Related papers: LGEM$^\text{+}$: a first-order logic framework for…

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…

Reasoning about hypotheses and updating knowledge through empirical observations are central to scientific discovery. In this work, we applied logic-based machine learning methods to drive biological discovery by guiding experimentation.…

The question-answering system for Life science research, which is characterized by the rapid pace of discovery, evolving insights, and complex interactions among knowledge entities, presents unique challenges in maintaining a comprehensive…

Phenotypic variability in a population of cells can work as the bet-hedging of the cells under an unpredictably changing environment, the typical example of which is the bacterial persistence. To understand the strategy to control such…

Genome-Scale Metabolic Models (GEMs) describe the interactions between genes, proteins, and the biochemical reactions that underpin an organism's metabolism aiming to computationally simulate functions at the cellular level. While many…

Scientific discovery is increasingly constrained by costly experiments and limited resources, underscoring the need for efficient optimization in AI for science. Bayesian Optimization (BO), though widely adopted for balancing exploration…

Large Language Models (LLMs) enhanced with retrieval -- commonly referred to as Retrieval-Augmented Generation (RAG) -- have demonstrated strong performance in knowledge-intensive tasks. However, RAG pipelines often fail when retrieved…

Imaging interferometric data in radio astronomy requires the use of non-linear algorithms that rely on different assumptions on the source structure and may produce non-unique results. This is especially true for Very Long Baseline…

Evidence-based medicine (EBM) plays a crucial role in the application of large language models (LLMs) in healthcare, as it provides reliable support for medical decision-making processes. Although it benefits from current…

Genome-scale metabolic models (GEMs) are essential tools for systems biology and rational chassis design, but conventional top-down reconstruction depends heavily on sequence homology and often leaves unknown enzymes and metabolic dark…

The vast amount of biomedical information available today presents a significant challenge for investigators seeking to digest, process, and understand these findings effectively. Large Language Models (LLMs) have emerged as powerful tools…

Many real world sequences such as protein secondary structures or shell logs exhibit a rich internal structures. Traditional probabilistic models of sequences, however, consider sequences of flat symbols only. Logical hidden Markov models…

Question answering is a natural language understanding task that involves reasoning over both explicit context, and unstated relevant domain knowledge. Despite the high cost of training, large language models (LLMs) -- the backbone of most…

Saccharomyces cerevisiae is increasingly recognised as a key source for single-cell protein (SCP) production, a rising solution to global protein-supply challenges. This study presents a computational framework combining the Yeast9…

Bayesian belief networks can be used to represent and to reason about complex systems with uncertain, incomplete and conflicting information. Belief networks are graphs encoding and quantifying probabilistic dependence and conditional…

Multi-step retrieval-augmented generation (RAG) has become a widely adopted strategy for enhancing large language models (LLMs) on tasks that demand global comprehension and intensive reasoning. Although many RAG systems incorporate a…

Retrieval-augmented Generation (RAG) has demonstrated potential in enhancing medical question-answering systems through the integration of large language models (LLMs) with external medical literature. LLMs can retrieve relevant medical…

Incomplete knowledge of metabolic processes hinders the accuracy of GEnome-scale Metabolic models (GEMs), which in turn impedes advancements in systems biology and metabolic engineering. Existing gap-filling methods typically rely on…

Hypothesis generation is a fundamental step in scientific discovery, yet it is increasingly challenged by information overload and disciplinary fragmentation. Recent advances in Large Language Models (LLMs) have sparked growing interest in…

Materials discovery requires navigating vast chemical and structural spaces while satisfying multiple, often conflicting, objectives. We present LLM-guided Evolution for MAterials discovery (LLEMA), a unified framework that couples the…