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In the past years, many computational methods have been developed to infer the structure of gene regulatory networks from time-series data. However, the applicability and accuracy presumptions of such algorithms remain unclear due to…

Recent advances in biological research have seen the emergence of high-throughput technologies with numerous applications that allow the study of biological mechanisms at an unprecedented depth and scale. A large amount of genomic data is…

One of the notable fields in studying the genetics of cancer is disease gene identification which affects disease treatment and drug discovery. Many researches have been done in this field. Genome-wide association studies (GWAS) are one of…

We propose a Multi-Layer Network based on the Bayesian framework of the Factor Graphs in Reduced Normal Form (FGrn) applied to a two-dimensional lattice. The Latent Variable Model (LVM) is the basic building block of a quadtree hierarchy…

Network inference has been attracting increasing attention in several fields, notably systems biology, control engineering and biomedicine. To develop a therapy, it is essential to understand the connectivity of biochemical units and the…

The recent proliferation of high-dimensional data, such as electronic health records and genetics data, offers new opportunities to find novel predictors of outcomes. Presented with a large set of candidate features, interest often lies in…

Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…

The problem of estimating high-dimensional network models arises naturally in the analysis of many physical, biological and socio-economic systems. Examples include stock price fluctuations in financial markets and gene regulatory networks…

Unraveling the complexities of Gene Regulatory Networks (GRNs) is crucial for understanding cellular processes and disease mechanisms. Traditional computational methods often struggle with the dynamic nature of these networks. This study…

Heterogeneous molecular entities and their interactions, commonly depicted as a network, are crucial for advancing our systems-level understanding of biology. With recent advancements in high-throughput data generation and a significant…

Network inference is the process of deciding what is the true unknown graph underlying a set of interactions between nodes. There is a vast literature on the subject, but most known methods have an important drawback: the inferred graph is…

Network inference approaches are widely used to shed light on regulatory interplay between molecular players such as genes and proteins. Biochemical processes underlying networks of interest (e.g. gene regulatory or protein signalling…

In healthcare, it is essential to explain the decision-making process of machine learning models to establish the trustworthiness of clinicians. This paper introduces BI-RADS-Net, a novel explainable deep learning approach for cancer…

Objective: Modelling the associations from high-throughput experimental molecular data has provided unprecedented insights into biological pathways and signalling mechanisms. Graphical models and networks have especially proven to be useful…

Metastasis is the leading cause of cancer-related mortality, yet most predictive models rely on shallow architectures and neglect patient-specific regulatory mechanisms. Here, we integrate classical machine learning and deep learning to…

We extend biologically-informed neural networks (BINNs) for genomic prediction (GP) and selection (GS) in crops by integrating thousands of single-nucleotide polymorphisms (SNPs) with multi-omics measurements and prior biological knowledge.…

Graphical models or networks describe the statistical dependence among multiple variables and are widely used in biology (e.g., gene regulatory networks). Under appropriate assumptions, directed edges may represent causal relationships. A…

We report a scalable hybrid quantum-classical machine learning framework to build Bayesian networks (BN) that captures the conditional dependence and causal relationships of random variables. The generation of a BN consists of finding a…

The main goal of this paper is to describe a method for exact inference in general hybrid Bayesian networks (BNs) (with a mixture of discrete and continuous chance variables). Our method consists of approximating general hybrid Bayesian…

We consider the problem of inferring the values of an arbitrary set of variables (e.g., risk of diseases) given other observed variables (e.g., symptoms and diagnosed diseases) and high-dimensional signals (e.g., MRI images or EEG). This is…