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Dec 5

Exploring the Capabilities of LLM Encoders for Image-Text Retrieval in Chest X-rays

Vision-language pretraining has advanced image-text alignment, yet progress in radiology remains constrained by the heterogeneity of clinical reports, including abbreviations, impression-only notes, and stylistic variability. Unlike general-domain settings where more data often leads to better performance, naively scaling to large collections of noisy reports can plateau or even degrade model learning. We ask whether large language model (LLM) encoders can provide robust clinical representations that transfer across diverse styles and better guide image-text alignment. We introduce LLM2VEC4CXR, a domain-adapted LLM encoder for chest X-ray reports, and LLM2CLIP4CXR, a dual-tower framework that couples this encoder with a vision backbone. LLM2VEC4CXR improves clinical text understanding over BERT-based baselines, handles abbreviations and style variation, and achieves strong clinical alignment on report-level metrics. LLM2CLIP4CXR leverages these embeddings to boost retrieval accuracy and clinically oriented scores, with stronger cross-dataset generalization than prior medical CLIP variants. Trained on 1.6M CXR studies from public and private sources with heterogeneous and noisy reports, our models demonstrate that robustness -- not scale alone -- is the key to effective multimodal learning. We release models to support further research in medical image-text representation learning.

  • 8 authors
·
Sep 17

SoftTiger: A Clinical Foundation Model for Healthcare Workflows

We introduce SoftTiger, a clinical large language model (CLaM) designed as a foundation model for healthcare workflows. The narrative and unstructured nature of clinical notes is a major obstacle for healthcare intelligentization. We address a critical problem of structuring clinical notes into clinical data, according to international interoperability standards. We collect and annotate data for three subtasks, namely, international patient summary, clinical impression and medical encounter. We then supervised fine-tuned a state-of-the-art LLM using public and credentialed clinical data. The training is orchestrated in a way that the target model can first support basic clinical tasks such as abbreviation expansion and temporal information extraction, and then learn to perform more complex downstream clinical tasks. Moreover, we address several modeling challenges in the healthcare context, e.g., extra long context window. Our blind pairwise evaluation shows that SoftTiger outperforms other popular open-source models and GPT-3.5, comparable to Gemini-pro, with a mild gap from GPT-4. We believe that LLMs may become a step-stone towards healthcare digitalization and democratization. Therefore, we publicly release SoftTiger models at scales of 13 billion and 70 billion parameters, as well as datasets and code for our innovative scalable evaluation, hopefully, making a significant contribution to the healthcare industry.

  • 5 authors
·
Feb 29, 2024

R2R: Efficiently Navigating Divergent Reasoning Paths with Small-Large Model Token Routing

Large Language Models (LLMs) achieve impressive reasoning capabilities at the cost of substantial inference overhead, posing substantial deployment challenges. Although distilled Small Language Models (SLMs) significantly enhance efficiency, their performance suffers as they fail to follow LLMs' reasoning paths. Luckily, we reveal that only a small fraction of tokens genuinely diverge reasoning paths between LLMs and SLMs. Most generated tokens are either identical or exhibit neutral differences, such as minor variations in abbreviations or expressions. Leveraging this insight, we introduce **Roads to Rome (R2R)**, a neural token routing method that selectively utilizes LLMs only for these critical, path-divergent tokens, while leaving the majority of token generation to the SLM. We also develop an automatic data generation pipeline that identifies divergent tokens and generates token-level routing labels to train the lightweight router. We apply R2R to combine R1-1.5B and R1-32B models from the DeepSeek family, and evaluate on challenging math, coding, and QA benchmarks. With an average activated parameter size of 5.6B, R2R surpasses the average accuracy of R1-7B by 1.6x, outperforming even the R1-14B model. Compared to R1-32B, it delivers a 2.8x wall-clock speedup with comparable performance, advancing the Pareto frontier of test-time scaling efficiency. Our code is available at https://github.com/thu-nics/R2R.

  • 9 authors
·
May 27 2

GTR-CoT: Graph Traversal as Visual Chain of Thought for Molecular Structure Recognition

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.

