搜索结果：Biomedical reports

Motivation: Biomedical question answering often requires evidence beyond topically retrieved literature, including gene alias resolution, database identifier normalization, and atlas-derived biological measurements. However, existing retrieval-augmented generation (RAG) systems typically follow a fixed workflow and lack an explicit mechanism for deciding when retrieved text is sufficient, when curated biomedical knowledge is required, or when executable evidence assembly over structured measurements should be invoked. This motivates a substrate-aware large language model (LLM) harness that selectively assembles sufficient evidence across literature, knowledge bases, and biological atlases. Results: We introduce BioHarness, an LLM harness for staged biomedical evidence assembly across literature retrieval, curated biomedical knowledge resources, and atlas-derived structured measurements. BioHarness first attempts to answer from reranked literature evidence and escalates through grounded cascade control to REPL-style evidence assembly only when the current evidence is uncertain, weakly grounded, or substrate-mismatched. Across 19,302 biomedical QA items spanning seven answer formats,

Corpus distillation for biomedical large language models (LLMs) seeks to address the pressing challenge of insufficient quantity and quality in open-source annotated scientific corpora, which remains a bottleneck for effective LLM training in biomedical research. This paper proposes a knowledge-driven, agentic framework for scientific corpus distillation, tailored explicitly for LLM training in the biomedical domain, addressing the challenge posed by the complex hierarchy of biomedical knowledge. Central to our approach is a collaborative multi-agent architecture, where specialized agents, each guided by the Medical Subject Headings (MeSH) hierarchy, work in concert to autonomously extract, synthesize, and self-evaluate high-quality textual data from vast scientific literature. This agentic framework collectively generates and refines domain-specific question-answer pairs, ensuring comprehensive coverage and consistency with biomedical ontologies while minimizing manual involvement. Extensive experimental results show that language models trained on our multi-agent distilled datasets achieve notable improvements in biomedical question-answering tasks, outperforming both strong life

Recent advancements in mixed-modal generative have opened new avenues for developing unified biomedical assistants capable of analyzing biomedical images, answering complex questions about them, and generating multimodal patient reports. However, existing datasets face challenges such as small sizes, limited coverage of biomedical tasks and domains, and a reliance on narrow sources. To address these gaps, we present MedMax, a large-scale multimodal biomedical instruction-tuning dataset for mixed-modal foundation models. With 1.47 million instances, MedMax encompasses a diverse range of tasks, including interleaved image-text generation, biomedical image captioning and generation, visual chat, and report understanding. These tasks span knowledge across diverse biomedical domains, including radiology and histopathology, grounded in medical papers and YouTube videos. Subsequently, we fine-tune a mixed-modal foundation model on the MedMax dataset, achieving significant performance improvements: a 26% gain over the Chameleon model and an 18.3% improvement over GPT-4o across 12 downstream biomedical visual question-answering tasks. Finally, we introduce a unified evaluation suite for bio

Biomedical named entity recognition (NER) and entity linking (EL) strongly depend on annotated corpora, but the utility of these resources for benchmarking is often assumed rather than characterized. We present a corpus-centric framework for diagnosing benchmark-relevant properties directly from corpus annotations, concept links, train-test splits, document metadata, and terminology mappings. The framework organizes standardized statistics into five families: (1) scale, density and label distribution, (2) lexical and conceptual structure, (3) train-test overlap, (4) metadata composition, and (5) terminology coverage where applicable. Applying the framework to nine corpora spanning diseases, chemicals, and cell types, we find that corpus properties can differ substantially, even when they address the same apparent task. We find differences in the evaluation signal they provide, the generalization demands they impose, the degree of train-test reuse they permit, and the regions of biomedical literature and concept space they represent. These differences suggest that commonly reported corpus statistics can be insufficient to characterize what biomedical NER and EL benchmarks evaluate.

