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Identifying genes associated with complex human diseases is one of the main challenges of human genetics and computational medicine. To answer this question, millions of genetic variants get screened to identify a few of importance. To…
Background: Patient recruitment in clinical trials is hindered by complex eligibility criteria and labor-intensive chart reviews. Prior research using text-only models have struggled to address this problem in a reliable and scalable way…
Pooled analyses that aggregate data from multiple studies are becoming increasingly common in collaborative epidemiologic research in order to increase the size and diversity of the study population. However, biomarker measurements from…
Test optimization contains test case selection and minimization, which is an important challenge in software testing and has been addressed with search-based approaches intensively in the past. Inspired by the recent advancement of using…
Open-source licenses establish the legal foundation for software reuse, yet license variants, including both modified standard licenses and custom-created alternatives, introduce significant compliance complexities. Despite their prevalence…
Software undergoes constant changes to support new requirements, address bugs, enhance performance, and ensure maintainability. Thus, developers spend a great portion of their workday trying to understand and review the code changes of…
A variety of genome-wide profiling techniques are available to probe complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher-level interactions that cannot be detected…
Cancer is a complex disease driven by genomic alterations, and tumor sequencing is becoming a mainstay of clinical care for cancer patients. The emergence of multi-institution sequencing data presents a powerful resource for learning…
Meeting summarization suffers from limited high-quality data, mainly due to privacy restrictions and expensive collection processes. We address this gap with FAME, a dataset of 500 meetings in English and 300 in German produced by MIMIC,…
Multimodal alignment of histopathology encoders with transcriptomic and genomic data has been shown to significantly improve performance in downstream diagnostic tasks. Hematological cytology is unique in that visual single-cell evaluation…
Mendelian randomization uses genetic variants to make causal inferences about the effect of a risk factor on an outcome. With fine-mapped genetic data, there may be hundreds of genetic variants in a single gene region any of which could be…
Background & Objective: Biomedical text data are increasingly available for research. Tokenization is an initial step in many biomedical text mining pipelines. Tokenization is the process of parsing an input biomedical sentence (represented…
Recent approaches to large language model (LLM) alignment typically require millions of human annotations or rely on external aligned models for synthetic data generation. This paper introduces ALMA: Alignment with Minimal Annotation,…
PyamilySeq is a Python-based tool designed for interpretable gene clustering and pangenomic inference, supporting analyses at both species and genus levels. It facilitates the clustering of gene sequences into families based on sequence…
Gene expression analysis is a critical method for cancer classification, enabling precise diagnoses through the identification of unique molecular signatures associated with various tumors. Identifying cancer-specific genes from gene…
Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods…
Patient recruitment remains a major bottleneck in clinical trials, calling for scalable and automated solutions. We present TrialMatchAI, an AI-powered recommendation system that automates patient-to-trial matching by processing…
The emergence of telomere-to-telomere (T2T) genome assemblies has opened new avenues for comparative genomics, yet effective tokenization strategies for genomic sequences remain underexplored. In this pilot study, we apply Byte Pair…
Prognostic signatures play an important role in clinical research, offering insights into the potential health outcomes of patients and guiding therapeutic decisions. Although single-gene prognostic biomarkers are valuable, multi-gene…
Data cleaning consumes about 80% of the time spent on data analysis for clinical research projects. This is a much bigger problem in the era of big data and machine learning in the field of medicine where large volumes of data are being…