Related papers: RuleVis: Constructing Patterns and Rules for Rule-…
Rule sets are often used in Machine Learning (ML) as a way to communicate the model logic in settings where transparency and intelligibility are necessary. Rule sets are typically presented as a text-based list of logical statements…
Despite extensive theoretical work on biologically plausible learning rules, clear evidence about whether and how such rules are implemented in the brain has been difficult to obtain. We consider biologically plausible supervised- and…
Impact analysis is concerned with the identification of consequences of changes and is therefore an important activity for software evolution. In modelbased software development, models are core artifacts, which are often used to generate…
Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…
Synaptic plasticity depends on the interaction between electrical activity in neurons and the synaptic proteome, the collection of over 1000 proteins in the post-synaptic density (PSD) of synapses. To construct models of synaptic plasticity…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
Rule sets are often used in Machine Learning (ML) as a way to communicate the model logic in settings where transparency and intelligibility are necessary. Rule sets are typically presented as a text-based list of logical statements…
State-of-the-art models represent proteins and molecules in separate embedding manifolds, limiting the modeling of systemic biological processes. We introduce ReactEmbed, a lightweight, plug-and-play module that bridges this gap. ReactEmbed…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
Traditional machine learning based intelligent systems assist users by learning patterns in data and making recommendations. However, these systems are limited in that the user has little means of understanding the rationale behind the…
Bigraphs are a versatile modelling formalism that allows easy expression of placement and connectivity relations in a graphical format. System evolution is user defined as a set of rewrite rules. This paper presents a practical, yet…
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
Association rule mining is intended for searching for the relationships between attributes in transaction databases. The whole process of rule discovery is very complex, and involves pre-processing techniques, a rule mining step, and…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
We develop a matrix-based approach to predict and verify indirect interactions in gene and protein regulatory networks. It is based on the approximate transitivity of indirect regulations (e.g. A regulates B and B regulates C often implies…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
This study proposed an exhaustive stable/reproducible rule-mining algorithm combined to a classifier to generate both accurate and interpretable models. Our method first extracts rules (i.e., a conjunction of conditions about the values of…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
The study of cellular signalling pathways and their deregulation in disease states, such as cancer, is a large and extremely complex task. Indeed, these systems involve many parts and processes but are studied piecewise and their…