Attribute Exploration of Gene Regulatory Processes

This thesis aims at the logical analysis of discrete processes, in particular of such generated by gene regulatory networks. States, transitions and operators from temporal logics are expressed in the language of Formal Concept Analysis. By the attribute exploration algorithm, an expert or a computer program is enabled to validate a minimal and complete set of implications, e.g. by comparison of predictions derived from literature with observed data. Here, these rules represent temporal dependencies within gene regulatory networks including coexpression of genes, reachability of states, invariants or possible causal relationships. This new approach is embedded into the theory of universal coalgebras, particularly automata, Kripke structures and Labelled Transition Systems. A comparison with the temporal expressivity of Description Logics is made. The main theoretical results concern the integration of background knowledge into the successive exploration of the defined data structures (formal contexts). Applying the method a Boolean network from literature modelling sporulation of Bacillus subtilis is examined. Finally, we developed an asynchronous Boolean network for extracellular matrix formation and destruction in the context of rheumatoid arthritis.Comment: 111 pages, 9 figures, file size 2.1 MB, PhD thesis University of Jena, Germany, Faculty of Mathematics and Computer Science, 2011. Online available at http://www.db-thueringen.de/servlets/DocumentServlet?id=1960

Contributions of Continuous Max-Flow Theory to Medical Image Processing

Discrete graph cuts and continuous max-flow theory have created a paradigm shift in many areas of medical image processing. As previous methods limited themselves to analytically solvable optimization problems or guaranteed only local optimizability to increasingly complex and non-convex functionals, current methods based now rely on describing an optimization problem in a series of general yet simple functionals with a global, but non-analytic, solution algorithms. This has been increasingly spurred on by the availability of these general-purpose algorithms in an open-source context. Thus, graph-cuts and max-flow have changed every aspect of medical image processing from reconstruction to enhancement to segmentation and registration. To wax philosophical, continuous max-flow theory in particular has the potential to bring a high degree of mathematical elegance to the field, bridging the conceptual gap between the discrete and continuous domains in which we describe different imaging problems, properties and processes. In Chapter 1, we use the notion of infinitely dense and infinitely densely connected graphs to transfer between the discrete and continuous domains, which has a certain sense of mathematical pedantry to it, but the resulting variational energy equations have a sense of elegance and charm. As any application of the principle of duality, the variational equations have an enigmatic side that can only be decoded with time and patience. The goal of this thesis is to show the contributions of max-flow theory through image enhancement and segmentation, increasing incorporation of topological considerations and increasing the role played by user knowledge and interactivity. These methods will be rigorously grounded in calculus of variations, guaranteeing fuzzy optimality and providing multiple solution approaches to addressing each individual problem

Autonomous Agents Modelling Other Agents: A Comprehensive Survey and Open Problems

Much research in artificial intelligence is concerned with the development of autonomous agents that can interact effectively with other agents. An important aspect of such agents is the ability to reason about the behaviours of other agents, by constructing models which make predictions about various properties of interest (such as actions, goals, beliefs) of the modelled agents. A variety of modelling approaches now exist which vary widely in their methodology and underlying assumptions, catering to the needs of the different sub-communities within which they were developed and reflecting the different practical uses for which they are intended. The purpose of the present article is to provide a comprehensive survey of the salient modelling methods which can be found in the literature. The article concludes with a discussion of open problems which may form the basis for fruitful future research.Comment: Final manuscript (46 pages), published in Artificial Intelligence Journal. The arXiv version also contains a table of contents after the abstract, but is otherwise identical to the AIJ version. Keywords: autonomous agents, multiagent systems, modelling other agents, opponent modellin

