Related papers: GenoTEX: An LLM Agent Benchmark for Automated Gene…

The gene set analysis (GSA) is a foundational approach for uncovering the molecular functions associated with a group of genes. Recently, LLM-powered methods have emerged to annotate gene sets with biological functions together with…

Large Language Models (LLMs) have demonstrated remarkable capabilities on various tasks, while the further evolvement is limited to the lack of high-quality training data. In addition, traditional training approaches rely too much on…

Large Language Models (LLMs) have transformed how people interact with artificial intelligence (AI) systems, achieving state-of-the-art results in various tasks, including scientific discovery and hypothesis generation. However, the lack of…

Large Language Models (LLMs) show promise as data analysis agents, but existing benchmarks overlook the iterative nature of the field, where experts' decisions evolve with deeper insights of the dataset. To address this, we introduce…

The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types.…

With the rise of large language models (LLMs), researchers are increasingly exploring their applications in var ious vertical domains, such as software engineering. LLMs have achieved remarkable success in areas including code generation…

Spreadsheets are ubiquitous across the World Wide Web, playing a critical role in enhancing work efficiency across various domains. Large language model (LLM) has been recently attempted for automatic spreadsheet manipulation but has not…

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

LLM-based reasoning models have enabled the development of agentic systems that act as co-scientists, assisting in multi-step scientific analysis. However, evaluating these systems is challenging, as it requires realistic, end-to-end…

A central problem in data integration and data cleansing is to find entities in different data sources that describe the same real-world object. Many existing methods for identifying such entities rely on explicit linkage rules which…

Large Language Models (LLMs) show promise in biomedicine but lack true causal understanding, relying instead on correlations. This paper envisions causal LLM agents that integrate multimodal data (text, images, genomics, etc.) and perform…

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of…

Large language model (LLM)-based mobile agents are increasingly popular due to their capability to interact directly with mobile phone Graphic User Interfaces (GUIs) and their potential to autonomously manage daily tasks. Despite their…

While Large Language Models (LLMs) have evolved into tool-using agents, they remain brittle in long-horizon interactions. Unlike mathematical reasoning where errors are often rectifiable via backtracking, tool-use failures frequently induce…

With the rapid development of Large Language Models (LLMs), it is crucial to have benchmarks which can evaluate the ability of LLMs on different domains. One common use of LLMs is performing tasks on scientific topics, such as writing…

Large Language Models (LLMs) and multi-agent systems have shown impressive capabilities in natural language tasks but face challenges in clinical trial applications, primarily due to limited access to external knowledge. Recognizing the…

Large Language Models (LLMs) have demonstrated impressive performance across diverse domains, yet they still encounter challenges such as insufficient domain-specific knowledge, biases, and hallucinations. This underscores the need for…

In this work, we investigate the potential of large language models (LLMs) based agents to automate data science tasks, with the goal of comprehending task requirements, then building and training the best-fit machine learning models.…

Autonomous agents powered by large language models (LLMs) promise to accelerate scientific discovery end-to-end, but rigorously evaluating their capacity for verifiable discovery remains a central challenge. Existing benchmarks face a…

Although traditional statistical techniques and machine learning methods have contributed significantly to genetics and, in particular, inherited disease diagnosis, they often struggle with complex, high-dimensional data, a challenge now…