Prostate cancer (PCa) is one of the most common cancers in men worldwide. Bi-parametric MRI (bp-MRI) and clinical variables are crucial for PCa identification and improving treatment decisions. However, this process is subjective to expert interpretations. Furthermore, most existing computer-aided diagnosis methods focus on imaging-based models, overlooking the clinical context and suffering from data scarcity, limiting their ability to learn robust representations. We propose a geometric multimodal Foundation Model (FM), named MFM-Geom, that learns representations from bp-MRI and clinical reports, encoding visual findings and information from the context of clinical variables. In the representations classification head, the approach leverages symmetric positive definite (SPD) matrices and Riemannian deep learning to integrate imaging-text representations from a biomedical multimodal FM. Using 10% of the training data, MFM-Geom outperformed baseline class token embedding-based classification (+8.3%, AUC-PR of 90.67). Generalization on external dataset confirmed the robustness of fine-tuning biomedical FM, achieving an AUC-PR of 90.6.

Biomedical Question Answering systems play a critical role in processing complex medical queries, yet they often struggle with the intricate nature of medical data and the demand for multi-hop reasoning. In this paper, we propose a model designed to effectively address both direct and sequential questions. While sequential questions are decomposed into a chain of sub-questions to perform reasoning across a chain of steps, direct questions are processed directly to ensure efficiency and minimise processing overhead. Additionally, we leverage multi-source information retrieval and in-context learning to provide rich, relevant context for generating answers. We evaluated our model on the BioCreative IX - MedHopQA Shared Task datasets. Our approach achieves an Exact Match score of 0.84, ranking second on the current leaderboard. These results highlight the model's capability to meet the challenges of Biomedical Question Answering, offering a versatile solution for advancing medical research and practice.

Purpose: We investigated the utilization of privacy-preserving, locally-deployed, open-source Large Language Models (LLMs) to extract diagnostic information from free-text cardiovascular magnetic resonance (CMR) reports. Materials and Methods: We evaluated nine open-source LLMs on their ability to identify diagnoses and classify patients into various cardiac diagnostic categories based on descriptive findings in 109 clinical CMR reports. Performance was quantified using standard classification metrics including accuracy, precision, recall, and F1 score. We also employed confusion matrices to examine patterns of misclassification across models. Results: Most open-source LLMs demonstrated exceptional performance in classifying reports into different diagnostic categories. Google's Gemma2 model achieved the highest average F1 score of 0.98, followed by Qwen2.5:32B and DeepseekR1-32B with F1 scores of 0.96 and 0.95, respectively. All other evaluated models attained average scores above 0.93, with Mistral and DeepseekR1-7B being the only exceptions. The top four LLMs outperformed our board-certified cardiologist (F1 score of 0.94) across all evaluation metrics in analyzing CMR reports.

Vision-language models pre-trained on large scale of unlabeled biomedical images and associated reports learn generalizable semantic representations. These multi-modal representations can benefit various downstream tasks in the biomedical domain. Contrastive learning is widely used to pre-train vision-language models for general natural images and associated captions. Despite its popularity, we found biomedical texts have complex and domain-specific semantics that are often neglected by common contrastive methods. To address this issue, we propose a novel method, perturbed report discrimination, for pre-train biomedical vision-language models. First, we curate a set of text perturbation methods that keep the same words, but disrupt the semantic structure of the sentence. Next, we apply different types of perturbation to reports, and use the model to distinguish the original report from the perturbed ones given the associated image. Parallel to this, we enhance the sensitivity of our method to higher level of granularity for both modalities by contrasting attention-weighted image sub-regions and sub-words in the image-text pairs. We conduct extensive experiments on multiple downstre

Objective: This study aims to review the recent advances in community challenges for biomedical text mining in China. Methods: We collected information of evaluation tasks released in community challenges of biomedical text mining, including task description, dataset description, data source, task type and related links. A systematic summary and comparative analysis were conducted on various biomedical natural language processing tasks, such as named entity recognition, entity normalization, attribute extraction, relation extraction, event extraction, text classification, text similarity, knowledge graph construction, question answering, text generation, and large language model evaluation. Results: We identified 39 evaluation tasks from 6 community challenges that spanned from 2017 to 2023. Our analysis revealed the diverse range of evaluation task types and data sources in biomedical text mining. We explored the potential clinical applications of these community challenge tasks from a translational biomedical informatics perspective. We compared with their English counterparts, and discussed the contributions, limitations, lessons and guidelines of these community challenges, whi

