Related papers: PyamilySeq: A Python Tool for Interpretable Gene (…
The study of research trends is pivotal for understanding scientific development on specific topics. Traditionally, this involves keyword analysis within scholarly literature, yet comprehensive tools for such analysis are scarce, especially…
In medical sciences, a biomarker is "a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention". Molecular…
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists due to its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina…
Single-cell RNA sequencing (scRNA-seq) enables researchers to analyze gene expression at single-cell level. One important task in scRNA-seq data analysis is unsupervised clustering, which helps identify distinct cell types, laying down the…
PySINDy is a Python package for the discovery of governing dynamical systems models from data. In particular, PySINDy provides tools for applying the sparse identification of nonlinear dynamics (SINDy) (Brunton et al. 2016) approach to…
Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular…
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…
In this work we introduce repro_eval - a tool for reactive reproducibility studies of system-oriented information retrieval (IR) experiments. The corresponding Python package provides IR researchers with measures for different levels of…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
Evaluating time series attribution methods is difficult because real-world datasets rarely provide ground truth for which time points drive a prediction. A common workaround is to generate synthetic data where class-discriminating features…
We introduce PyQBench, an innovative open-source framework for benchmarking gate-based quantum computers. PyQBench can benchmark NISQ devices by verifying their capability of discriminating between two von Neumann measurements. PyQBench…
Large language models (LLMs) have demonstrated significant advancements in reasoning and code generation, but efficiently creating new benchmarks to evaluate these capabilities remains a challenge. Traditional benchmark creation relies on…
pyspeckit is a toolkit and library for spectroscopic analysis in Python. We describe the pyspeckit package and highlight some of its capabilities, such as interactively fitting a model to data, akin to the historically widely-used splot…
Motivation: The ability to perform operations on encrypted data has a growing number of applications in bioinformatics, with implications for data privacy in health care and biosecurity. The SEAL library is a popular implementation of fully…
PyGALAX is a Python package for geospatial analysis that integrates automated machine learning (AutoML) and explainable artificial intelligence (XAI) techniques to analyze spatial heterogeneity in both regression and classification tasks.…
Motivation: A major challenge in the development of machine learning based methods in computational biology is that data may not be accurately labeled due to the time and resources required for experimentally annotating properties of…
In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
PEACH Tree is an easy-to-use, online tool for displaying multiple sequence alignments and phylogenetic trees side-by-side. PEACH Tree is powerful for rapidly tracing evolutionary and transmission histories by filtering invariant sites out…
Recommender systems have demonstrated significant impact across diverse domains, yet ensuring the reproducibility of experimental findings remains a persistent challenge. A primary obstacle lies in the fragmented and often opaque data…