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Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains formidable due to the complexity of multiple large, semi-structured files and the need for extensive domain…

The adoption of machine learning (ML) and deep learning methods has revolutionized molecular medicine by driving breakthroughs in genomics, transcriptomics, drug discovery, and biological systems modeling. The increasing quantity,…

Comprehending genomic information is essential for biomedical research, yet extracting data from complex distributed databases remains challenging. Large language models (LLMs) offer potential for genomic Question Answering (QA) but face…

Gene set knowledge discovery is essential for advancing human functional genomics. Recent studies have shown promising performance by harnessing the power of Large Language Models (LLMs) on this task. Nonetheless, their results are subject…

Creating end-to-end bioinformatics workflows requires diverse domain expertise, which poses challenges for both junior and senior researchers as it demands a deep understanding of both genomics concepts and computational techniques. While…

Large language models (LLMs) are being used in data science code generation tasks, but they often struggle with complex sequential tasks, leading to logical errors. Their application to geospatial data processing is particularly challenging…

Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and…

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge…

Large Language Models (LLMs) excel at generating synthetic data, but ensuring its quality and diversity remains challenging. We propose Genetic Prompt, a novel framework that combines genetic algorithms with LLMs to augment synthetic data…

Autonomous coding agents built on large language models (LLMs) can now solve many general software and machine learning tasks, but they remain ineffective on complex, domain-specific scientific problems. Medical imaging is a particularly…

Generative AI agents, software systems powered by Large Language Models (LLMs), are emerging as a promising approach to automate cybersecurity tasks. Among the others, penetration testing is a challenging field due to the task complexity…

Large-scale single-cell and Perturb-seq investigations routinely involve clustering cells and subsequently annotating each cluster with Gene-Ontology (GO) terms to elucidate the underlying biological programs. However, both stages,…

Training capable Large Language Model (LLM) agents is critically bottlenecked by the high cost and static nature of real-world interaction data. We address this by introducing GenEnv, a framework that establishes a difficulty-aligned…

Modern engineering increasingly relies on vast datasets generated by experiments and simulations, driving a growing demand for efficient, reliable, and broadly applicable modeling strategies. There is also heightened interest in developing…

Large Language Models (LLMs) have shown promising performance in time series modeling tasks, but do they truly understand time series data? While multiple benchmarks have been proposed to answer this fundamental question, most are manually…

The intricate relationship between genetic variation and human diseases has been a focal point of medical research, evidenced by the identification of risk genes regarding specific diseases. The advent of advanced genome sequencing…

Context: Manual qualitative data analysis is time-intensive and can compromise validity and replicability, affecting analysis design, implementation, and reporting. Large Language Models (LLMs) enable human-bot collaboration in Software…

GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…

Hypothesis generation in biomedical research has traditionally centered on uncovering hidden relationships within vast scientific literature, often using methods like Literature-Based Discovery (LBD). Despite progress, current approaches…

From professional research to everyday planning, many tasks are bottlenecked by wide-scale information seeking, which is more repetitive than cognitively complex. With the rapid development of Large Language Models (LLMs), automated search…