The growing public demand for accessible biomedical information calls for scalable text simplification. While large language models (LLMs) offer solutions, they too struggle with balancing improved readability against preservation of meaning. This report empirically compares how two LLMs - instruction-tuned Mistral-Small 3 24B and the reasoning-augmented QWen2.5 32B- navigate this trade-off in biomedical text simplification, benchmarked against human performance. Our analysis highlights how each model applies distinct operational strategies when simplifying biomedical text. Mistral exhibits a tempered lexical simplification approach that consistently enhances readability across multiple metrics while preserving discourse fidelity (BERTScore: 0.91, statistically comparable to that of humans). In comparison, QWen also attains enhanced readability performance and a reasonable BERTScore of 0.89, but presents a disconnect in balancing between readability and accuracy. Additionally, a comprehensive correlation analysis of a suite of 21 metrics confirms strong functional redundancies in metrics and informs adaptation requirements.

Large language models (LLMs) are increasingly evident for accurate question answering across various domains. However, rigorous evaluation of their performance on complex question-answering (QA) capabilities is essential before deployment in real-world biomedical and healthcare applications. This paper presents our approach to the MedHopQA track of the BioCreative IX shared task, which focuses on multi-hop biomedical question answering involving diseases, genes, and chemicals. We adopt a supervised fine-tuning strategy leveraging LLaMA 3 8B, enhanced with a curated biomedical question-answer dataset compiled from external sources including BioASQ, MedQuAD, and TREC. Three experimental setups are explored: fine-tuning on combined short and long answers, short answers only, and long answers only. While our models demonstrate strong domain understanding, achieving concept-level accuracy scores of up to 0.8, their Exact Match (EM) scores remain significantly lower, particularly in the test phase. We introduce a two-stage inference pipeline for precise short-answer extraction to mitigate verbosity and improve alignment with evaluation metrics. Despite partial improvements, challenges pe

Prion diseases are rare, rapidly progressive, and fatal neurodegenerative disorders that remain difficult to diagnose, particularly in their early stages because of nonspecific clinical presentations. However, to our knowledge, there is no publicly available prion-disease-focused dataset designed to capture a broad range of clinically relevant entities from the biomedical literature. We introduce PrionNER, a manually annotated named entity recognition dataset for prion disease clinical information in PubMed abstracts. The current release comprises 317 abstracts, 2,943 sentences, and 6,955 text-bound entity annotations spanning 15 coarse-grained and 31 fine-grained clinically oriented entity types covering diseases, symptoms, diagnostics, findings, anatomy, treatments, and temporal and statistical evidence. Inter-annotator agreement reaches 81.78 exact-match F1, indicating strong annotation consistency. We benchmark supervised BERT baselines, W2NER, and zero-shot extractors on PrionNER. W2NER is the strongest supervised model, and Gemma-4-31B is the strongest zero-shot model, but the benchmark remains challenging, especially for structurally complex mentions and fine-grained clinica

Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT signif

Accurate histopathologic interpretation is key for clinical decision-making; however, current deep learning models for digital pathology are often overconfident and poorly calibrated in out-of-distribution (OOD) settings, which limit trust and clinical adoption. Safety-critical medical imaging workflows benefit from intrinsic uncertainty-aware properties that can accurately reject OOD input. We implement the Spectral-normalized Neural Gaussian Process (SNGP), a set of lightweight modifications that apply spectral normalization and replace the final dense layer with a Gaussian process layer to improve single-model uncertainty estimation and OOD detection. We evaluate SNGP vs. deterministic and MonteCarlo dropout on six datasets across three biomedical classification tasks: white blood cells, amyloid plaques, and colorectal histopathology. SNGP has comparable in-distribution performance while significantly improving uncertainty estimation and OOD detection. Thus, SNGP or related models offer a useful framework for uncertainty-aware classification in digital pathology, supporting safe deployment and building trust with pathologists.

