Related papers: BIOGEN: Evidence-Grounded Multi-Agent Reasoning Fr…

Translating single-cell RNA sequencing (scRNA-seq) data into mechanistic biological hypotheses remains a critical bottleneck, as agentic AI systems lack direct access to transcriptomic representations while expression foundation models…

Knowledge graphs and large language models (LLMs) are key tools for biomedical knowledge integration and reasoning, facilitating structured organization of scientific articles and discovery of complex semantic relationships. However,…

Retrieval augmented generation (RAG) has shown great power in improving Large Language Models (LLMs). However, most existing RAG-based LLMs are dedicated to retrieving single modality information, mainly text; while for many real-world…

We present BioLangFusion, a simple approach for integrating pre-trained DNA, mRNA, and protein language models into unified molecular representations. Motivated by the central dogma of molecular biology (information flow from gene to…

Single-cell RNA sequencing (scRNA-seq) data analysis is crucial for biological research, as it enables the precise characterization of cellular heterogeneity. However, manual manipulation of various tools to achieve desired outcomes can be…

Motivation: Modelling methods that find structure in data are necessary with the current large volumes of genomic data, and there have been various efforts to find subsets of genes exhibiting consistent patterns over subsets of treatments.…

Large language models (LLMs) offer new opportunities for constructing knowledge graphs (KGs) from unstructured clinical narratives. However, existing approaches often rely on structured inputs and lack robust validation of factual accuracy…

Emergency departments worldwide face rising patient volumes, workforce shortages, and variability in triage decisions that threaten the delivery of timely and accurate care. Current triage methods rely primarily on vital signs, routine…

Single-cell RNA-sequencing (scRNA-seq) stands as a powerful tool for deciphering cellular heterogeneity and exploring gene expression profiles at high resolution. However, its high cost renders it impractical for extensive sample cohorts…

Metagenomic disease prediction commonly relies on species abundance tables derived from large, incomplete reference catalogs, constraining resolution and discarding valuable information contained in DNA reads. To overcome these limitations,…

Retrieval-Augmented Generation (RAG) helps large language models (LLMs) answer knowledge-intensive and time-sensitive questions by conditioning generation on external evidence. However, most RAG systems still retrieve unstructured chunks…

Multimodal Retrieval-Augmented Generation (MRAG) addresses key limitations of Multimodal Large Language Models (MLLMs), such as hallucination and outdated knowledge. However, current MRAG systems struggle to distinguish whether retrieved…

Despite theoretical advantages, causal methods for Gene Regulatory Network (GRN) inference from single-cell RNA-seq data consistently fail to match or outperform correlation-based baselines in many realistic benchmarks, a persistent puzzle…

Biomedical knowledge resources often either preserve evidence as unstructured text or compress it into flat triples that omit study design, provenance, and quantitative support. Here we present EvidenceNet, a disease-specific dataset of…

Biomedical semantic question answering rooted in information retrieval can play a crucial role in keeping up to date with vast, rapidly evolving and ever-growing biomedical literature. A robust system can help researchers, healthcare…

Modern networks generate vast, heterogeneous traffic that must be continuously analyzed for security and performance. Traditional network traffic analysis systems, whether rule-based or machine learning-driven, often suffer from high false…

Multimodal Large Language Models (MLLMs) in healthcare suffer from severe confirmation bias, often hallucinating visual details to support initial, potentially erroneous diagnostic hypotheses. Existing Chain-of-Thought (CoT) approaches lack…

The growing use of large language models (LLMs) for biomedical question answering raises concerns about the accuracy and evidentiary support of their responses. To address this, we present Answered with Evidence, a framework for evaluating…

Prevalent in biomedical applications (e.g., human phenotype research), multimodal datasets can provide valuable insights into the underlying physiological mechanisms. However, current machine learning (ML) models designed to analyze these…

Epilepsy diagnosis and treatment require evidence-intensive reasoning across heterogeneous clinical knowledge, including biosignal patterns, genetic mechanisms, pharmacogenomics, treatment strategies, and patient outcomes. In this work, we…