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Microbiome research has immense potential for unlocking insights into human health and disease. A common goal in human microbiome research is identifying subgroups of individuals with similar microbial composition that may be linked to…
Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…
Bit arrays, or bitmaps, are used to significantly speed up set operations in several areas, such as data warehousing, information retrieval, and data mining, to cite a few. However, bitmaps usually use a large storage space, thus requiring…
Although considerable efforts have been devoted to transformer-based ranking models for document search, the relevance-efficiency tradeoff remains a critical problem for ad-hoc ranking. To overcome this challenge, this paper presents BECR…
Multiple datasets containing different types of features may be available for a given task. For instance, users' profiles can be used to group users for recommendation systems. In addition, a model can also use users' historical behaviors…
With distributed machine learning being a prominent technique for large-scale machine learning tasks, communication complexity has become a major bottleneck for speeding up training and scaling up machine numbers. In this paper, we propose…
Disentangled distributed representations of data are desirable for machine learning, since they are more expressive and can generalize from fewer examples. However, for complex data, the distributed representations of multiple objects…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
Two successful approaches for the segmentation of biomedical images are (1) the selection of segment candidates from a merge-tree, and (2) the clustering of small superpixels by solving a Multi-Cut problem. In this paper, we introduce a…
Document clustering is an unsupervised approach in which a large collection of documents (corpus) is subdivided into smaller, meaningful, identifiable, and verifiable sub-groups (clusters). Meaningful representation of documents and…
Medical imaging is vital in computer assisted intervention. Particularly cone beam computed tomography (CBCT) with defacto real time and mobility capabilities plays an important role. However, CBCT images often suffer from artifacts, which…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…
A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work leverages the sparsity of the assembly graph to find $r$-dominating sets which enable…