, there are currently no clear evidences on whether and how language-image pre-training could benefit from long captions. To figure this out, we first re-caption 30M images with detailed descriptions using a pre-trained Multi-modality Large Language Model (MLLM), and then study the usage of the resulting captions under a contrastive learning framework. We observe that, each sentence within a long caption is very likely to describe the image partially (e.g., an object). Motivated by this, we propose to dynamically sample sub-captions from the text label to construct multiple positive pairs, and introduce a grouping loss to match the embeddings of each sub-caption with its corresponding local image patches in a self-supervised manner. Experimental results on a wide rage of downstream tasks demonstrate the consistent superiority of our method, termed DreamLIP, over previous alternatives, highlighting its fine-grained representational capacity. It is noteworthy that, on the tasks of image-text retrieval and semantic segmentation, our model trained with 30M image-text pairs achieves on par or even better performance than CLIP trained with 400M pairs. Project page is available at https://zyf0619sjtu.github.io/dream-lip.

Image Captioning, the task of automatic generation of image captions, has attracted attentions from researchers in many fields of computer science, being computer vision, natural language processing and machine learning in recent years. This paper contributes to research on Image Captioning task in terms of extending dataset to a different language - Vietnamese. So far, there is no existed Image Captioning dataset for Vietnamese language, so this is the foremost fundamental step for developing Vietnamese Image Captioning. In this scope, we first build a dataset which contains manually written captions for images from Microsoft COCO dataset relating to sports played with balls, we called this dataset UIT-ViIC. UIT-ViIC consists of 19,250 Vietnamese captions for 3,850 images. Following that, we evaluate our dataset on deep neural network models and do comparisons with English dataset and two Vietnamese datasets built by different methods. UIT-ViIC is published on our lab website for research purposes.

Generative vision-language models (VLMs) exhibit strong high-level image understanding but lack spatially dense alignment between vision and language modalities, as our findings indicate. Orthogonal to advancements in generative VLMs, another line of research has focused on representation learning for vision-language alignment, targeting zero-shot inference for dense tasks like segmentation. In this work, we bridge these two directions by densely aligning images with synthetic descriptions generated by VLMs. Synthetic captions are inexpensive, scalable, and easy to generate, making them an excellent source of high-level semantic understanding for dense alignment methods. Empirically, our approach outperforms prior work on standard zero-shot open-vocabulary segmentation benchmarks/datasets, while also being more data-efficient.

We address the challenge of representing long captions in vision-language models, such as CLIP. By design these models are limited by fixed, absolute positional encodings, restricting inputs to a maximum of 77 tokens and hindering performance on tasks requiring longer descriptions. Although recent work has attempted to overcome this limit, their proposed approaches struggle to model token relationships over longer distances and simply extend to a fixed new token length. Instead, we propose a generalizable method, named TULIP, able to upgrade the token length to any length for CLIP-like models. We do so by improving the architecture with relative position encodings, followed by a training procedure that (i) distills the original CLIP text encoder into an encoder with relative position encodings and (ii) enhances the model for aligning longer captions with images. By effectively encoding captions longer than the default 77 tokens, our model outperforms baselines on cross-modal tasks such as retrieval and text-to-image generation.

Image captioning, like many tasks involving vision and language, currently relies on Transformer-based architectures for extracting the semantics in an image and translating it into linguistically coherent descriptions. Although successful, the attention operator only considers a weighted summation of projections of the current input sample, therefore ignoring the relevant semantic information which can come from the joint observation of other samples. In this paper, we devise a network which can perform attention over activations obtained while processing other training samples, through a prototypical memory model. Our memory models the distribution of past keys and values through the definition of prototype vectors which are both discriminative and compact. Experimentally, we assess the performance of the proposed model on the COCO dataset, in comparison with carefully designed baselines and state-of-the-art approaches, and by investigating the role of each of the proposed components. We demonstrate that our proposal can increase the performance of an encoder-decoder Transformer by 3.7 CIDEr points both when training in cross-entropy only and when fine-tuning with self-critical sequence training. Source code and trained models are available at: https://github.com/aimagelab/PMA-Net.

Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. However, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. This work introduces MoleculeNet, a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. However, this result comes with caveats. Learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. For quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm.

We present Pix2Cap-COCO, the first panoptic pixel-level caption dataset designed to advance fine-grained visual understanding. To achieve this, we carefully design an automated annotation pipeline that prompts GPT-4V to generate pixel-aligned, instance-specific captions for individual objects within images, enabling models to learn more granular relationships between objects and their contexts. This approach results in 167,254 detailed captions, with an average of 22.94 words per caption. Building on Pix2Cap-COCO, we introduce a novel task, panoptic segmentation-captioning, which challenges models to recognize instances in an image and provide detailed descriptions for each simultaneously. To benchmark this task, we design a robust baseline based on X-Decoder. The experimental results demonstrate that Pix2Cap-COCO is a particularly challenging dataset, as it requires models to excel in both fine-grained visual understanding and detailed language generation. Furthermore, we leverage Pix2Cap-COCO for Supervised Fine-Tuning (SFT) on large multimodal models (LMMs) to enhance their performance. For example, training with Pix2Cap-COCO significantly improves the performance of GPT4RoI, yielding gains in CIDEr +1.4%, ROUGE +0.4%, and SPICE +0.5% on Visual Genome dataset, and strengthens its region understanding ability on the ViP-BENCH, with an overall improvement of +5.1%, including notable increases in recognition accuracy +11.2% and language generation quality +22.2%.

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs propose can often be challenging to make, and are almost never compatible with automated synthesis approaches. To better enable the discovery of functional small molecules, LLMs need to learn a new molecular language that is more effective in predicting properties and inherently synced with automated synthesis technology. Current molecule LLMs are limited by representing molecules based on atoms. In this paper, we argue that just like tokenizing texts into meaning-bearing (sub-)word tokens instead of characters, molecules should be tokenized at the level of functional building blocks, i.e., parts of molecules that bring unique functions and serve as effective building blocks for real-world automated laboratory synthesis. This motivates us to propose mCLM, a modular Chemical-Language Model that comprises a bilingual language model that understands both natural language descriptions of functions and molecular blocks. mCLM front-loads synthesizability considerations while improving the predicted functions of molecules in a principled manner. mCLM, with only 3B parameters, achieves improvements in synthetic accessibility relative to 7 other leading generative AI methods including GPT-5. When tested on 122 out-of-distribution medicines using only building blocks/tokens that are compatible with automated modular synthesis, mCLM outperforms all baselines in property scores and synthetic accessibility. mCLM can also reason on multiple functions and iteratively self-improve to rescue drug candidates that failed late in clinical trials ("fallen angels").

Large datasets of paired images and text have become increasingly popular for learning generic representations for vision and vision-and-language tasks. Such datasets have been built by querying search engines or collecting HTML alt-text -- since web data is noisy, they require complex filtering pipelines to maintain quality. We explore alternate data sources to collect high quality data with minimal filtering. We introduce RedCaps -- a large-scale dataset of 12M image-text pairs collected from Reddit. Images and captions from Reddit depict and describe a wide variety of objects and scenes. We collect data from a manually curated set of subreddits, which give coarse image labels and allow us to steer the dataset composition without labeling individual instances. We show that captioning models trained on RedCaps produce rich and varied captions preferred by humans, and learn visual representations that transfer to many downstream tasks.

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5{Github}.

