Related papers: Introgression Browser: High throughput whole-genom…

We present our ongoing work NeuroMapper, an in-browser visualization tool that helps machine learning (ML) developers interpret the evolution of a model during training, providing a new way to monitor the training process and visually…

Despite the success of existing tensor factorization methods, most of them conduct a multilinear decomposition, and rarely exploit powerful modeling frameworks, like deep neural networks, to capture a variety of complicated interactions in…

Traffic anomalies and attacks are commonplace in today's networks and identifying them rapidly and accurately is critical for large network operators. For a statistical intrusion detection system (IDS), it is crucial to detect at the…

Over the last few years, the number of precision farming projects has increased specifically in harvesting robots and many of which have made continued progress from identifying crops to grasping the desired fruit or vegetable. One of the…

PURPOSE: The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools monitoring and prioritizing the literature to understand the clinical implications of the pathogenic genetic variants. We…

We introduce DNABERT-S, a tailored genome model that develops species-aware embeddings to naturally cluster and segregate DNA sequences of different species in the embedding space. Differentiating species from genomic sequences (i.e., DNA…

In the global challenge of understanding and characterizing biodiversity, short species-specific genomic sequences known as DNA barcodes play a critical role, enabling fine-grained comparisons among organisms within the same kingdom of…

Data visualisation is a key tool in data mining for understanding big datasets. Many visualisation methods have been proposed, including the well-regarded state-of-the-art method t-Distributed Stochastic Neighbour Embedding. However, the…

Intrusion detection system (IDS) is a piece of hardware or software that looks for malicious activity or policy violations in a network. It looks for malicious activity or security flaws on a network or system. IDS protects hosts or…

Summary: TreeGrafter is a new software tool for annotating protein sequences using annotated phylogenetic trees. Cur-rently, the tool provides annotations to Gene Ontology terms, and PANTHER protein class, family and subfamily. The…

Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…

We have developed observation control software for the Immersion GRating INfrared Spectrometer (IGRINS) slit-viewing camera module, which maintains the position of an astronomical target on the spectroscopic slit. It is composed of several…

In this article we are describing a new algorithm for detecting and validating partial horizontal gene transfers (HGT). The presented algorithm is based on a sliding window procedure which analyzes fragments of the given multiple sequence…

We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing…

Despite much progress over the past decade, current Single Nucleotide Polymorphism (SNP) genotyping technologies still offer an insufficient degree of multiplexing when required to handle user-selected sets of SNPs. In this paper we propose…

Variant calling refinement is crucial for distinguishing true genetic variants from technical artifacts in high-throughput sequencing data. Manual review is time-consuming while heuristic filtering often lacks optimal solutions. Traditional…

Intelligence analysts have long struggled with an abundance of data that must be investigated on a daily basis. In the U.S. Army, this activity involves reconciling information from various sources, a process that has been automated to a…

With the advent of Next-Generation (NG) sequencing, it has become possible to sequence an entire genome quickly and inexpensively. However, in some experiments one only needs to extract and assembly a portion of the sequence reads, for…

In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…

Genetic transfers are pervasive across both prokaryotes and eukaryotes, encompassing canonical genomic introgression between species or genera and horizontal gene transfer (HGT) across kingdoms. However, DNA transfer between…