Automatic concept learning via information lattices

Concept learning is about distilling interpretable rules and concepts from data, a prelude to more advanced knowledge discovery and problem solving in creative domains such as art and science. While concept learning is pervasive in humans, current artificial intelligent (AI) systems are mostly good at either applying human-distilled rules (rule-based AI) or capturing patterns in a task-driven fashion (pattern recognition), but not at learning concepts in a human-interpretable way similar to human-induced rules and theory. This thesis introduces a new learning problem---Automatic Concept Learning (ACL)---targeting self-explanation and self-exploration as the two principal pursuits; correspondingly, it proposes a new learning model---Information Lattice Learning (ILL)---combining computational abstraction and probabilistic rule learning as the two principal components. Woven around the core idea of abstraction, the entire ACL framework is presented as a generalization of Shannon’s information lattice that further brings learning into the picture. The core idea of abstraction is cast as a hierarchical, interpretable, data-free, and task-free clustering problem, seeded from universal priors such as simple algebra and symmetries. The main body of the thesis comprises three self-contained yet close-knit parts: theory, algorithms, and applications. The theory part presents the mathematical exposition of ACL, formalizing the key notions of abstraction, concept, probabilistic rule, and further the entire concept learning problem. The goal is to lay down a solid path towards algorithmic means that are computationally feasible, reliable, and human-interpretable. The algorithms part presents the computational development of ACL, that is, ILL. It puts together computational abstraction and statistical learning in the same algorithmic picture, creating a bridge that connects deductive (rule-based) and inductive (data-driven) approaches in AI. Aiming for human interpretability and model transparency in particular, ILL in many ways mimics human learning. This includes mechanism-driven abstraction generation, as well as a "teacher-student" loop that can distill customizable traces of rules for data summarization and data explanation. The applications part recapitulates the theory and algorithms through concrete examples. Music is used for demonstration and automatic music concept learning is thoroughly studied. This part details the implementation of MUS-ROVER, an automatic music theorist that distills music composition rules from sheet music. To better support music ACL and music AI in general, the twin system MUS-NET is built as a crowdsourcing platform for making and serving digital sheet music data sets

A computational framework of human causal generalization

How do people decide how general a causal relationship is, in terms of the entities or situations it applies to? How can people make these difficult judgments in a fast, efficient way? To address these questions, I designed a novel online experiment interface that systematically measures how people generalize causal relationships, and developed a computational modeling framework that combines program induction (about the hidden causal laws) with non-parametric category inference (about their domains of influence) to account for unique patterns in human causal generalization. In particular, by introducing adaptor grammars to standard Bayesian-symbolic models, this framework formalizes conceptual bootstrapping as a general online inference algorithm that gives rise to compositional causal concepts. Chapter 2 investigates one-shot causal generalization, where I find that participants’ inferences are shaped by the order of the generalization questions they are asked. Chapter 3 looks into few-shot cases, and finds an asymmetry in the formation of causal categories: participants preferentially identify causal laws with features of the agent objects rather than recipients, but this asymmetry disappears when visual cues to causal agency are challenged. The proposed modeling approach can explain both the generalizationorder effect and the causal asymmetry, outperforming a naïve Bayesian account while providing a computationally plausible mechanism for real-world causal generalization. Chapter 4 further extends this framework with adaptor grammars, using a dynamic conceptual repertoire that is enriched over time, allowing the model to cache and later reuse elements of earlier insights. This model predicts systematically different learned concepts when the same evidence is processed in different orders, and across four experiments people’s learning outcomes indeed closely resembled this model’s, differing significantly from alternative accounts

CLADAG 2021 BOOK OF ABSTRACTS AND SHORT PAPERS

The book collects the short papers presented at the 13th Scientific Meeting of the Classification and Data Analysis Group (CLADAG) of the Italian Statistical Society (SIS). The meeting has been organized by the Department of Statistics, Computer Science and Applications of the University of Florence, under the auspices of the Italian Statistical Society and the International Federation of Classification Societies (IFCS). CLADAG is a member of the IFCS, a federation of national, regional, and linguistically-based classification societies. It is a non-profit, non-political scientific organization, whose aims are to further classification research

Seventh Annual Workshop on Space Operations Applications and Research (SOAR 1993), volume 1

This document contains papers presented at the Space Operations, Applications and Research Symposium (SOAR) Symposium hosted by NASA/Johnson Space Center (JSC) on August 3-5, 1993, and held at JSC Gilruth Recreation Center. SOAR included NASA and USAF programmatic overview, plenary session, panel discussions, panel sessions, and exhibits. It invited technical papers in support of U.S. Army, U.S. Navy, Department of Energy, NASA, and USAF programs in the following areas: robotics and telepresence, automation and intelligent systems, human factors, life support, and space maintenance and servicing. SOAR was concerned with Government-sponsored research and development relevant to aerospace operations. More than 100 technical papers, 17 exhibits, a plenary session, several panel discussions, and several keynote speeches were included in SOAR '93