Related papers: Assay2Mol: large language model-based drug design …
This paper introduces a simple yet effective query expansion approach, denoted as query2doc, to improve both sparse and dense retrieval systems. The proposed method first generates pseudo-documents by few-shot prompting large language…
Machine learning (ML) is revolutionising drug discovery by expediting the prediction of small molecule properties essential for developing new drugs. These properties -- including absorption, distribution, metabolism and excretion (ADME)--…
Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model…
Molecular property prediction is an increasingly critical task within drug discovery and development. Typically, neural networks can learn molecular properties using graph-based, language-based or feature-based methods. Recent advances in…
Modeling the relationship between chemical structure and molecular activity is a key goal in drug development. Many benchmark tasks have been proposed for molecular property prediction, but these tasks are generally aimed at specific,…
The rapid advancement of Large Language Models (LLMs) has significantly influenced various domains, leveraging their exceptional few-shot and zero-shot learning capabilities. In this work, we aim to explore and understand the LLMs-based…
Language modeling has seen impressive progress over the last years, mainly prompted by the invention of the Transformer architecture, sparking a revolution in many fields of machine learning, with breakthroughs in chemistry and biology. In…
The BioModels database is one of the premier databases for computational models in systems biology. The database contains over 1000 curated models and an even larger number of non-curated models. All the models are stored in the…
Molecular representation learning is pivotal for various molecular property prediction tasks related to drug discovery. Robust and accurate benchmarks are essential for refining and validating current methods. Existing molecular property…
Multimodal learning, a rapidly evolving field in artificial intelligence, seeks to construct more versatile and robust systems by integrating and analyzing diverse types of data, including text, images, audio, and video. Inspired by the…
The increasing integration of Visual Language Models (VLMs) into AI systems necessitates robust model alignment, especially when handling multimodal content that combines text and images. Existing evaluation datasets heavily lean towards…
In tackling the challenges of large language model (LLM) performance for Text-to-SQL tasks, we introduce CHASE-SQL, a new framework that employs innovative strategies, using test-time compute in multi-agent modeling to improve candidate…
While generative models have recently become ubiquitous in many scientific areas, less attention has been paid to their evaluation. For molecular generative models, the state-of-the-art examines their output in isolation or in relation to…
Academic literature reviews have traditionally relied on techniques such as keyword searches and accumulation of relevant back-references, using databases like Google Scholar or IEEEXplore. However, both the precision and accuracy of these…
Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how…
Statistical methodology for the design and analysis of clinical Phase II dose response studies, with related software implementation, are well developed for the case of a normally distributed, homoscedastic response considered for a single…
Generative artificial intelligence (AI) models, such as diffusion models and OpenAI's ChatGPT, are transforming medicine by enhancing diagnostic accuracy and automating clinical workflows. The field has advanced rapidly, evolving from…
This study proposes a text classification algorithm based on large language models, aiming to address the limitations of traditional methods in capturing long-range dependencies, understanding contextual semantics, and handling class…
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…
Pretraining molecular representations is crucial for drug and material discovery. Recent methods focus on learning representations from geometric structures, effectively capturing 3D position information. Yet, they overlook the rich…