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A self-organizing approach is proposed for gene finding based on the model of codon usage for coding regions and positional preference for noncoding regions. The symmetry between the direct and reverse coding regions is adopted for reducing…
Backpropagation of error (backprop) is a powerful algorithm for training machine learning architectures through end-to-end differentiation. However, backprop is often criticised for lacking biological plausibility. Recently, it has been…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
A reduced-order model based on Proper Orthogonal Decomposition (POD) is proposed for the bidomain equations of cardiac electrophysiology. Its accuracy is assessed through electrocardiograms in various configurations, including myocardium…
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…
Causal discovery is the challenging task of inferring causal structure from data. Motivated by Pearl's Causal Hierarchy (PCH), which tells us that passive observations alone are not enough to distinguish correlation from causation, there…
We consider a generic representation problem of internal coordinates (bond lengths, valence angles, and dihedral angles) and their transformation to 3-dimensional Cartesian coordinates of a biomolecule. We show that the…
Neutron computed tomography (nCT) is a 3D characterization technique used to image the internal morphology or chemical composition of samples in biology and materials sciences. A typical workflow involves placing the sample in the path of a…
The CUR decomposition is a technique for low-rank approximation that selects small subsets of the columns and rows of a given matrix to use as bases for its column and rowspaces. It has recently attracted much interest, as it has several…
Iteration methods based on barycentric rational interpolation are derived that exhibit accelerating orders of convergence. For univariate root search, the derivative-free methods approach quadratic convergence and the first-derivative…
This paper presents a multi-lead fusion method for the accurate and automated detection of the QRS complex location in 12 lead ECG (Electrocardiogram) signals. The proposed multi-lead fusion method accurately delineates the QRS complex by…
Several statistical approaches based on reproducing kernels have been proposed to detect abrupt changes arising in the full distribution of the observations and not only in the mean or variance. Some of these approaches enjoy good…
We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such…
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 recent times, deep neural networks achieved outstanding predictive performance on various classification and pattern recognition tasks. However, many real-world prediction problems have ordinal response variables, and this ordering…
Background: Identification of causal SNPs in most genome wide association studies relies on approaches that consider each SNP individually. However, there is a strong correlation structure among SNPs that need to be taken into account.…
Code retrieval helps developers reuse the code snippet in the open-source projects. Given a natural language description, code retrieval aims to search for the most relevant code among a set of code. Existing state-of-the-art approaches…
In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably…
Behavioral cloning has proven to be effective for learning sequential decision-making policies from expert demonstrations. However, behavioral cloning often suffers from the causal confusion problem where a policy relies on the noticeable…
A hypercomplex representation of DNA is proposed to facilitate comparison of DNA sequences with fuzzy composition. Using hypercomplex number representation, conventional sequence analysis method, such as, dot matrix analysis, dynamic…