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

Image captioning is a crucial task with applications in a wide range of domains, including healthcare and education. Despite extensive research on English image captioning datasets, the availability of such datasets for Vietnamese remains limited, with only two existing datasets. In this study, we introduce KTVIC, a comprehensive Vietnamese Image Captioning dataset focused on the life domain, covering a wide range of daily activities. This dataset comprises 4,327 images and 21,635 Vietnamese captions, serving as a valuable resource for advancing image captioning in the Vietnamese language. We conduct experiments using various deep neural networks as the baselines on our dataset, evaluating them using the standard image captioning metrics, including BLEU, METEOR, CIDEr, and ROUGE. Our findings underscore the effectiveness of the proposed dataset and its potential contributions to the field of image captioning in the Vietnamese context.

Image captions serve as efficient surrogates for visual content in multimodal systems such as retrieval, recommendation, and multi-step agentic inference pipelines. Yet current evaluation practices miss a fundamental question: Can captions stand-in for images in real downstream tasks? We propose a utility-based benchmark, CaptionQA, to evaluate model-generated captions, where caption quality is measured by how well it supports downstream tasks. CaptionQA is an extensible domain-dependent benchmark covering 4 domains--Natural, Document, E-commerce, and Embodied AI--each with fine-grained taxonomies (25 top-level and 69 subcategories) that identify useful information for domain-specific tasks. CaptionQA builds 33,027 densely annotated multiple-choice questions (50.3 per image on average) that explicitly require visual information to answer, providing a comprehensive probe of caption utility. In our evaluation protocol, an LLM answers these questions using captions alone, directly measuring whether captions preserve image-level utility and are utilizable by a downstream LLM. Evaluating state-of-the-art MLLMs reveals substantial gaps between the image and its caption utility. Notably, models nearly identical on traditional image-QA benchmarks lower by up to 32% in caption utility. We release CaptionQA along with an open-source pipeline for extension to new domains. The code is available at https://github.com/bronyayang/CaptionQA.

Video captioning aims to generate natural language descriptions according to the content, where representation learning plays a crucial role. Existing methods are mainly developed within the supervised learning framework via word-by-word comparison of the generated caption against the ground-truth text without fully exploiting linguistic semantics. In this work, we propose a hierarchical modular network to bridge video representations and linguistic semantics from three levels before generating captions. In particular, the hierarchy is composed of: (I) Entity level, which highlights objects that are most likely to be mentioned in captions. (II) Predicate level, which learns the actions conditioned on highlighted objects and is supervised by the predicate in captions. (III) Sentence level, which learns the global semantic representation and is supervised by the whole caption. Each level is implemented by one module. Extensive experimental results show that the proposed method performs favorably against the state-of-the-art models on the two widely-used benchmarks: MSVD 104.0% and MSR-VTT 51.5% in CIDEr score.

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.

Text-based foundation models have become an important part of scientific discovery, with molecular foundation models accelerating advancements in material science and molecular design.However, existing models are constrained by closed-vocabulary tokenizers that capture only a fraction of molecular space. In this work, we systematically evaluate 34 tokenizers, including 19 chemistry-specific ones, and reveal significant gaps in their coverage of the SMILES molecular representation. To assess the impact of tokenizer choice, we introduce n-gram language models as a low-cost proxy and validate their effectiveness by pretraining and finetuning 18 RoBERTa-style encoders for molecular property prediction. To overcome the limitations of existing tokenizers, we propose two new tokenizers -- Smirk and Smirk-GPE -- with full coverage of the OpenSMILES specification. The proposed tokenizers systematically integrate nuclear, electronic, and geometric degrees of freedom; facilitating applications in pharmacology, agriculture, biology, and energy storage. Our results highlight the need for open-vocabulary modeling and chemically diverse benchmarks in cheminformatics.

