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Leveraging artificial intelligence (AI)-driven electronic design and automation (EDA) tools, high-performance computing, and parallelized algorithms are essential for next-generation microprocessor innovation, ensuring continued progress in…
Although conservation of thermodynamics is much less studied than of sequences and structures, thermodynamic details are biophysical features different from but as important as structural features. As a succession of previous research which…
Linear mixture models have proven very useful in a plethora of applications, e.g., topic modeling, clustering, and source separation. As a critical aspect of the linear mixture models, identifiability of the model parameters is…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs which play a significant role in several biological processes. RNA-seq based transcriptome sequencing has been extensively used for identification of lncRNAs. However, accurate…
The rapid development of pretrained Machine Learning Interatomic Potentials (MLIPs) that cover a wide range of molecular species has made it challenging to select the best model for a given application. We benchmark 15 pretrained MLIPs,…
In this paper, we propose a novel approach for mining different program features by analysing the internal behaviour of a deep neural network trained on source code. Using an unlabelled dataset of Java programs and three different embedding…
Much of the recent research work in image retrieval, has been focused around using Neural Networks as the core component. Many of the papers in other domain have shown that training multiple models, and then combining their outcomes,…
Classification, the process of assigning a label (or class) to an observation given its features, is a common task in many applications. Nonetheless in most real-life applications, the labels can not be fully explained by the observed…
Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
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…
Atypical mitosis marks a deviation in the cell division process that has been shown be an independent prognostic marker for tumor malignancy. However, atypical mitosis classification remains challenging due to low prevalence, at times…
Modern methods often formulate the counting of cells from microscopic images as a regression problem and more or less rely on expensive, manually annotated training images (e.g., dot annotations indicating the centroids of cells or…
The selection of features is an essential data preprocessing stage in data mining. The core principle of feature selection seems to be to pick a subset of possible features by excluding features with almost no predictive information as well…
Acute myeloid leukemia (AML) involves a block in terminal differentiation of the myeloid lineage and uncontrolled proliferation of a progenitor state. Using phorbol myristate acetate (PMA), it is possible to overcome this block in THP-1…
Molecular and morphological characters, as important parts of biological taxonomy, are contradictory but need to be integrated. Organism's image recognition and bioinformatics are emerging and hot problems nowadays but with a gap between…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
Identification of minerals in the field is a task that is wrought with many challenges. Traditional approaches are prone to errors where there is no enough experience and expertise. Several existing techniques mainly make use of features of…