Related papers: FastRemap: A Tool for Quickly Remapping Reads betw…
Fast, efficient and reliable algorithms for pairwise alignment of protein structures are in ever increasing demand for analyzing the rapidly growing data of protein structures. CLePAPS is a tool developed for this purpose. It distinguishes…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Large language models (LLMs) are rapidly transforming various domains, including biomedicine and healthcare, and demonstrate remarkable potential from scientific research to new drug discovery. Graph-based retrieval-augmented generation…
Repository-scale code reasoning is a cornerstone of modern AI-assisted software engineering, enabling Large Language Models (LLMs) to handle complex workflows from program comprehension to complex debugging. However, balancing accuracy with…
Recently, crossbar array based in-memory accelerators have been gaining interest due to their high throughput and energy efficiency. While software and compiler support for the in-memory accelerators has also been introduced, they are…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Combinations of spectroscopic analysis and microscopic techniques are used across many disciplines of scientific research, including material science, chemistry and biology. X-ray spectromicroscopy, in particular, is a powerful tool used…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
Distributed approaches based on the map-reduce programming paradigm have started to be proposed in the bioinformatics domain, due to the large amount of data produced by the next-generation sequencing techniques. However, the use of…
Applications in science and engineering often require huge computational resources for solving problems within a reasonable time frame. Parallel supercomputers provide the computational infrastructure for solving such problems. A…
The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…
To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a…
We introduce DualMap, an online open-vocabulary mapping system that enables robots to understand and navigate dynamically changing environments through natural language queries. Designed for efficient semantic mapping and adaptability to…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
Finetuning on domain-specific data is a well-established method for enhancing LLM performance on downstream tasks. Training on each dataset produces a new set of model weights, resulting in a multitude of checkpoints saved in-house or on…
MetaScope is a fast and accurate tool for analyzing (host-associated) metagenome datasets. Sequence alignment of reads against the host genome (if requested) and against microbial Genbank is performed using a new DNA aligner called SASS.…
Motivation: The rapid growth in genome-wide association studies (GWAS) in plants and animals has brought about the need for a central resource that facilitates i) performing GWAS, ii) accessing data and results of other GWAS, and iii)…
Deep learning models require the configuration of many layers and parameters in order to get good results. However, there are currently few systematic guidelines for how to configure a successful model. This means model builders often have…
We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples. SIMLR…