Related papers: Constructing a Knowledge Base for Gene Regulatory …
Fighting criminal activities in our modern societies required the engagement of intelligent information systems that can analyze crime data geographically and enable new concepts to be deduced from it. These information systems should be…
What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic…
This paper outlines a general formal framework for reasoning systems, intended to support future analysis of inference architectures across domains. We model reasoning systems as structured tuples comprising phenomena, explanation space,…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
Mathematical models are fundamental building blocks in the design of dynamical control systems. As control systems are becoming increasingly complex and networked, approaches for obtaining such models based on first principles reach their…
The theory of distributed conceptual structures, as outlined in this paper, is concerned with the distribution and conception of knowledge. It rests upon two related theories, Information Flow and Formal Concept Analysis, which it seeks to…
Mining specifications from execution traces presents an automated way of capturing characteristic system behaviors. However, existing approaches are largely restricted to Boolean abstractions of events, limiting their ability to express…
We present a novel approach to the automatic acquisition of taxonomies or concept hierarchies from a text corpus. The approach is based on Formal Concept Analysis (FCA), a method mainly used for the analysis of data, i.e. for investigating…
The vast growth of data has rendered traditional manual inspection infeasible, necessitating the adoption of computational methods for efficient data exploration. Topic modeling has emerged as a powerful tool for analyzing large-scale…
One of the basic frameworks in science views behavioral products as a process within a dynamic system. The mechanism might be seen as a representation of many instances of centralized control in real time. Many real systems, however,…
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
The ability to flexibly compose previously acquired skills to execute intelligent behaviors is a hallmark of natural intelligence. Such compositional flexibility is often attributed to context-dependent gating mechanisms that determine how…
We are concerned with the analysis of normative texts - documents based on the deontic notions of obligation, permission, and prohibition. Our goal is to make queries about these notions and verify that a text satisfies certain properties…
Nowadays data sets are available in very complex and heterogeneous ways. Mining of such data collections is essential to support many real-world applications ranging from healthcare to marketing. In this work, we focus on the analysis of…
Prior work has shown that text-conditioned diffusion models can learn to identify and manipulate primitive concepts underlying a compositional data-generating process, enabling generalization to entirely novel, out-of-distribution…
Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires…
This paper studies the role that ontologies can play in establishing conceptual data models during the process of information systems development. A mapping algorithm has been proposed and embedded in a special purpose Transformation-Engine…
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…
In real-world systems, phase transitions often materialize abruptly, making it difficult to design appropriate controls that help uncover underlying processes. Some agent-based computational models display transformations similar to phase…