Related papers: TROM: A Testing-based Method for Finding Transcrip…
Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them.…
In this paper, we introduce the Protocol Genome, a self-supervised learning system that learns correlations from DICOM headers and achieves AUROC 0.901 (vs 0.847 baseline) and ECE 0.036 (vs 0.058) on fully held-out external validation. Our…
Large-scale statistical analysis of data sets associated with genome sequences plays an important role in modern biology. A key component of such statistical analyses is the computation of $p$-values and confidence bounds for statistics…
Large-scale simultaneous mRNA translation and the resulting competition for the available ribosomes has important implications to the cell's functioning and evolution. Developing a better understanding of the intricate correlations between…
The simultaneous orthogonal matching pursuit (SOMP) algorithm aims to find the joint support of a set of sparse signals acquired under a multiple measurement vector model. Critically, the analysis of SOMP depends on the maximal inner…
System modeling is a classical approach to ensure their reliability since it is suitable both for a formal verification and for software testing techniques. In the context of model-based testing an approach combining random testing and…
Reasoning about time is essential for understanding the nuances of events described in natural language. Previous research on this topic has been limited in scope, characterized by a lack of standardized benchmarks that would allow for…
Ontology matching (OM) plays an essential role in enabling semantic interoperability and integration across heterogeneous knowledge sources, particularly in the biomedical domain which contains numerous complex concepts related to diseases…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the…
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…
In many transcriptomic studies, the correlation of genes might fluctuate with quantitative factors such as genetic ancestry. We propose a method that models the covariance between two variables to vary against a continuous covariate. For…
We present STRUM (Spectral Transcription and Rhythm Understanding Model), an audio-to-chart pipeline that converts raw recordings into playable Clone Hero / YARG charts for drums, guitar, bass, vocals, and keys without any oracle metadata.…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
Recently, model-based retrieval has emerged as a new paradigm in text retrieval that discards the index in the traditional retrieval model and instead memorizes the candidate corpora using model parameters. This design employs a…
DNA microarray experiments, a well-established experimental technique, aim at understanding the function of genes in some biological processes. One of the most common experiments in functional genomics research is to compare two groups of…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Automatic transcription of guitar strumming is an underrepresented and challenging task in Music Information Retrieval (MIR), particularly for extracting both strumming directions and chord progressions from audio signals. While existing…
The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…