搜索结果：Biomedical research (Tokyo, Japan)

Biomedical knowledge graphs (KGs) encode vast, heterogeneous information spanning literature, genes, pathways, drugs, diseases, and clinical trials, but leveraging them collectively for scientific discovery remains difficult. Their structural differences, continual evolution, and limited cross-resource alignment require substantial manual integration, limiting the depth and scale of knowledge exploration. We introduce DeepEvidence, an AI-agent framework designed to perform Deep Research across various heterogeneous biomedical KGs. Unlike generic Deep Research systems that rely primarily on internet-scale text, DeepEvidence incorporates specialized knowledge-graph tooling and coordinated exploration strategies to systematically bridge heterogeneous resources. At its core is an orchestrator that directs two complementary agents: Breadth-First ReSearch (BFRS) for broad, multi-graph entity search, and Depth-First ReSearch (DFRS) for multi-hop, evidence-focused reasoning. An internal, incrementally built evidence graph provides a structured record of retrieved entities, relations, and supporting evidence. To operate at scale, DeepEvidence includes unified interfaces for querying diverse

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its ba

Synthetic data generation using large language models (LLMs) demonstrates substantial promise in addressing biomedical data challenges and shows increasing adoption in biomedical research. This study systematically reviews recent advances in synthetic data generation for biomedical applications and clinical research, focusing on how LLMs address data scarcity, utility, and quality issues with different modalities. We conducted a scoping review following PRISMA-ScR guidelines and searched literature published between 2020 and 2025 through PubMed, ACM, Web of Science, and Google Scholar. A total of 59 studies were included based on relevance to synthetic data generation in biomedical contexts. Among the reviewed studies, the predominant data modalities were unstructured texts (78.0\%), tabular data (13.6\%), and multimodal sources (8.4\%). Common generation methods included LLM prompting (74.6\%), fine-tuning (20.3\%), and specialized models (5.1\%). Evaluations were heterogeneous: intrinsic metrics (27.1\%), human-in-the-loop assessments (44.1\%), and LLM-based evaluations (13.6\%). However, limitations and key barriers persist in data modalities, domain utility, resource and model

The analysis of existing institutional research proposal databases can provide novel insights into science funding parity. The purpose of this study was to analyze the relationship between race/ethnicity and extramural research proposal and award rates across a medical school faculty and to determine whether there was evidence that researchers changed their submission strategies because of differential inequities across submission categories. The authors performed an analysis of 14,263 biomedical research proposals with proposed start dates between 2010-2022 from the University of Michigan Medical School, measuring the proposal submission and award rates for each racial/ethnic group across 4 possible submission categories (R01 & Equivalent programs, other federal, industry, and non-profit). Biomedical researchers from different racial/ethnic groups follow markedly different proposal submission strategies within the University of Michigan Medical School. There is also a clear relationship between race/ethnicity and rates of proposal award. Black/African American and Asian researchers appear disadvantaged across all submission categories relative to White researchers. This study

This paper presents the setup and results of the second edition of the BioLaySumm shared task on the Lay Summarisation of Biomedical Research Articles, hosted at the BioNLP Workshop at ACL 2024. In this task edition, we aim to build on the first edition's success by further increasing research interest in this important task and encouraging participants to explore novel approaches that will help advance the state-of-the-art. Encouragingly, we found research interest in the task to be high, with this edition of the task attracting a total of 53 participating teams, a significant increase in engagement from the previous edition. Overall, our results show that a broad range of innovative approaches were adopted by task participants, with a predictable shift towards the use of Large Language Models (LLMs).

The integration of AI-assisted biomedical image analysis into clinical practice demands AI-generated findings that are not only accurate but also interpretable to clinicians. However, existing biomedical AI models generally lack the ability to simultaneously generate diagnostic findings and localize corresponding biomedical objects. This limitation makes it challenging for clinicians to correlate AI-generated findings with visual evidence (e.g., tiny lesions) in images and interpret the results of AI models. To address this challenge, we introduce UniBiomed, the first universal foundation model for grounded biomedical image interpretation, which is capable of generating accurate diagnostic findings and simultaneously segmenting the corresponding biomedical targets. UniBiomed is based on a novel integration of Multi-modal Large Language Model and Segment Anything Model, which can effectively unify diverse biomedical tasks in universal training for advancing grounded interpretation. To develop UniBiomed, we curate a large-scale dataset comprising over 27 million triplets of images, region annotations, and text descriptions across ten biomedical imaging modalities. Extensive validatio

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

This paper presents a scientometric analysis of research output from the University of Lagos, focusing on the two decades spanning 2004 to 2023. Using bibliometric data retrieved from the Web of Science, we examine trends in publication volume, collaboration patterns, citation impact, and the most prolific authors, departments, and research domains at the university. The study reveals a consistent increase in research productivity, with the highest publication output recorded in 2023. Health Sciences, Engineering, and Social Sciences are identified as dominant fields, reflecting the university's interdisciplinary research strengths. Collaborative efforts, both locally and internationally, show a positive correlation with higher citation impact, with the United States and the United Kingdom being the leading international collaborators. Notably, open-access publications account for a significant portion of the university's research output, enhancing visibility and citation rates. The findings offer valuable insights into the university's research performance over the past two decades, providing a foundation for strategic planning and policy formulation to foster research excellence

