Related papers: SeqMate: A Novel Large Language Model Pipeline for…

Motivation: Single-cell RNA sequencing (scRNA-seq) is a groundbreaking technology extensively utilized in biological research, facilitating the examination of gene expression at the individual cell level within a given tissue sample. While…

Natural Language Processing (NLP) is widely used to supply summarization ability from long context to structured information. However, extracting structured knowledge from scientific text by NLP models remains a challenge because of its…

Large Language Models (LLMs) are increasingly utilized for large-scale extraction and organization of unstructured data owing to their exceptional Natural Language Processing (NLP) capabilities. Empowering materials design, vast amounts of…

This research pioneers the use of fine-tuned Large Language Models (LLMs) to automate Systematic Literature Reviews (SLRs), presenting a significant and novel contribution in integrating AI to enhance academic research methodologies. Our…

Unstructured text has long been difficult to automatically analyze at scale. Large language models (LLMs) now offer a way forward by enabling {\em semantic data processing}, where familiar data processing operators (e.g., map, reduce,…

The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…

Investigative journalists routinely confront large document collections. Large language models (LLMs) with retrieval-augmented generation (RAG) capabilities promise to accelerate the process of document discovery, but newsroom adoption…

Large language models (LLMs) have shown impressive promise in code generation, yet their progress remains limited by the shortage of large-scale datasets that are both diverse and well-aligned with human reasoning. Most existing resources…

With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for…

The prediction of chemical synthesis pathways plays a pivotal role in materials science research. Challenges, such as the complexity of synthesis pathways and the lack of comprehensive datasets, currently hinder our ability to predict these…

Conversational user interfaces powered by large language models (LLMs) have significantly lowered the technical barriers to database querying. However, existing tools still encounter several challenges, such as misinterpretation of user…

Creation of large-scale databases for Visual Question Answering tasks pertaining to the text data in a scene (text-VQA) involves skilful human annotation, which is tedious and challenging. With the advent of foundation models that handle…

Table Question Answering (TQA) aims to answer natural language questions over structured tables. Large Language Models (LLMs) enable promising solutions to this problem, with operator-centric solutions that generate table manipulation…

Evaluating outputs of large language models (LLMs) is challenging, requiring making -- and making sense of -- many responses. Yet tools that go beyond basic prompting tend to require knowledge of programming APIs, focus on narrow domains,…

This paper introduces LLAssist, an open-source tool designed to streamline literature reviews in academic research. In an era of exponential growth in scientific publications, researchers face mounting challenges in efficiently processing…

Supervised fine-tuning (SFT) is a standard approach for adapting large language models to specialized domains, yet its application to protein sequence modeling and protein language models (PLMs) remains ad hoc. This is in part because…

Large Language Models (LLMs) have showcased their remarkable capabilities in diverse domains, encompassing natural language understanding, translation, and even code generation. The potential for LLMs to generate harmful content is a…

Natural Question Answering (QA) datasets play a crucial role in evaluating the capabilities of large language models (LLMs), ensuring their effectiveness in real-world applications. Despite the numerous QA datasets that have been developed…

Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…

Large Language Models, particularly decoder-only generative models such as GPT, are increasingly used to automate Software Engineering tasks. These models are primarily guided through natural language prompts, making prompt engineering a…