Related papers: SlopMap: a software application tool for quick and…
Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…
In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting…
Real-world graphs exhibit increasing heterophily, where nodes no longer tend to be connected to nodes with the same label, challenging the homophily assumption of classical graph neural networks (GNNs) and impeding their performance.…
NeuroNet is a deep convolutional neural network mimicking multiple popular and state-of-the-art brain segmentation tools including FSL, SPM, and MALPEM. The network is trained on 5,000 T1-weighted brain MRI scans from the UK Biobank Imaging…
Bloom filter is a space-efficient probabilistic data structure for checking elements' membership in a set. Given multiple sets, however, a standard Bloom filter is not sufficient when looking for the items to which an element or a set of…
FlowMapper.org is a web-based framework for automated production and design of origin-destination flow maps (https://flowmapper.org). FlowMapper has four major features that contribute to the advancement of existing flow mapping systems.…
Background: Many efforts have been put into the use of automated approaches, such as natural language processing (NLP), to mine or extract data from free-text medical records to construct comprehensive patient profiles for delivering better…
Spiking Neural Network (SNN) naturally inspires hardware implementation as it is based on biology. For learning, spike time dependent plasticity (STDP) may be implemented using an energy efficient waveform superposition on memristor based…
Machine- and deep-learning approaches for biological sequences depend critically on transforming raw DNA, RNA, and protein FASTA files into informative numerical representations. However, this process is often fragmented across multiple…
Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…
We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…
Semi-supervised learning (SSL) has emerged as a promising paradigm in medical image segmentation, offering competitive performance while substantially reducing the need for extensive manual annotation. When combined with active learning…
Single-particle tracking (SPT) grants unprecedented insight into cellular function at the molecular scale [1]. Throughout the cell, the movement of single-molecules is generally heterogeneous and complex. Hence, there is an imperative to…
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can…
Pedigree data contain family history information that is used to analyze hereditary diseases. These clinical data sets may contain duplicate records due to the same family visiting a clinic multiple times or a clinician entering multiple…
Aligning reads to a reference sequence is a fundamental step in numerous bioinformatics pipelines. As a consequence, the sensitivity and precision of the mapping tool, applied with certain parameters to certain data, can critically affect…
We present a data-parallel software package for fitting Gaussian Approximation Potentials (GAPs) on multiple nodes using the ScaLAPACK library with MPI and OpenMP. Until now the maximum training set size for GAP models has been limited by…
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…
Recent years in NLP have seen the continued development of domain-specific information extraction tools for scientific documents, alongside the release of increasingly multimodal pretrained transformer models. While the opportunity for…
Discovering research expertise at institutions can be a difficult task. Manually curated university directories easily become out of date and they often lack the information necessary for understanding a researcher's interests and past…