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Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic…

In The Cancer Genome Atlas (TCGA) data set, there are many interesting nonlinear dependencies between pairs of genes that reveal important relationships and subtypes of cancer. Such genomic data analysis requires a rapid, powerful and…

Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…

We preprocess the raw NMR spectrum and extract key characteristic features by using two different methodologies, called equidistant sampling and peak sampling for subsequent substructure pattern recognition; meanwhile may provide the…

Systems biology is an emerging interdisciplinary area of research that focuses on study of complex interactions in a biological system, such as gene regulatory networks. The discovery of gene regulatory networks leads to a wide range of…

We present a systematic study of Tensor Network (TN) models $\unicode{x2013}$ Matrix Product States (MPS) and Tree Tensor Networks (TTN) $\unicode{x2013}$ for real-time jet tagging in high-energy physics, with a focus on low-latency…

Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…

Retrosynthesis, which predicts the reactants of a given target molecule, is an essential task for drug discovery. In recent years, the machine learing based retrosynthesis methods have achieved promising results. In this work, we introduce…

Recently, two new parallel algorithms for on-the-fly model checking of LTL properties were presented at the same conference: Automated Technology for Verification and Analysis, 2011. Both approaches extend Swarmed NDFS, which runs several…

The deep Convolutional Neural Network (CNN) is the state-of-the-art solution for large-scale visual recognition. Following basic principles such as increasing the depth and constructing highway connections, researchers have manually…

Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…

Natural Language Inference (NLI) is a fundamental and challenging task in Natural Language Processing (NLP). Most existing methods only apply one-pass inference process on a mixed matching feature, which is a concatenation of different…

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

The astounding performance of transformers in natural language processing (NLP) has motivated researchers to explore their applications in computer vision tasks. DEtection TRansformer (DETR) introduces transformers to object detection tasks…

The fully-connected tensor network (FCTN) decomposition has gained prominence in the field of tensor completion owing to its powerful capacity to capture the low-rank characteristics of tensors. Nevertheless, the recovery of local details…

This work addresses the problem of range-Doppler multiple target detection in a radar system in the presence of slow-time correlated and heavy-tailed distributed clutter. Conventional target detection algorithms assume Gaussian-distributed…

Reconstructing nonlinear dynamical systems (DS) from data (DSR) is a fundamental challenge in science and engineering, but it inherently relies on sequential models. Recent breakthroughs for sequential models have produced algorithms that…

The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…

Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic…

Previously, we presented PanelPRO, now known as Fam3PRO, an open-source R package for multi-gene, multi-cancer risk modeling with pedigree data. The initial release could not handle pedigrees that contained cyclic structures called loops,…