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Optical Character Recognition has been a challenging field in the advent of digital computers. It is needed where information is to be readable both to humans and machines. The process of OCR is composed of a set of pre and post processing…
A eukaryotic gene consists of multiple exons (protein coding regions) and introns (non-coding regions), and a splice junction refers to the boundary between a pair of exon and intron. Precise identification of spice junctions on a gene is…
We devise a novel inference algorithm to effectively solve the cancer progression model reconstruction problem. Our empirical analysis of the accuracy and convergence rate of our algorithm, CAncer PRogression Inference (CAPRI), shows that…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
Academic documents are packed with texts, equations, tables, and figures, requiring comprehensive understanding for accurate Optical Character Recognition (OCR). While end-to-end OCR methods offer improved accuracy over layout-based…
The manuscript describes efficient algorithms for the computation of the CUR and ID decompositions. The methods used are based on simple modifications to the classical truncated pivoted QR decomposition, which means that highly optimized…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
Thanks to rapidly evolving sequencing techniques, the amount of genomic data at our disposal is growing increasingly large. Determining the gene structure is a fundamental requirement to effectively interpret gene function and regulation.…
Retrieving fine-grained visual content based on user intent remains a challenge in multi-modal systems. Although current Composed Image Retrieval (CIR) methods combine reference images with retrieval texts, they are constrained to…
Splice sites play a crucial role in gene expression, and accurate prediction of these sites in DNA sequences is essential for diagnosing and treating genetic disorders. We address the challenge of splice site prediction by introducing…
Software developers frequently reuse source code from repositories as it saves development time and effort. Code clones accumulated in these repositories hence represent often repeated functionalities and are candidates for reuse in an…
Worm origin identification and propagation path reconstruction are essential problems in digital forensics. However, a small number of studies have specifically investigated these problems so far. In this paper, we extend a distributed…
CUR matrix decomposition is a randomized algorithm that can efficiently compute the low rank approximation for a given rectangle matrix. One limitation with the existing CUR algorithms is that they require an access to the full matrix A for…
Core decomposition is a classic technique for discovering densely connected regions in a graph with large range of applications. Formally, a $k$-core is a maximal subgraph where each vertex has at least $k$ neighbors. A natural extension of…
Integrating extracted knowledge from the Web to knowledge graphs (KGs) can facilitate tasks like question answering. We study relation integration that aims to align free-text relations in subject-relation-object extractions to relations in…
Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment strategies. Many…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the bloodstream and contribute to a pool of…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Many learning problems require predicting sets of objects when the number of objects is not known beforehand. Examples include object detection, molecular modeling, and scientific inference tasks such as astrophysical source detection.…