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Swift and accurate blood smear analysis is an effective diagnostic method for leukemia and other hematological malignancies. However, manual leukocyte count and morphological evaluation using a microscope is time-consuming and prone to…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NP-hard even for datasets known to only contain siblings. Some recent methods have been…
In recent years, supervised person re-identification (re-ID) models have received increasing studies. However, these models trained on the source domain always suffer dramatic performance drop when tested on an unseen domain. Existing…
Visually similar characters, or homoglyphs, can be used to perform social engineering attacks or to evade spam and plagiarism detectors. It is thus important to understand the capabilities of an attacker to identify homoglyphs --…
(Hyper)Graph decomposition is a family of problems that aim to break down large (hyper)graphs into smaller sub(hyper)graphs for easier analysis. The importance of this lies in its ability to enable efficient computation on large and complex…
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…
Simplicial complexes are higher-order combinatorial structures which have been used to represent real-world complex systems. In this paper, we concentrate on the local patterns in simplicial complexes called simplets, a generalization of…
Representing images by compact hash codes is an attractive approach for large-scale content-based image retrieval. In most state-of-the-art hashing-based image retrieval systems, for each image, local descriptors are first aggregated as a…
The repeat content and heterozygosity rate of a target genome are important factors in determining the feasibility of achieving a complete telomere-to-telomere assembly. The mathematical relationship between the required coverage and read…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue…
Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they…
Background: Regions with copy number variations (in germline cells) or copy number alteration (in somatic cells) are of great interest for human disease gene mapping and cancer studies. They represent a new type of mutation and are…
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…
We present a two-layer hidden Markov model to detect structure of haplotypes for unrelated individuals. This allows modeling two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
The objective of this work is to learn a compact embedding of a set of descriptors that is suitable for efficient retrieval and ranking, whilst maintaining discriminability of the individual descriptors. We focus on a specific example of…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…