Related papers: Constructing a Knowledge Base for Gene Regulatory …

Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics…

This paper presents an automatic formal controller synthesis method for nonlinear sampled-data systems with safety and reachability specifications. Fundamentally, the presented method is not restricted to polynomial systems and controllers.…

Conceptual Graphs (CGs) are a formalism to represent knowledge. However producing a CG database is complex. To the best of our knowledge, existing methods do not fully use the expressivity of CGs. It is particularly troublesome as it is…

This review article highlights state-of-the-art data-driven techniques to discover, encode, surrogate, or emulate constitutive laws that describe the path-independent and path-dependent response of solids. Our objective is to provide an…

Networks pervade many disciplines of science for analyzing complex systems with interacting components. In particular, this concept is commonly used to model interactions between genes and identify closely associated genes forming…

The pursuit of decision safety in clinical applications highlights the potential of concept-based methods in medical imaging. While these models offer active interpretability, they often suffer from concept leakages, where unintended…

Continual learning aims to update models under distribution shift without forgetting, yet many high-stakes deployments, such as healthcare, also require interpretability. In practice, models that adapt well (e.g., deep networks) are often…

Formal Concept Analysis (FCA) begins from a context, given as a binary relation between some objects and some attributes, and derives a lattice of concepts, where each concept is given as a set of objects and a set of attributes, such that…

Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…

This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The…

Dialectical frameworks are a unifying model of formal argumentation, where argumentative relations between arguments are represented by assigning acceptance conditions to atomic arguments. Their generality allow them to cover a number of…

Genetic and pharmacological perturbation experiments, such as deleting a gene and monitoring gene expression responses, are powerful tools for studying cellular signal transduction pathways. However, it remains a challenge to automatically…

Generating a huge number of association rules reduces their utility in the decision making process, done by domain experts. In this context, based on the theory of Formal Concept Analysis, we propose to extend the notion of Formal Concept…

We develop a method to control discrete-time systems with constant but initially unknown parameters from linear temporal logic (LTL) specifications. We introduce the notions of (non-deterministic) parametric and adaptive transition systems…

We propose a novel approach for the formal verification of biological systems based on the use of a modal linear logic. We show how such a logic can be used, with worlds as instants of time, as an unified framework to encode both biological…

Humans engage in informal debates on a daily basis. By expressing their opinions and ideas in an argumentative fashion, they are able to gain a deeper understanding of a given problem and in some cases, find the best possible course of…

In this paper the problems of deriving a taxonomy from a text and concept-oriented text segmentation are approached. Formal Concept Analysis (FCA) method is applied to solve both of these linguistic problems. The proposed segmentation…

In this paper we describe a mechanism to improve Information Retrieval (IR) on the web. The method is based on Formal Concepts Analysis (FCA) that it is makes semantical relations during the queries, and allows a reorganizing, in the shape…

Statistical inference of genetic regulatory networks is essential for understanding temporal interactions of regulatory elements inside the cells. For inferences of large networks, identification of network structure is typical achieved…

Data lakes are widely used to store extensive and heterogeneous datasets for advanced analytics. However, the unstructured nature of data in these repositories introduces complexities in exploiting them and extracting meaningful insights.…