Related papers: Dynamic read mapping and online consensus calling …
Motivation: Identifying genomic variants is an essential step for connecting genotype and phenotype. The usual approach consists of statistical inference of variants from alignments of sequencing reads. State-of-the-art variant callers can…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
Thousands of users consult digital archives daily, but the information they can access is unrepresentative of the diversity of documentary history. The sequence-to-sequence architecture typically used for optical character recognition (OCR)…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Online Continual Learning (OCL) aims to learn from endless non\text{-}stationary data streams, yet most existing methods assume a flat label space and overlook the hierarchical organization of real\text{-}world concepts that evolves both…
The use of local detectors and descriptors in typical computer vision pipelines work well until variations in viewpoint and appearance change become extreme. Past research in this area has typically focused on one of two approaches to this…
Maintaining a dynamic $k$-core decomposition is an important problem that identifies dense subgraphs in dynamically changing graphs. Recent work by Liu et al. [SPAA 2022] presents a parallel batch-dynamic algorithm for maintaining an…
In the era of the big data, we create and collect lots of data from all different kinds of sources: the Internet, the sensors, the consumer market, and so on. Many of the data are coming sequentially, and would like to be processed and…
The mutations of a complex systemic disease like cancer can be modeled as stuck-at faults in the Boolean system paradigm. For a class of multiple faults, the fault identification is exceptionally significant under the incomplete access of…
A change point problem occurs in many statistical applications. If there exist change points in a model, it is harmful to make a statistical analysis without any consideration of the existence of the change points and the results derived…
Inference scaling methods for LLMs often rely on decomposing problems into steps (or groups of tokens), followed by sampling and selecting the best next steps. However, these steps and their sizes are often predetermined or manually…
Capturing the dynamics in user preference is crucial to better predict user future behaviors because user preferences often drift over time. Many existing recommendation algorithms -- including both shallow and deep ones -- often model such…
Variant calling is a fundamental task in genomic research, essential for detecting genetic variations such as single nucleotide polymorphisms (SNPs) and insertions or deletions (indels). This paper presents an enhancement to DeepChem, a…
Embedding is a useful technique to project a high-dimensional feature into a low-dimensional space, and it has many successful applications including link prediction, node classification and natural language processing. Current approaches…
The rapid growth of Cloud Computing and Internet of Things (IoT) has significantly increased the interconnection of computational resources, creating an environment where malicious software (malware) can spread rapidly. To address this…
Decision making for dynamic systems is challenging due to the scale and dynamicity of such systems, and it is comprised of decisions at strategic, tactical, and operational levels. One of the most important aspects of decision making is…
Continual learning is the problem of learning and retaining knowledge through time over multiple tasks and environments. Research has primarily focused on the incremental classification setting, where new tasks/classes are added at discrete…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
The use-case diagram is a software artifact. Thus, as with any software artifact, the use-case diagrams change across time through the software development life cycle. Therefore, several versions of the same diagram are existed at distinct…
Aligning reads to a reference sequence is a fundamental step in numerous bioinformatics pipelines. As a consequence, the sensitivity and precision of the mapping tool, applied with certain parameters to certain data, can critically affect…