Related papers: Meraculous2: fast accurate short-read assembly of …
Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…
The field of connectomics faces unprecedented "big data" challenges. To reconstruct neuronal connectivity, automated pixel-level segmentation is required for petabytes of streaming electron microscopy data. Existing algorithms provide…
This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves…
The study of plasticity in spiking neural networks is an active area of research. However, simulations that involve complex plasticity rules, dense connectivity/high synapse counts, complex neuron morphologies, or extended simulation times…
Multi-view echocardiographic sequences segmentation is crucial for clinical diagnosis. However, this task is challenging due to limited labeled data, huge noise, and large gaps across views. Here we propose a recurrent aggregation learning…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
Combinatorial algorithms such as those that arise in graph analysis, modeling of discrete systems, bioinformatics, and chemistry, are often hard to parallelize. The Combinatorial BLAS library implements key computational primitives for…
We develop Morphlux, a server-scale programmable photonic fabric to interconnect accelerators within servers. We show that augmenting state-of-the-art torus-based ML data-centers with Morphlux can improve the bandwidth of tenant compute…
A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
Calibrating statistical models using Bayesian inference often requires both accurate and timely estimates of parameters of interest. Particle Markov Chain Monte Carlo (p-MCMC) and Sequential Monte Carlo Squared (SMC$^2$) are two methods…
Biclustering has proved to be a powerful data analysis technique due to its wide success in various application domains. However, the existing literature presents efficient solutions only for enumerating maximal biclusters with constant…
Probabilistic reasoning is an essential tool for robust decision-making systems because of its ability to explicitly handle real-world uncertainty, constraints and causal relations. Consequently, researchers are developing hybrid models by…
The discrete distribution clustering algorithm, namely D2-clustering, has demonstrated its usefulness in image classification and annotation where each object is represented by a bag of weighed vectors. The high computational complexity of…
To increase performance and efficiency, systems use FPGAs as reconfigurable accelerators. A key challenge in designing these systems is partitioning computation between processors and an FPGA. An appropriate division of labor may be…
Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…
{\tt AbstractSimplicialComplexes.m2} is a computer algebra package written for the computer algebra system {\tt Macaulay2} \cite{M2}. It provides new infrastructure to work with abstract simplicial complexes and related homological…
Most genome assemblers construct point estimates, choosing a genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov Chain Monte Carlo approach to sequence assembly that instead generates…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…