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Despite the remarkable successes of Convolutional Neural Networks (CNNs) in computer vision, it is time-consuming and error-prone to manually design a CNN. Among various Neural Architecture Search (NAS) methods that are motivated to…

Long event sequences (termed traces) and large data logs that originate from sensors and prediction models are becoming increasingly common in our data-rich world. In such scenarios, conformance checking-validating a data log against an…

Aqueous solubility (AS) is a key physiochemical property that plays a crucial role in drug discovery and material design. We report a novel unified approach to predict and infer chemical compounds with the desired AS based on simple…

Aligning large language models (LLMs) with human values is crucial for safe deployment. Inference-time techniques offer granular control over generation; however, they rely on model uncertainty, meaning an internal estimate of how likely…

The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome -- millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of…

Motivation: RNA thermometers (RNATs) are cis-regulatory ele- ments that change secondary structure upon temperature shift. Often involved in the regulation of heat shock, cold shock and virulence genes, RNATs constitute an interesting…

Antibody-facilitated immune responses are central to the body's defense against pathogens, viruses, and other foreign invaders. The ability of antibodies to specifically bind and neutralize antigens is vital for maintaining immunity. Over…

Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…

Recent advances in deep learning have shown that uncertainty estimation is becoming increasingly important in applications such as medical imaging, natural language processing, and autonomous systems. However, accurately quantifying…

Machine Learning (ML) algorithms are increasingly used as surrogate models to increase the efficiency of stochastic reliability analyses in geotechnical engineering. This paper presents a highly efficient ML aided reliability technique that…

One key task in virtual screening is to accurately predict the binding affinity ($\triangle$$G$) of protein-ligand complexes. Recently, deep learning (DL) has significantly increased the predicting accuracy of scoring functions due to the…

We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the…

The 2024 Nobel Prize in Chemistry was awarded in part for protein structure prediction using AlphaFold2, an artificial intelligence/machine learning (AI/ML) model trained on vast amounts of sequence and 3D structure data. AlphaFold2 and…

Protein design using structure prediction models such as AlphaFold2 has shown remarkable success, but existing approaches like relaxed sequence optimization (RSO) rely on single-path gradient descent and ignore sequence-space constraints,…

An approximation model based on convolutional neural networks (CNNs) is proposed for flow field predictions. The CNN is used to predict the velocity and pressure field in unseen flow conditions and geometries given the pixelated shape of…

We propose Linear Oscillatory State-Space models (LinOSS) for efficiently learning on long sequences. Inspired by cortical dynamics of biological neural networks, we base our proposed LinOSS model on a system of forced harmonic oscillators.…

Learning to solve complex tasks with signal temporal logic (STL) specifications is crucial to many real-world applications. However, most previous works only consider fixed or parametrized STL specifications due to the lack of a diverse STL…

Classification and identification of amino acids in aqueous solutions is important in the study of biomacromolecules. Laser Induced Breakdown Spectroscopy (LIBS) uses high energy laser-pulses for ablation of chemical compounds whose…

Spiking neural networks (SNNs) are becoming a promising alternative to conventional artificial neural networks (ANNs) due to their rich neural dynamics and the implementation of energy-efficient neuromorphic chips. However, the…

We present InvMSAFold, an inverse folding method for generating protein sequences that is optimized for diversity and speed. For a given structure, InvMSAFold generates the parameters of a probability distribution over the space of…