biomedical data teams

Abstract: Latent embeddings have become a central data abstraction in modern machine learning, especially in biomedicine, where foundation models are increasingly used to encode multimodal data like clinical text, medical images, omics, and physiological signals. However, the utility and value of these representations depends on understanding their quality, structure, and the information they encode. Existing analysis workflows for evaluating representations remain fragmented across custom scripts, isolated metrics, and most importantly lack multimodal analysis, limiting accessibility and reproducibility. We present LatentVerse, a representation analysis resource that combines a web-based visual analytics platform for accessible, report-driven exploration with a command-line interface for scalable technical workflows. LatentVerse unifies diagnostics for various representation quality metrics and extends to multimodal settings by decomposing embeddings into shared and modality-specific components. We evaluate LatentVerse through controlled unimodal and multimodal simulations, discovery-oriented analyses on real biomedical embeddings, and a user study across diverse use cases. By supporting thorough and interpretable evaluation of latent spaces, LatentVerse makes foundation model representations more understandable in biomedical and data science applications.

Abstract: Large language models (LLMs) can generate biomedical hypotheses, but it remains unclear whether they truly reason from scientific evidence or simply produce convincing-sounding ideas. To study this, we combine three major biological databases: the Kyoto Encyclopedia of Genes and Genomes (KEGG), Rhea, and UniProt, into a unified biochemical knowledge graph and construct a benchmark of 550 paths connecting enzyme sources to rare disease endpoints, yielding 13,200 hypotheses from six LLMs under four conditions varying the biological information each model receives: source enzyme only, full biological path, or source and disease endpoint only. Hypotheses are scored using an expert-derived five-criterion rubric on a 1-5 scale per criterion. We find that models given both the source and disease endpoint often produce the highest-scoring hypotheses, showing that LLMs can generate compelling ideas from minimal information. However, these hypotheses are less grounded in the evidence. In contrast, models given the full biological path generate hypotheses more consistent with known mechanistic relationships. We call this evidence-disciplined reasoning. To confirm this effect, we shuffled intermediate path steps while keeping endpoints fixed. Evidence grounding dropped significantly (delta = -0.793, p < 0.001), confirming models genuinely used path structure during reasoning. Our findings show that knowledge graphs support hypothesis generation in two ways: they identify biological endpoint pairs absent from the literature, and their mechanistic paths guide how LLMs reason between them.

Abstract: Large language models generate fluent text that can contain unfaithful claims -- a phenomenon known as hallucination. We present a multi-signal detection pipeline combining fine-tuned DeBERTa-v3 classification, Monte Carlo (MC) Dropout uncertainty quantification, and temperature-scaled calibration for response-level hallucination detection. Evaluated on the HaluEval benchmark, our pipeline achieves F1=0.915 and AUROC=0.977 on general-domain tasks, with per-task F1 scores of 0.97 (QA), 0.96 (Summarization), and 0.82 (Dialogue). MC Dropout inference further improves accuracy to 93.2%. A context ablation study confirms the model performs genuine entailment reasoning rather than exploiting surface patterns, with summarization F1 dropping 24% when knowledge context is removed. Learning curve analysis reveals that 25% of training data captures 77% of full-data performance. Beyond detection, we apply Direct Preference Optimization (DPO) to a Qwen2.5-0.5B generator, reducing its hallucination rate from 85.5% to 37.7% (55.9% relative reduction) as measured by our detector. Cross-domain evaluation on the SciFact biomedical benchmark shows that general-domain training transfers poorly (F1=0.52), motivating domain-specific fine-tuning. PubMedBERT fine-tuned on SciFact achieves F1=0.63 and AUROC=0.81, demonstrating that domain-matched pre-training is the strongest adaptation strategy. Code and models are available at https://github.com/varunteja99/hallucination-detection-nlp

Abstract: We introduce OntologyBench, a tiered biomedical retrieval benchmark comprising 471,854 training and 125,744 evaluation query-document relevance pairs across concept grounding, relational retrieval, and compositional phenotype-based retrieval. Although these tasks can be tractable using ontology-aware reference methods, across task tiers, embedding performance is generally lower on relational and compositional tasks than on concept-grounding tasks. Fine-tuning on ontology-derived supervision improves performance on several relational and compositional tasks, whereas the evaluated reranking and LLM-based candidate-scoring methods provide little or no end-to-end improvement. Errors frequently reflect diseases matching only subsets of the phenotype evidence. These findings indicate that the evaluated embedding and reranking configurations do not reliably recover the compatibility encoded by the selected ontology relations and phenotype combinations and motivate retrieval systems that better integrate learned representations with structured biomedical knowledge.