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Many practical problems in almost all scientific and technological disciplines have been classified as computationally hard (NP-hard or even NP-complete). In life sciences, combinatorial optimization problems frequently arise in molecular…
The emergence of diverse generative vision models has recently enabled the synthesis of visually realistic images, underscoring the critical need for effectively detecting these generated images from real photos. Despite advances in this…
Variability in illumination is a primary factor limiting deep learning robustness for field-based plant disease detection. This study evaluates Histogram Matching (HM), a technique that transforms the pixel intensity distribution of an…
In histopathological image analysis, feature extraction for classification is a challenging task due to the diversity of histology features suitable for each problem as well as presence of rich geometrical structure. In this paper, we…
Aggregation-based assays, using micro- and nano-particles have been widely accepted as an efficient and cost-effective bio-sensing tool, particularly in microbiology, where particle clustering events are used as a metric to infer the…
The target of Electronic Health Record (EHR) coding is to find the diagnostic codes according to the EHRs. In previous research, researchers have preferred to do multi-classification on the EHR coding task; most of them encode the EHR first…
Despite the superior performance of Deep Learning (DL) on numerous segmentation tasks, the DL-based approaches are notoriously overconfident about their prediction with highly polarized label probability. This is often not desirable for…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
We present an approach, called the "Shadow Method," for the identification of disease loci from dense genetic marker maps in complex, potentially incomplete pedigrees. "Shadow" is a simple method based on an analysis of the patterns of…
To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies between all DNA segment pairs across the genome. As Hi-C data sets often are massive,…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
The remarkable success of foundation models has sparked growing interest in their application to single-cell biology. Models like Geneformer and scGPT promise to serve as versatile tools in this specialized field. However, representing a…
Many datasets take the form of a bipartite graph where two types of nodes are connected by relationships, like the movies watched by a user or the tags associated with a file. The partitioning of the bipartite graph could be used to fasten…
Detection of rare variants by resequencing is important for the identification of individuals carrying disease variants. Rapid sequencing by new technologies enables low-cost resequencing of target regions, although it is still prohibitive…
Fashion attribute classification is of great importance to many high-level tasks such as fashion item search, fashion trend analysis, fashion recommendation, etc. The task is challenging due to the extremely imbalanced data distribution,…
The human genotope is the convex hull of all allele frequency vectors that can be obtained from the genotypes present in the human population. In this paper we take a few initial steps towards a description of this object, which may be…
Complex networks constitute the backbones of many complex systems such as social networks. Detecting the community structure in a complex network is both a challenging and a computationally expensive task. In this paper, we present the…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…