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Machine learning interatomic potentials (MLIPs) provide an effective approach for accurately and efficiently modeling atomic interactions, expanding the capabilities of atomistic simulations to complex systems. However, a priori feature…

The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…

We review enzymatic systems which involve biocatalytic reactions utilized for information processing (biocomputing). Extensive ongoing research in biocomputing, mimicking Boolean logic gates has been motivated by potential applications in…

Surface electromyography (sEMG) signal-based activity recognition has attracted increasing research attention in recent years. To develop accurate sEMG signal-based activity recognizers, numerous approaches have been proposed. Some studies…

Machine-learning methods in biochemistry commonly represent molecules as graphs of pairwise intermolecular interactions for property and structure predictions. Most methods operate on a single graph, typically the minimal free energy (MFE)…

There is growing interest in using machine learning (ML) to support clinical diagnosis, but most approaches rely on static, fully observed datasets and fail to reflect the sequential, resource-aware reasoning clinicians use in practice.…

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that…

Recent advances in natural language processing (NLP) owe their success to pre-training language models on large amounts of unstructured data. Still, there is an increasing effort to combine the unstructured nature of LMs with structured…

A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…

Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis…

Efficient materials discovery requires reducing costly first-principles calculations for training machine-learned interatomic potentials (MLIPs). We develop an active learning (AL) framework that iteratively selects informative structures…

Understanding how Large Language Models (LLMs) perform logical reasoning internally remains a fundamental challenge. While prior mechanistic studies focus on identifying taskspecific circuits, they leave open the question of what…

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…

We demonstrate that deep learning techniques can be used to predict motility induced phase separation (MIPS) in suspensions of active Brownian particles (ABPs) by creating a notion of phase at the particle level. Using a fully connected…

Active learning (AL) accelerates scientific discovery by prioritizing the most informative experiments, but traditional machine learning (ML) models used in AL suffer from cold-start limitations and domain-specific feature engineering,…

Large Language Models (LLMs) based agents excel at diverse tasks, yet they suffer from brittle procedural memory that is manually engineered or entangled in static parameters. In this work, we investigate strategies to endow agents with a…

Molecular dynamics (MD) employing machine-learned interatomic potentials (MLIPs) serve as an efficient, urgently needed complement to ab initio molecular dynamics (aiMD). By training these potentials on data generated from ab initio…

Can we leverage LLMs to model the process of discovering novel language model (LM) architectures? Inspired by real research, we propose a multi-agent LLM approach that simulates the conventional stages of research, from ideation and…

Discovery of the molecular candidates for applications in drug targets, biomolecular systems, catalysts, photovoltaics, organic electronics, and batteries, necessitates development of machine learning algorithms capable of rapid exploration…

Biological machine learning is often bottlenecked by a lack of scaled data. One promising route to relieving data bottlenecks is through high throughput screens, which can experimentally test the activity of $10^6-10^{12}$ protein sequences…