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During the diagnostic process, doctors incorporate multimodal information including imaging and the medical history - and similarly medical AI development has increasingly become multimodal. In this paper we tackle a more subtle challenge:…
Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce…
In this paper, we introduce the Dynamic Modularity-Spectral Algorithm (DynMSA), a novel approach to identify clusters of stocks with high intra-cluster correlations and low inter-cluster correlations by combining Random Matrix Theory with…
Missing data present challenges in data analysis. Naive analyses such as complete-case and available-case analysis may introduce bias and loss of efficiency, and produce unreliable results. Multiple imputation (MI) is one of the most widely…
Feature extraction is an unavoidable task, especially in the critical step of preprocessing biological sequences. This step consists for example in transforming the biological sequences into vectors of motifs where each motif is a…
A common and natural intuition among software testers is that test cases need to differ if a software system is to be tested properly and its quality ensured. Consequently, much research has gone into formulating distance measures for how…
We have extended our analytically derived PDB-NMA formulation, ATMAN [1], to include protein dimers using mixed internal and Cartesian coordinates. A test case on a 1.3\AA\ resolution model of a small homodimer, ActVA-ORF6, consisting of…
Evolution is an extraordinary engine for enzymatic diversity, yet the chemistry it has explored remains a narrow slice of what DNA can encode. Deep generative models can design new proteins that bind ligands, but none have created enzymes…
Enzymes and proteins are live driven biochemicals, which has a dramatic impact over the environment, in which it is active. So, therefore, it is highly looked-for to build such a robust and highly accurate automatic and computational model…
Functional MRI (fMRI) has been widely used to study activity patterns in the human brain. It infers neuronal activity from the associated hemodynamic response, which fundamentally limits its spatial and temporal specificity. In mice, the…
The distribution of objective vectors in a Pareto Front Approximation (PFA) is crucial for representing the associated manifold accurately. Distribution Indicators (DIs) assess the distribution of a PFA numerically, utilizing concepts like…
In a research context, image acquisition will often involve a pre-defined static protocol and the data will be of high quality. If we are to build applications that work in hospitals without significant operational changes in care delivery,…
Recent works leveraging Graph Neural Networks to approach graph matching tasks have shown promising results. Recent progress in learning discrete distributions poses new opportunities for learning graph matching models. In this work, we…
In microbiome studies, it is often of great interest to identify clusters or partitions of microbiome profiles within a study population and to characterize the distinctive attributes of each resulting microbial community. While raw counts…
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…
Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language…
Genome-wide association studies have become increasingly common due to advances in technology and have permitted the identification of differences in single nucleotide polymorphism (SNP) alleles that are associated with diseases. However,…
Dynamo is a full-stack software solution for scientific data management. Dynamo's architecture is modular, extensible, and customizable, making the software suitable for managing data in a wide range of installation scales, from a few…
Food authenticity studies are concerned with determining if food samples have been correctly labeled or not. Discriminant analysis methods are an integral part of the methodology for food authentication. Motivated by food authenticity…
Subsampling from a large data set is useful in many supervised learning contexts to provide a global view of the data based on only a fraction of the observations. Diverse (or space-filling) subsampling is an appealing subsampling approach…