Modeling and Simulation of Biological Systems through Electronic Design Automation techniques

Modeling and simulation of biological systems is a key requirement for integrating invitro and in-vivo experimental data. In-silico simulation allows testing different experimental conditions, thus helping in the discovery of the dynamics that regulate the system. These dynamics include errors in the cellular information processing that are responsible for diseases such as cancer, autoimmunity, and diabetes as well as drug effects to the system (Gonalves, 2013). In this context, modeling approaches can be classified into two categories: quantitative and qualitative models. Quantitative modeling allows for a natural representation of molecular and gene networks and provides the most precise prediction. Nevertheless, the lack of kinetic data (and of quantitative data in general) hampers its use for many situations (Le Novere, 2015). In contrast, qualitative models simplify the biological reality and are often able to reproduce the system behavior. They cannot describe actual concentration levels nor realistic time scales. As a consequence, they cannot be used to explain and predict the outcome of biological experiments that yield quantitative data. However, given a biological network consisting of input (e.g., receptors), intermediate, and output (e.g., transcription factors) signals, they allow studying the input-output relationships through discrete simulation (Samaga, 2013). Boolean models are gaining an increasing interest in reproducing dynamic behaviors, understanding processes, and predicting emerging properties of cellular signaling networks through in-silico experiments. They are emerging as a valid alternative to the quantitative approaches (i.e., based on ordinary differential equations) for exploratory modeling when little is known about reaction kinetics or equilibrium constants in the context of gene expression or signaling. Even though several approaches and software have been recently proposed for logic modeling of biological systems, they are limited to specific contexts and they lack of automation in analyzing biological properties such as complex attractors, and molecule vulnerability. This thesis proposes a platform based on Electronic Design Automation (EDA) technologies for qualitative modeling and simulation of Biological Systems. It aims at overtaking limitations that affect the most recent qualitative tools

Topological Foundations of Cognitive Science

A collection of papers presented at the First International Summer Institute in Cognitive Science, University at Buffalo, July 1994, including the following papers: ** Topological Foundations of Cognitive Science, Barry Smith ** The Bounds of Axiomatisation, Graham White ** Rethinking Boundaries, Wojciech Zelaniec ** Sheaf Mereology and Space Cognition, Jean Petitot ** A Mereotopological Definition of 'Point', Carola Eschenbach ** Discreteness, Finiteness, and the Structure of Topological Spaces, Christopher Habel ** Mass Reference and the Geometry of Solids, Almerindo E. Ojeda ** Defining a 'Doughnut' Made Difficult, N .M. Gotts ** A Theory of Spatial Regions with Indeterminate Boundaries, A.G. Cohn and N.M. Gotts ** Mereotopological Construction of Time from Events, Fabio Pianesi and Achille C. Varzi ** Computational Mereology: A Study of Part-of Relations for Multi-media Indexing, Wlodek Zadrozny and Michelle Ki

Intelligent Data Storage and Retrieval for Design Optimisation – an Overview

This paper documents the findings of a literature review conducted by the Sir Lawrence Wackett Centre for Aerospace Design Technology at RMIT University. The review investigates aspects of a proposed system for intelligent design optimisation. Such a system would be capable of efficiently storing (and compressing if required) a range of types of design data into an intelligent database. This database would be accessed by the system during subsequent design processes, allowing for search of relevant design data for re-use in later designs, allowing it to become very efficient in reducing the time for later designs as the database grows in size. Extensive research has been performed, in both theoretical aspects of the project, and practical examples of current similar systems. This research covers the areas of database systems, database queries, representation and compression of design data, geometric representation and heuristic methods for design applications.

CLiFF Notes: Research In Natural Language Processing at the University of Pennsylvania

The Computational Linguistics Feedback Forum (CLIFF) is a group of students and faculty who gather once a week to discuss the members\u27 current research. As the word feedback suggests, the group\u27s purpose is the sharing of ideas. The group also promotes interdisciplinary contacts between researchers who share an interest in Cognitive Science. There is no single theme describing the research in Natural Language Processing at Penn. There is work done in CCG, Tree adjoining grammars, intonation, statistical methods, plan inference, instruction understanding, incremental interpretation, language acquisition, syntactic parsing, causal reasoning, free word order languages, ... and many other areas. With this in mind, rather than trying to summarize the varied work currently underway here at Penn, we suggest reading the following abstracts to see how the students and faculty themselves describe their work. Their abstracts illustrate the diversity of interests among the researchers, explain the areas of common interest, and describe some very interesting work in Cognitive Science. This report is a collection of abstracts from both faculty and graduate students in Computer Science, Psychology and Linguistics. We pride ourselves on the close working relations between these groups, as we believe that the communication among the different departments and the ongoing inter-departmental research not only improves the quality of our work, but makes much of that work possible

Legal knowledge engineering: Computing, logic and law

The general problem approached in this thesis is that of building computer based legal advisory programs (otherwise known as expert systems or Intelligent Knowledge Based Systems). Such computer systems should be able to provide an individual with advice about either the general legal area being investigated, or advice about how the individual should proceed in a given case. In part the thesis describes a program (the ELl program) which attempts to confront some of the problems inherent in the building of these systems. The ELl system is seen as an experimental program (currently handling welfare rights legislation) and development vehicle. It is not presented as a final commercially implementable program. We present a detailed criticism of the type of legal knowledge contained within the system. The second, though in part intertwined, major subject of the thesis describes the jurisprudential aspects of the attempt to model the law by logic, a conjunction which is seen to be at the heart of the computer/law problem. We suggest that the conjunction offers very little to those who are interested in the real application of the real law, and that this is most forcefully seen when a working computer system models that conjunction. Our conclusion is that neither logic nor rule-based methods are sufficient for handling legal knowledge. The novelty and import of this thesis is not simply that it presents a negative conclusion; rather that it offers a sound theoretical and pragmatic framework for understanding why these methods are insufficient - the limits to the field are, in fact, defined