Image captioning, which generates natural language descriptions of the visual information in an image, is a crucial task in vision-language research. Previous models have typically addressed this task by aligning the generative capabilities of machines with human intelligence through statistical fitting of existing datasets. While effective for normal images, they may struggle to accurately describe those where certain parts of the image are obscured or edited, unlike humans who excel in such cases. These weaknesses they exhibit, including hallucinations and limited interpretability, often hinder performance in scenarios with shifted association patterns. In this paper, we present a generic image captioning framework that employs causal inference to make existing models more capable of interventional tasks, and counterfactually explainable. Our approach includes two variants leveraging either total effect or natural direct effect. Integrating them into the training process enables models to handle counterfactual scenarios, increasing their generalizability. Extensive experiments on various datasets show that our method effectively reduces hallucinations and improves the model's faithfulness to images, demonstrating high portability across both small-scale and large-scale image-to-text models. The code is available at https://github.com/Aman-4-Real/See-or-Guess.

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

Massive web datasets play a key role in the success of large vision-language models like CLIP and Flamingo. However, the raw web data is noisy, and existing filtering methods to reduce noise often come at the expense of data diversity. Our work focuses on caption quality as one major source of noise, and studies how generated captions can increase the utility of web-scraped datapoints with nondescript text. Through exploring different mixing strategies for raw and generated captions, we outperform the best filtering method proposed by the DataComp benchmark by 2% on ImageNet and 4% on average across 38 tasks, given a candidate pool of 128M image-text pairs. Our best approach is also 2x better at Flickr and MS-COCO retrieval. We then analyze what makes synthetic captions an effective source of text supervision. In experimenting with different image captioning models, we also demonstrate that the performance of a model on standard image captioning benchmarks (e.g., NoCaps CIDEr) is not a reliable indicator of the utility of the captions it generates for multimodal training. Finally, our experiments with using generated captions at DataComp's large scale (1.28B image-text pairs) offer insights into the limitations of synthetic text, as well as the importance of image curation with increasing training data quantity.

Attention-based neural encoder-decoder frameworks have been widely adopted for image captioning. Most methods force visual attention to be active for every generated word. However, the decoder likely requires little to no visual information from the image to predict non-visual words such as "the" and "of". Other words that may seem visual can often be predicted reliably just from the language model e.g., "sign" after "behind a red stop" or "phone" following "talking on a cell". In this paper, we propose a novel adaptive attention model with a visual sentinel. At each time step, our model decides whether to attend to the image (and if so, to which regions) or to the visual sentinel. The model decides whether to attend to the image and where, in order to extract meaningful information for sequential word generation. We test our method on the COCO image captioning 2015 challenge dataset and Flickr30K. Our approach sets the new state-of-the-art by a significant margin.

In this paper we describe the Microsoft COCO Caption dataset and evaluation server. When completed, the dataset will contain over one and a half million captions describing over 330,000 images. For the training and validation images, five independent human generated captions will be provided. To ensure consistency in evaluation of automatic caption generation algorithms, an evaluation server is used. The evaluation server receives candidate captions and scores them using several popular metrics, including BLEU, METEOR, ROUGE and CIDEr. Instructions for using the evaluation server are provided.

Writing Assistants (e.g., Grammarly, Microsoft Copilot) traditionally generate diverse image captions by employing syntactic and semantic variations to describe image components. However, human-written captions prioritize conveying a central message alongside visual descriptions using pragmatic cues. To enhance pragmatic diversity, it is essential to explore alternative ways of communicating these messages in conjunction with visual content. To address this challenge, we propose RONA, a novel prompting strategy for Multi-modal Large Language Models (MLLM) that leverages Coherence Relations as an axis for variation. We demonstrate that RONA generates captions with better overall diversity and ground-truth alignment, compared to MLLM baselines across multiple domains. Our code is available at: https://github.com/aashish2000/RONA

Understanding biological processes, drug development, and biotechnological advancements requires detailed analysis of protein structures and sequences, a task in protein research that is inherently complex and time-consuming when performed manually. To streamline this process, we introduce ProteinGPT, a state-of-the-art multi-modal protein chat system, that allows users to upload protein sequences and/or structures for comprehensive protein analysis and responsive inquiries. ProteinGPT seamlessly integrates protein sequence and structure encoders with linear projection layers for precise representation adaptation, coupled with a large language model (LLM) to generate accurate and contextually relevant responses. To train ProteinGPT, we construct a large-scale dataset of 132,092 proteins with annotations, and optimize the instruction-tuning process using GPT-4o. This innovative system ensures accurate alignment between the user-uploaded data and prompts, simplifying protein analysis. Experiments show that ProteinGPT can produce promising responses to proteins and their corresponding questions.

