Computational Methods in Systems Biology
21st International Conference, CMSB 2023, Luxembourg City, Luxembourg, September 13–15, 2023, Proceedings
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Book and Conference Proceedings
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Chapter and Conference Paper
Core SBML and Its Formal Semantics
The systems biology markup language (SBML) permits to represent biological models mixing reaction networks, algebraic equations, differential equations, and events. Its main objective is to exchange biological...
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Chapter and Conference Paper
Earliest Query Answering for Deterministic Stepwise Hedge Automata
Earliest query answering (EQA) is the problem to enumerate certain query answers on streams at the earliest events. We consider \( EQA \) ...
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Chapter and Conference Paper
Subhedge Projection for Stepwise Hedge Automata
We show how to evaluate stepwise hedge automata (Shas) with subhedge projection. Since this requires passing finite state information top-down, we introduce the notion of downward stepwise hedge automata. We use ...
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Chapter and Conference Paper
Abstract Simulation of Reaction Networks via Boolean Networks
We propose to simulate chemical reaction networks with the deterministic semantics abstractly, without any precise knowledge on the initial concentrations. For this, the concentrations of species are abstracte...
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Chapter and Conference Paper
Nested Regular Expressions Can Be Compiled to Small Deterministic Nested Word Automata
We study the problem of whether regular expressions for nested words can be compiled to small deterministic nested word automata (NWAs). In theory, we obtain a positive answer for small deterministic regular expr...
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Chapter and Conference Paper
Regular Matching and Inclusion on Compressed Tree Patterns with Context Variables
We study the complexity of regular matching and inclusion for compressed tree patterns extended by context variables. The addition of context variables to tree patterns permits us to properly capture compresse...
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Chapter and Conference Paper
Computing Difference Abstractions of Metabolic Networks Under Kinetic Constraints
Algorithms based on abstract interpretation were proposed recently for predicting changes of reaction networks with partial kinetic information. Their prediction precision, however, depends heavily on which he...
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Chapter and Conference Paper
Certain Query Answering on Compressed String Patterns: From Streams to Hyperstreams
We study the problem of certain query answering (Cqa) on compressed string patterns. These are incomplete singleton context-free grammars, that can model systems of multiple streams with references to others, cal...
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Chapter and Conference Paper
Equivalence of Symbolic Tree Transducers
Symbolic tree transducers are programs that transform data trees with an infinite signature. In this paper, we show that the equivalence problem of deterministic symbolic top-down tree transducers (DTop) can be r...
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Chapter and Conference Paper
Normalizing Chemical Reaction Networks by Confluent Structural Simplification
Reaction networks can be simplified by eliminating linear intermediate species in partial steady states. In this paper, we study the question whether this rewrite procedure is confluent, so that for any given ...
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Chapter and Conference Paper
Projection for Nested Word Automata Speeds up XPath Evaluation on XML Streams
We present an evaluator for navigational XPath on Xml streams with projection. The idea is to project away those parts of an Xml stream that are irrelevant for evaluating a given XPath query. This task is relevan...
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Chapter and Conference Paper
A Uniform Programmning Language for Implementing XML Standards
We propose X-Fun, a core language for implementing various Xml standards in a uniform manner. X-Fun is a higher-order functional programming language for transforming data trees based on node selection queries. I...
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Chapter and Conference Paper
Structural Simplification of Chemical Reaction Networks Preserving Deterministic Semantics
We study the structural simplification of chemical reaction networks preserving the deterministic kinetics. We aim at finding simplification rules that can eliminate intermediate molecules while preserving the...
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Chapter and Conference Paper
Qualitative Reasoning for Reaction Networks with Partial Kinetic Information
We propose a formal modeling language for reaction networks with partial kinetic information. The language has a graphical syntax reminiscent to Petri nets. The kinetics of reactions need to be described only ...
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Chapter and Conference Paper
Logics for Unordered Trees with Data Constraints on Siblings
We study counting monadic second-order logics (CMso) for unordered data trees. Our objective is to enhance this logic with data constraints for comparing string data values attached to sibling edges of a data ...
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Chapter and Conference Paper
Sublinear DTD Validity
We present an efficient algorithm for testing approximate dtd validity modulo the strong tree edit distance. Our algorithm inspects xml documents in a probabilistic manner. It detects with high probability the no...
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Chapter and Conference Paper
Learning Sequential Tree-to-Word Transducers
We study the problem of learning sequential top-down tree-to-word transducers (stws). First, we present a Myhill-Nerode characterization of the corresponding class of sequential tree-to-word transformations ( ...
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Chapter and Conference Paper
Attractor Equivalence: An Observational Semantics for Reaction Networks
We study observational semantics for networks of chemical reactions as used in systems biology. Reaction networks without kinetic information, as we consider, can be identified with Petri nets. We present a ne...
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Chapter and Conference Paper
Early Nested Word Automata for XPath Query Answering on XML Streams
Algorithms for answering XPath queries on Xml streams have been studied intensively in the last decade. Nevertheless, there still exists no solution with high efficiency and large coverage. In this paper, we intr...