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,

Demographic data collection is essential in education research, as demographic data allows researchers to better describe the participant population they study and to contextualize findings. However, current research practices for neurodiversity demographics often rely on prescriptive methods (e.g., requiring participants to report official diagnoses) rather than allowing participants to self-identify. This approach can: a) not allow participants to express their intersecting identities in ways that are authentic; and b) limit trustworthiness and reliability of the data and interpretation. In addition, inconsistent dissemination and representation of demographic data across studies hinder the accessibility and usability of this work. Through a literature review of neurodivergent student experiences with learning and performing STEM, we identified widespread discrepancies in how demographic information is collected and reported. This paper explores how neurodivergent identities can be more accurately and inclusively represented in education research. We present findings of a thematic analysis on the ways neurodivergent demographic data collection is done in the literature using data

Preliminary evidence suggests that women, including female researchers, are disproportionately affected by the COVID-19 pandemic in terms of unequal distribution of childcare, elderly care and other kinds of domestic and emotional labor. Sudden lockdowns and abrupt shifts in daily routines have disproportionate consequences on their productivity, which is reflected by a sudden drop in research output in biomedical research, consequently affecting the number of female authors of scientific publications. We investigate the proportion of male and female researchers who published scientific papers during the COVID-19 pandemic, using bibliometric data from biomedical preprint servers and selected Springer-Nature journals. Our findings document a decrease in the number of publications by female authors in biomedical field during the global pandemic. This effect is particularly pronounced for papers related to COVID-19, indicating that women are producing fewer publications related to COVID-19 research. This sudden increase in the gender gap is persistent across the ten countries with the highest number of researchers. These results should be used to inform the scientific community of the

Biomedical relation extraction (BioRE) extracts structured knowledge from biomedical literature for applications such as knowledge base construction and hypothesis generation. Traditional symbolic systems such as SemRep provide high precision but limited recall, while large language models (LLMs) offer stronger contextual reasoning but remain prone to false-positive predictions. We developed ANCHOR-RE, a framework that integrates ontology-guided reasoning, external knowledge grounding, and data-driven verification rules into LLM inference. We evaluated it on three BioRE benchmarks (SemRepGS, DDI, and ChemProt) using both proprietary and open-weight LLMs. To assess generalizability beyond benchmark datasets while reducing potential evaluation bias from LLM pretraining contamination, we conducted a temporal evaluation using 100 biomedical articles published in 2026. With the proprietary backbone, ANCHOR-RE outperformed direct LLM prompting, improving micro-F1 from 0.654 to 0.676 on SemRepGS, from 0.769 to 0.872 on DDI, and from 0.939 to 0.941 on ChemProt. On DDI and ChemProt, it also outperformed previously reported inference-only methods and approached fine-tuned or instruction-tune

Scientific activity plays a major role in innovation for biomedicine and healthcare. For instance, fundamental research on disease pathologies and mechanisms can generate potential targets for drug therapy. This co-evolution is punctuated by papers which provide new perspectives and open new domains. Despite the relationship between scientific discovery and biomedical advancement, identifying these research milestones that truly impact biomedical innovation can be difficult and is largely based solely on the opinions of subject matter experts. Here, we consider whether a new class of citation algorithms that identify seminal scientific works in a field, Reference Publication Year Spectroscopy (RPYS) and multi-RPYS, can identify the connections between innovation (e.g. therapeutic treatments) and the foundational research underlying them. Specifically, we assess whether the results of these analytic techniques converge with expert opinions on research milestones driving biomedical innovation in the treatment of Basal Cell Carcinoma. Our results show that these algorithms successfully identify the majority of milestone papers detailed by experts (Wong and Dlugosz 2014) thereby valida

This scientometric study analyzes Avian Influenza research from 2014 to 2023 using bibliographic data from the Web of Science database. We examined publication trends, sources, authorship, collaborative networks, document types, and geographical distribution to gain insights into the global research landscape. Results reveal a steady increase in publications, with high contributions from Chinese and American institutions. Journals such as PLoS One and the Journal of Virology published the highest number of studies, indicating their influence in this field. The most prolific institutions include the Chinese Academy of Sciences and the University of Hong Kong, while the College of Veterinary Medicine at South China Agricultural University emerged as the most productive department. China and the USA lead in publication volume, though developed nations like the United Kingdom and Germany exhibit a higher rate of international collaboration. "Articles" are the most common document type, constituting 84.6% of the total, while "Reviews" account for 7.6%. This study provides a comprehensive view of global trends in Avian Influenza research, emphasizing the need for collaborative efforts ac

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.

We introduce PubMedQA, a novel biomedical question answering (QA) dataset collected from PubMed abstracts. The task of PubMedQA is to answer research questions with yes/no/maybe (e.g.: Do preoperative statins reduce atrial fibrillation after coronary artery bypass grafting?) using the corresponding abstracts. PubMedQA has 1k expert-annotated, 61.2k unlabeled and 211.3k artificially generated QA instances. Each PubMedQA instance is composed of (1) a question which is either an existing research article title or derived from one, (2) a context which is the corresponding abstract without its conclusion, (3) a long answer, which is the conclusion of the abstract and, presumably, answers the research question, and (4) a yes/no/maybe answer which summarizes the conclusion. PubMedQA is the first QA dataset where reasoning over biomedical research texts, especially their quantitative contents, is required to answer the questions. Our best performing model, multi-phase fine-tuning of BioBERT with long answer bag-of-word statistics as additional supervision, achieves 68.1% accuracy, compared to single human performance of 78.0% accuracy and majority-baseline of 55.2% accuracy, leaving much r

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.

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

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