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We introduce VerifAI, an open-source expert system for biomedical question answering that integrates retrieval-augmented generation (RAG) with a novel post-hoc claim verification mechanism. Unlike standard RAG systems, VerifAI ensures…

Recent progress in retrieval-augmented generation (RAG) has led to more accurate and interpretable multi-hop question answering (QA). Yet, challenges persist in integrating iterative reasoning steps with external knowledge retrieval. To…

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the interconnectedness between core biomedical concepts, enable…

With the abundant amount of available online and offline text data, there arises a crucial need to extract the relation between phrases and summarize the main content of each document in a few words. For this purpose, there have been many…

Laboratory workflows in pharmaceutical and biomedical research encode substantial tacit knowledge -- expert judgment about failure conditions, decision branching logic, and contextual dependencies -- that remains inaccessible to protocol…

In the era of Big Knowledge Graphs, Question Answering (QA) systems have reached a milestone in their performance and feasibility. However, their applicability, particularly in specific domains such as the biomedical domain, has not gained…

Modern searches for physics beyond the Standard Model produce rapidly expanding literature containing heterogeneous information, including textual analyses, numerical datasets, and graphical exclusion limits. Integrating these distributed…

Explainable AI (XAI) in medical histopathology is essential for enhancing the interpretability and clinical trustworthiness of deep learning models in cancer diagnosis. However, the black-box nature of these models often limits their…

Question Answering (QA) systems provide easy access to the vast amount of knowledge without having to know the underlying complex structure of the knowledge. The research community has provided ad hoc solutions to the key QA tasks,…

Diagram question answering (Diagram QA) requires reasoning-level attribution that links each question-answer pair to all visual regions needed to derive the answer, rather than only the region containing the final response. Creating such…

Multimodal Large Language Models are increasingly applied to biomedical imaging, yet scientific reasoning for microscopy remains limited by the scarcity of large-scale, high-quality training data. We introduce MicroVQA++, a three-stage,…

Recognizing biomedical concepts in the text is vital for ontology refinement, knowledge graph construction, and concept relationship discovery. However, traditional concept recognition methods, relying on explicit mention identification,…

Knowledge graphs (KGs) are powerful tools for modelling complex, multi-relational data and supporting hypothesis generation, particularly in applications like drug repurposing. However, for predictive methods to gain acceptance as credible…

The rapid expansion of publicly-available medical data presents a challenge for clinicians and researchers alike, increasing the gap between the volume of scientific literature and its applications. The steady growth of studies and findings…

This study applies Large Language Models (LLMs) to two foundational Electronic Health Record (EHR) data science tasks: structured data querying (using programmatic languages, Python/Pandas) and information extraction from unstructured…

Foundation models (FMs) are able to leverage large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently…

This paper describes a machine learning and data science pipeline for structured information extraction from documents, implemented as a suite of open-source tools and extensions to existing tools. It centers around a methodology for…

This work presents a Biomedical Literature Question Answering (Q&A) system based on a Retrieval-Augmented Generation (RAG) architecture, designed to improve access to accurate, evidence-based medical information. Addressing the shortcomings…

The rapid growth of biomedical literature and curated databases has made it increasingly difficult for researchers to systematically connect biomarker mechanisms to actionable drug combination hypotheses. We present AI Co-Scientist (CoDHy),…

Recent advances in Natural Language Processing (NLP), and specifically automated Question Answering (QA) systems, have demonstrated both impressive linguistic fluency and a pernicious tendency to reflect social biases. In this study, we…