While image captioning has gained significant attention, the potential of captioning time-series images, prevalent in areas like finance and healthcare, remains largely untapped. Existing time-series captioning methods typically offer generic, domain-agnostic descriptions of time-series shapes and struggle to adapt to new domains without substantial retraining. To address these limitations, we introduce TADACap, a retrieval-based framework to generate domain-aware captions for time-series images, capable of adapting to new domains without retraining. Building on TADACap, we propose a novel retrieval strategy that retrieves diverse image-caption pairs from a target domain database, namely TADACap-diverse. We benchmarked TADACap-diverse against state-of-the-art methods and ablation variants. TADACap-diverse demonstrates comparable semantic accuracy while requiring significantly less annotation effort.

Captions are crucial for understanding scientific visualizations and documents. Existing captioning methods for scientific figures rely on figure-caption pairs extracted from documents for training, many of which fall short with respect to metrics like helpfulness, explainability, and visual-descriptiveness [15] leading to generated captions being misaligned with reader preferences. To enable the generation of high-quality figure captions, we introduce FigCaps-HF a new framework for figure-caption generation that can incorporate domain expert feedback in generating captions optimized for reader preferences. Our framework comprises of 1) an automatic method for evaluating quality of figure-caption pairs, 2) a novel reinforcement learning with human feedback (RLHF) method to optimize a generative figure-to-caption model for reader preferences. We demonstrate the effectiveness of our simple learning framework by improving performance over standard fine-tuning across different types of models. In particular, when using BLIP as the base model, our RLHF framework achieves a mean gain of 35.7%, 16.9%, and 9% in ROUGE, BLEU, and Meteor, respectively. Finally, we release a large-scale benchmark dataset with human feedback on figure-caption pairs to enable further evaluation and development of RLHF techniques for this problem.

Although Multimodal Large Language Models (MLLMs) have demonstrated proficiency in video captioning, practical applications require captions that follow specific user instructions rather than generating exhaustive, unconstrained descriptions. Current benchmarks, however, primarily assess descriptive comprehensiveness while largely overlooking instruction-following capabilities. To address this gap, we introduce IF-VidCap, a new benchmark for evaluating controllable video captioning, which contains 1,400 high-quality samples. Distinct from existing video captioning or general instruction-following benchmarks, IF-VidCap incorporates a systematic framework that assesses captions on two dimensions: format correctness and content correctness. Our comprehensive evaluation of over 20 prominent models reveals a nuanced landscape: despite the continued dominance of proprietary models, the performance gap is closing, with top-tier open-source solutions now achieving near-parity. Furthermore, we find that models specialized for dense captioning underperform general-purpose MLLMs on complex instructions, indicating that future work should simultaneously advance both descriptive richness and instruction-following fidelity.

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

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score. The dataset and the benchmark are available at https://huggingface.co/datasets/tsynbio/ProteinLMBench.

In recent years, automatic generation of image descriptions (captions), that is, image captioning, has attracted a great deal of attention. In this paper, we particularly consider generating Japanese captions for images. Since most available caption datasets have been constructed for English language, there are few datasets for Japanese. To tackle this problem, we construct a large-scale Japanese image caption dataset based on images from MS-COCO, which is called STAIR Captions. STAIR Captions consists of 820,310 Japanese captions for 164,062 images. In the experiment, we show that a neural network trained using STAIR Captions can generate more natural and better Japanese captions, compared to those generated using English-Japanese machine translation after generating English captions.