相关论文: GenePheno: Interpretable Gene Knockout-Induced Phe…
Much of the natural variation for a complex trait can be explained by variation in DNA sequence levels. As part of sequence variation, gene-gene interaction has been ubiquitously observed in nature, where its role in shaping the development…
A good feature representation is a determinant factor to achieve high performance for many machine learning algorithms in terms of classification. This is especially true for techniques that do not build complex internal representations of…
There is growing consensus among neuroscientists that neural circuits critical for survival are the result of genomic decompression processes. We introduce SynaptoGen, a novel computational framework--member of the Connectome Models…
Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous studies have primarily focused on generating gene expression or haplotype…
Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…
The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
The analysis of DNA sequences has become critical in numerous fields, from evolutionary biology to understanding gene regulation and disease mechanisms. While deep neural networks can achieve remarkable predictive performance, they…
The genotype-phenotype map is an essential object in our understanding of organismal complexity and adaptive properties, determining at once genomic plasticity and those constraints that may limit the ability of genomes to attain…
The advent of high--throughput transcription profiling technologies has enabled identification of genes and pathways associated with disease, providing new avenues for precision medicine. A key challenge is to analyze this data in the…
Genetic mutations can cause disease by disrupting normal gene function. Identifying the disease-causing mutations from millions of genetic variants within an individual patient is a challenging problem. Computational methods which can…
A primary goal of computational phenotype research is to conduct medical diagnosis. In hospital, physicians rely on massive clinical data to make diagnosis decisions, among which laboratory tests are one of the most important resources.…
Detailed phenotype information is fundamental to accurate diagnosis and risk estimation of diseases. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However,…
Recently, Graph Neural Networks (GNNs) have significantly advanced the performance of machine learning tasks on graphs. However, this technological breakthrough makes people wonder: how does a GNN make such decisions, and can we trust its…
Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental…
Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence…
Survival analysis plays a vital role in making clinical decisions. However, the models currently in use are often difficult to interpret, which reduces their usefulness in clinical settings. Prototype learning presents a potential solution,…
Complex biological functions are carried out by the interaction of genes and proteins. Uncovering the gene regulation network behind a function is one of the central themes in biology. Typically, it involves extensive experiments of…