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Advances in high-throughput sequencing technology have led to significant progress in measuring gene expressions at the single-cell level. The amount of publicly available single-cell RNA-seq (scRNA-seq) data is already surpassing 50M…

Repurposing existing drugs to treat new diseases is a cost-effective alternative to de novo drug development, but there are millions of potential drug-disease combinations to be considered with only a small fraction being viable. In silico…

The prediction of RNA-small molecule binding sites is crucial for the discovery of effective drugs. Various computational methods have been developed to address this challenge, using information about the structure and sequence of RNA. In…

Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…

There is a critical need for standard approaches to assess, report, and compare the technical performance of genome-scale differential gene expression experiments. We assess technical performance with a proposed "standard" dashboard of…

There are numerous advantages of deep neural network surrogate modeling for response time-history prediction. However, due to the high cost of refined numerical simulations and actual experiments, the lack of data has become an unavoidable…

Sequential Recommender Systems (SRS) aim to model sequential behaviors of users to capture their interests which usually evolve over time. Transformer-based SRS have achieved distinguished successes recently. However, studies reveal…

Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex…

Current machine learning has made great progress on computer vision and many other fields attributed to the large amount of high-quality training samples, while it does not work very well on genomic data analysis, since they are notoriously…

Deep learning and signal processing are closely correlated in many IoT scenarios such as anomaly detection to empower intelligence of things. Many IoT processors utilize digital signal processors (DSPs) for signal processing and build deep…

Image Representation learning via input reconstruction is a common technique in machine learning for generating representations that can be effectively utilized by arbitrary downstream tasks. A well-established approach is using…

With the introduction of SNIP [arXiv:1810.02340v2], it has been demonstrated that modern neural networks can effectively be pruned before training. Yet, its sensitivity criterion has since been criticized for not propagating training signal…

MicroRNAs (miRNAs) are small endogenous regulatory molecules that modulate gene expression post-transcriptionally. Although differential expression of miRNAs have been implicated in many diseases (including cancers), the underlying…

Many studies have been conducted to improve the efficiency of Transformer from quadric to linear. Among them, the low-rank-based methods aim to learn the projection matrices to compress the sequence length. However, the projection matrices…

Accurate prediction of drug response in precision medicine requires models that capture how specific chemical substructures interact with cellular pathway states. However, most existing deep learning approaches treat chemical and…

Objective. Deep neural networks (DNNs) have shown unprecedented success in various brain-machine interface applications such as epileptic seizure prediction. However, existing approaches typically train models in a patient-specific fashion…

Difference-in-Differences (DiD) and Synthetic Control (SC) are widely used methods for causal inference in panel data, each with distinct strengths and limitations. We propose a novel method for short-panel causal inference that integrates…

Physics-Informed Neural Networks (PINNs) are becoming a popular method for solving PDEs, due to their mesh-free nature and their ability to handle high-dimensional problems where traditional numerical solvers often struggle. Despite their…

RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures using…

Effective integration of AI agents into daily life requires them to understand and adapt to individual human preferences, particularly in collaborative roles. Although recent studies on embodied intelligence have advanced significantly,…