Physics-informed machine learning (PIML) is emerging as a potentially transformative paradigm for modeling complex biomedical systems by integrating parameterized physical laws with data-driven methods. Here, we review three main classes of PIML frameworks: physics-informed neural networks (PINNs), neural ordinary differential equations (NODEs), and neural operators (NOs), highlighting their growing role in biomedical science and engineering. We begin with PINNs, which embed governing equations into deep learning models and have been successfully applied to biosolid and biofluid mechanics, mechanobiology, and medical imaging among other areas. We then review NODEs, which offer continuous-time modeling, especially suited to dynamic physiological systems, pharmacokinetics, and cell signaling. Finally, we discuss deep NOs as powerful tools for learning mappings between function spaces, enabling efficient simulations across multiscale and spatially heterogeneous biological domains. Throughout, we emphasize applications where physical interpretability, data scarcity, or system complexity make conventional black-box learning insufficient. We conclude by identifying open challenges and fu

Large language models often perform well on biomedical NLP tasks but may fail to link ontology terms to their correct identifiers. We investigate why these failures occur by analyzing predictions across two major ontologies, Human Phenotype Ontology and Gene Ontology, and two high-performing models, GPT-4o and LLaMa 3.1 405B. We evaluate nine candidate features related to term familiarity, identifier usage, morphology, and ontology structure. Univariate and multivariate analyses show that exposure to ontology identifiers is the strongest predictor of linking success.

Deep neural networks for medical image diagnosis often achieve high predictive accuracy while relying on spurious or clinically irrelevant visual cues, limiting their trustworthiness in practice. Post-hoc explanation methods are widely used to visualize model decisions in the form of saliency maps; however, these explanations do not influence how models learn during training, allowing non-causal or confounding features to persist. This motivates the incorporation of explanation supervision directly into the training objective to guide model attention toward clinically meaningful regions and promote clinically grounded decision-making. This paper presents a systematic approach to integrate explanation loss into model training and analyzes how different explanation loss designs and supervision strengths influence both predictive performance and spatial faithfulness of explanations. To quantitatively assess interpretability, two complementary explanation performance metrics-annotation coverage and saliency precision-are introduced, enabling rigorous evaluation beyond qualitative visualization. Our experimental results reveal a clear trade-off between explanation quality and explanatio

Domain adaptation is a widely used method in natural language processing (NLP) to improve the performance of a language model within a specific domain. This method is particularly common in the biomedical domain, which sees regular publication of numerous scientific articles. PubMed, a significant corpus of text, is frequently used in the biomedical domain. The primary objective of this study is to explore whether refining a pre-training dataset using specific quality metrics for scientific papers can enhance the performance of the resulting model. To accomplish this, we employ two straightforward journal impact metrics and conduct experiments by continually pre-training BERT on various subsets of the complete PubMed training set, we then evaluate the resulting models on biomedical language understanding tasks from the BLURB benchmark. Our results show that pruning using journal impact metrics is not efficient. But we also show that pre-training using fewer abstracts (but with the same number of training steps) does not necessarily decrease the resulting model's performance.

Hallucinated outputs from large language models (LLMs) pose risks in the medical domain, especially for lay audiences making health-related decisions. Existing automatic factual consistency evaluation methods, such as entailment- and question-answering (QA) -based, struggle with plain language summarization (PLS) due to elaborative explanation phenomenon, which introduces external content (e.g., definitions, background, examples) absent from the scientific abstract to enhance comprehension. To address this, we introduce PlainQAFact, an automatic factual consistency evaluation metric trained on a fine-grained, human-annotated dataset PlainFact, for evaluating factual consistency of both source-simplified and elaborately explained sentences. PlainQAFact first classifies sentence type, then applies a retrieval-augmented QA scoring method. Empirical results show that existing evaluation metrics fail to evaluate the factual consistency in PLS, especially for elaborative explanations, whereas PlainQAFact consistently outperforms them across all evaluation settings. We further analyze PlainQAFact's effectiveness across external knowledge sources, answer extraction strategies, answer overl