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The ability to predict future events or patterns based on previous experience is crucial for many applications such as traffic control, weather forecasting, or supply chain management. While modern supervised Machine Learning approaches…

Numerous machine learning (ML) models employed in protein function and structure prediction depend on evolutionary information, which is captured through multiple-sequence alignments (MSA) or position-specific scoring matrices (PSSM) as…

Generating peptides with desired properties is crucial for drug discovery and biotechnology. Traditional sequence-based and structure-based methods often require extensive datasets, which limits their effectiveness. In this study, we…

Inverse material design is a cornerstone challenge in materials science, with significant applications across many industries. Traditional approaches that invert the structure-property (SP) linkage to identify microstructures with targeted…

Mimicking the perceptual functions of human cutaneous mechanoreceptors, artificial skins or flexible pressure sensors can transduce tactile stimuli to quantitative electrical signals. Conventional methods to design such devices follow a…

Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query…

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…

Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…

A linear regression-based machine learned interatomic potential (MLIP) was developed for the silicon-carbon system. The MLIP was predominantly trained on structures discovered through a genetic algorithm, encompassing the entire…

The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…

We present the MSA-to-protein transformer, a generative model of protein sequences conditioned on protein families represented by multiple sequence alignments (MSAs). Unlike existing approaches to learning generative models of protein…

Protein language models (pLMs) have demonstrated success at generating functional proteins across vast sequence spaces but lack the ability to design high-fitness variants on demand. Here, we iteratively guide pLMs toward user-defined…

The synthesis of nanocrystals has been highly dependent on trial-and-error, due to the complex correlation between synthesis parameters and physicochemical properties. Although deep learning offers a potential methodology to achieve…

Designing novel functional proteins remains a slow and expensive process due to a variety of protein engineering challenges; in particular, the number of protein variants that can be experimentally tested in a given assay pales in…

Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…

Spike-Timing-Dependent Plasticity (STDP) provides a biologically grounded learning rule for spiking neural networks (SNNs), but its reliance on precise spike timing and pairwise updates limits fast learning of weights. We introduce a…

Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…

In this paper, we propose persistent spectral based machine learning (PerSpect ML) models for drug design. Persistent spectral models, including persistent spectral graph, persistent spectral simplicial complex and persistent spectral…

Modeling biological soft tissue is complex in part due to material heterogeneity. Microstructural patterns, which play a major role in defining the mechanical behavior of these tissues, are both challenging to characterize, and difficult to…

Improving the ability to predict protein function can potentially facilitate research in the fields of drug discovery and precision medicine. Technically, the properties of proteins are directly or indirectly reflected in their sequence and…