Precise Legal Sentence Boundary Detection for Retrieval at Scale: NUPunkt and CharBoundary

We present NUPunkt and CharBoundary, two sentence boundary detection libraries optimized for high-precision, high-throughput processing of legal text in large-scale applications such as due diligence, e-discovery, and legal research. These libraries address the critical challenges posed by legal documents containing specialized citations, abbreviations, and complex sentence structures that confound general-purpose sentence boundary detectors. Our experimental evaluation on five diverse legal datasets comprising over 25,000 documents and 197,000 annotated sentence boundaries demonstrates that NUPunkt achieves 91.1% precision while processing 10 million characters per second with modest memory requirements (432 MB). CharBoundary models offer balanced and adjustable precision-recall tradeoffs, with the large model achieving the highest F1 score (0.782) among all tested methods. Notably, NUPunkt provides a 29-32% precision improvement over general-purpose tools while maintaining exceptional throughput, processing multi-million document collections in minutes rather than hours. Both libraries run efficiently on standard CPU hardware without requiring specialized accelerators. NUPunkt is implemented in pure Python with zero external dependencies, while CharBoundary relies only on scikit-learn and optional ONNX runtime integration for optimized performance. Both libraries are available under the MIT license, can be installed via PyPI, and can be interactively tested at https://sentences.aleainstitute.ai/. These libraries address critical precision issues in retrieval-augmented generation systems by preserving coherent legal concepts across sentences, where each percentage improvement in precision yields exponentially greater reductions in context fragmentation, creating cascading benefits throughout retrieval pipelines and significantly enhancing downstream reasoning quality.

  • 3 authors
·
Apr 5

TexPrax: A Messaging Application for Ethical, Real-time Data Collection and Annotation

Collecting and annotating task-oriented dialog data is difficult, especially for highly specific domains that require expert knowledge. At the same time, informal communication channels such as instant messengers are increasingly being used at work. This has led to a lot of work-relevant information that is disseminated through those channels and needs to be post-processed manually by the employees. To alleviate this problem, we present TexPrax, a messaging system to collect and annotate problems, causes, and solutions that occur in work-related chats. TexPrax uses a chatbot to directly engage the employees to provide lightweight annotations on their conversation and ease their documentation work. To comply with data privacy and security regulations, we use an end-to-end message encryption and give our users full control over their data which has various advantages over conventional annotation tools. We evaluate TexPrax in a user-study with German factory employees who ask their colleagues for solutions on problems that arise during their daily work. Overall, we collect 202 task-oriented German dialogues containing 1,027 sentences with sentence-level expert annotations. Our data analysis also reveals that real-world conversations frequently contain instances with code-switching, varying abbreviations for the same entity, and dialects which NLP systems should be able to handle.

  • 7 authors
·
Aug 16, 2022

GUESS:GradUally Enriching SyntheSis for Text-Driven Human Motion Generation

In this paper, we propose a novel cascaded diffusion-based generative framework for text-driven human motion synthesis, which exploits a strategy named GradUally Enriching SyntheSis (GUESS as its abbreviation). The strategy sets up generation objectives by grouping body joints of detailed skeletons in close semantic proximity together and then replacing each of such joint group with a single body-part node. Such an operation recursively abstracts a human pose to coarser and coarser skeletons at multiple granularity levels. With gradually increasing the abstraction level, human motion becomes more and more concise and stable, significantly benefiting the cross-modal motion synthesis task. The whole text-driven human motion synthesis problem is then divided into multiple abstraction levels and solved with a multi-stage generation framework with a cascaded latent diffusion model: an initial generator first generates the coarsest human motion guess from a given text description; then, a series of successive generators gradually enrich the motion details based on the textual description and the previous synthesized results. Notably, we further integrate GUESS with the proposed dynamic multi-condition fusion mechanism to dynamically balance the cooperative effects of the given textual condition and synthesized coarse motion prompt in different generation stages. Extensive experiments on large-scale datasets verify that GUESS outperforms existing state-of-the-art methods by large margins in terms of accuracy, realisticness, and diversity. Code is available at https://github.com/Xuehao-Gao/GUESS.

  • 6 authors
·
Jan 4, 2024

Generative Large Language Models Are All-purpose Text Analytics Engines: Text-to-text Learning Is All Your Need

Objective To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning. Methods We formulated 7 key clinical NLP tasks as text-to-text learning and solved them using one unified generative clinical LLM, GatorTronGPT, developed using GPT-3 architecture and trained with up to 20 billion parameters. We adopted soft prompts (i.e., trainable vectors) with frozen LLM, where the LLM parameters were not updated (i.e., frozen) and only the vectors of soft prompts were updated, known as prompt tuning. We added additional soft prompts as a prefix to the input layer, which were optimized during the prompt tuning. We evaluated the proposed method using 7 clinical NLP tasks and compared them with previous task-specific solutions based on Transformer models. Results and Conclusion The proposed approach achieved state-of-the-art performance for 5 out of 7 major clinical NLP tasks using one unified generative LLM. Our approach outperformed previous task-specific transformer models by ~3% for concept extraction and 7% for relation extraction applied to social determinants of health, 3.4% for clinical concept normalization, 3.4~10% for clinical abbreviation disambiguation, and 5.5~9% for natural language inference. Our approach also outperformed a previously developed prompt-based machine reading comprehension (MRC) model, GatorTron-MRC, for clinical concept and relation extraction. The proposed approach can deliver the ``one model for all`` promise from training to deployment using a unified generative LLM.

  • 9 authors
·
Dec 10, 2023

MARK: Memory Augmented Refinement of Knowledge

Large Language Models (LLMs) assist in specialized tasks but struggle to align with evolving domain knowledge without costly fine-tuning. Domain knowledge consists of: Knowledge: Immutable facts (e.g., 'A stone is solid') and generally accepted principles (e.g., ethical standards); Refined Memory: Evolving insights shaped by business needs and real-world changes. However, a significant gap often exists between a domain expert's deep, nuanced understanding and the system's domain knowledge, which can hinder accurate information retrieval and application. Our Memory-Augmented Refinement of Knowledge (MARK) framework enables LLMs to continuously learn without retraining by leveraging structured refined memory, inspired by the Society of Mind. MARK operates through specialized agents, each serving a distinct role: Residual Refined Memory Agent: Stores and retrieves domain-specific insights to maintain context over time; User Question Refined Memory Agent: Captures user-provided facts, abbreviations, and terminology for better comprehension; LLM Response Refined Memory Agent: Extracts key elements from responses for refinement and personalization. These agents analyse stored refined memory, detect patterns, resolve contradictions, and improve response accuracy. Temporal factors like recency and frequency prioritize relevant information while discarding outdated insights. MARK enhances LLMs in multiple ways: Ground Truth Strategy: Reduces hallucinations by establishing a structured reference; Domain-Specific Adaptation: Essential for fields like healthcare, law, and manufacturing, where proprietary insights are absent from public datasets; Personalized AI Assistants: Improves virtual assistants by remembering user preferences, ensuring coherent responses over time.

  • 3 authors
·
May 8

StochasTok: Improving Fine-Grained Subword Understanding in LLMs

Subword-level understanding is integral to numerous tasks, including understanding multi-digit numbers, spelling mistakes, abbreviations, rhyming, and wordplay. Despite this, current large language models (LLMs) still often struggle with seemingly simple subword-level tasks like How many 'r's in 'strawberry'?. A key factor behind these failures is tokenization which obscures the fine-grained structure of words. Current alternatives, such as character-level and dropout tokenization methods, significantly increase computational costs and provide inconsistent improvements. In this paper we revisit tokenization and introduce StochasTok, a simple, efficient stochastic tokenization scheme that randomly splits tokens during training, allowing LLMs to 'see' their internal structure. Our experiments show that pretraining with StochasTok substantially improves LLMs' downstream performance across multiple subword-level language games, including character counting, substring identification, and math tasks. Furthermore, StochasTok's simplicity allows seamless integration at any stage of the training pipeline; and we demonstrate that post-training with StochasTok can instill improved subword understanding into existing pretrained models, thus avoiding costly pretraining from scratch. These dramatic improvements achieved with a minimal change suggest StochasTok holds exciting potential when applied to larger, more capable models. Code open-sourced at: https://github.com/anyasims/stochastok.

  • 8 authors
·
Jun 2