Computational Methods in Systems Biology: 21st International Conference, CMSB 2023, Luxembourg City, Luxembourg, September 13–15, 2023, Proceedings (Lecture Notes in Bioinformatics)

Preface
Organization
Abstracts of Invited Talks
Causal Dynamical Network Inference: From Theory to Applications in Biology
Optimizing NonRibosomal Peptide Synthesis by Biocomputing Approaches
Integrating Machine Learning and Mechanistic Modeling: Unlocking the Potential of Hybrid Approaches in the Life Sciences
Contents
A Formal Approach for Tuning Stochastic Oscillators
1 Introduction
1.1 Related Work
2 Background
2.1 HASL Model Checking
2.2 Approximate Bayesian Computation
3 ABC-HASL Method for Tuning Oscillators
3.1 Characterising of Noisy Periodicity
3.2 An Automaton for the Distance from a Target Period
3.3 HASL-ABC Method for Tuning Oscillators
4 Case Studies
5 Conclusion
References
Phenotype Control of Partially Specified Boolean Networks
1 Introduction
2 Theory
2.1 Boolean Networks
2.2 Partially Specified Boolean Networks
2.3 Phenotype Control of Partially Specified Boolean Networks
3 Methods
3.1 Symbolic Computation Model
3.2 Control Algorithm
4 Evaluation
4.1 Performance
4.2 MAPK Case Study
5 Conclusion
References
A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI
1 Background
2 Annotation-Based Compact Representation for Splines
3 User-Friendly Insertion of Splines into SBML Models
4 Parsing and Simulating Splines from an SBML Model
5 A Real-World Example
6 Discussion
References
Intuitive Modelling and Formal Analysis of Collective Behaviour in Foraging Ants
1 Introduction
2 Modelling
3 Analysis
4 Related Work
5 Conclusions
References
Cell-Level Pathway Scoring Comparison with a Biologically Constrained Variational Autoencoder
1 Introduction
2 Materials and Methods
2.1 Dataset
2.2 Sources of Biological Information
2.3 Model Design
2.4 Visualization and Comparison of the Signaling Activity
2.5 Code Availability
3 Results
3.1 Pathway Activity at Single-Cell Resolution Using KEGG as Prior Knowledge
3.2 Pathway Activity at Single-Cell Resolution Using Reactome as Prior Knowledge
3.3 Gene-Set Precision
3.4 Numerical Performance
4 Conclusions
References
On Estimating Derivatives of Input Signals in Biochemistry
1 Introduction
2 Preliminaries on CRNs
2.1 Reactions and Equations
2.2 CRN Computational Frameworks
3 Differentiation CRN
3.1 Biological Intuition Using a Membrane
3.2 Core Differentiation CRN
4 Mathematical Analysis of the Quality of the Estimation
5 Validation on Simple Examples
5.1 Verification of the Delay-Approximation
5.2 Approximation of the Derivative
5.3 Using Signal Derivatives for Online Computations
6 Biological Examples
6.1 BioModels Repository
6.2 Circadian Clock
6.3 Bistable Switch
7 Conclusion and Perspectives
References
Harissa: Stochastic Simulation and Inference of Gene Regulatory Networks Based on Transcriptional Bursting
1 Introduction
2 Theory
3 Usage
4 Conclusions
A Appendices
A.1 Reduced Model
A.2 Inference Algorithm
A.3 Repressilator Network
References
Approximate Constrained Lumping of Polynomial Differential Equations
1 Introduction
2 Preliminaries
3 Approximate Constrained Lumping
4 Computing Constrained Approximated Lumping
4.1 Lumping Algorithm
4.2 Heuristic Search of Lumping Tolerance
5 Evaluation
6 Conclusion
References
Core SBML and Its Formal Semantics
1 Introduction
2 Preliminaries
3 SBML
4 Core SBML
5 Compiler from a SBML Fragment to Core SBML
6 Compiler of Core SBML to BioCham
7 Conclusion
References
Average Sensitivity of Nested Canalizing Multivalued Functions
1 Introduction
2 Nested Canalizing Multivalued Functions
2.1 Definition
2.2 Example: Logical Modelling of the Phage Lambda
3 Weakly Nested Canalizing Multivalued Functions
3.1 Definition
3.2 Examples of WNC Non NC Functions
3.3 Back to the Phage Lambda Example
3.4 Properties of WNC Functions
4 Average Sensitivity
4.1 Boolean-Valued Boolean Functions
4.2 Multivalued Functions
5 Upper Bound on the Average Sensitivity of WNC Multivalued Functions
6 Concluding Remarks
References
Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks
1 Introduction
2 Preliminaries
2.1 Boolean Networks and Trap Spaces
2.2 The Marker Reprogramming Problem
2.3 The Synthesis Problem
2.4 Counter-Example-Guided Abstraction Refinement (CEGAR)
3 A CEGAR for Minimal Trap Spaces
3.1 Generalizing Counter-Examples for Refinement
3.2 Necessary Condition on Perturbations
3.3 Generalization to the Synthesis Problem
3.4 Complexity
4 Implementation and Performance Evaluation
4.1 Datasets
4.2 Protocol
4.3 Results
5 Discussion
References
SAF: SAT-Based Attractor Finder in Asynchronous Automata Networks
1 Introduction
2 Architecture and Implementation
3 Performance
4 Availability
5 Conclusion
A Input File and Web Interface of SAF
References
Condition for Periodic Attractor in 4-Dimensional Repressilators
1 Introduction
2 Discrete Modeling of Gene Regulatory Networks
3 4-Dimensional Repressilator
4 Condition for a Periodic Attractor
4.1 Feature Selection and Search of Candidate Condition Based on Decision Tree
4.2 Condition Simplification
4.3 Number of Oscillatory Dimensions in a Periodic Attractor
5 Conclusion
References
Attractor Identification in Asynchronous Boolean Dynamics with Network Reduction
1 Introduction
2 Background
2.1 Boolean Networks
2.2 Reduction
3 Method
3.1 Implementation
3.2 Results
4 Discussion
References
3D Hybrid Cellular Automata for Cardiac Electrophysiology: A Concept Study
1 Introduction
2 Methodology
2.1 Hybrid Cellular Automata (HCA) Concept
2.2 Global Transition Function
2.3 Neighborhood Stencil
2.4 Incoming Signals
2.5 Activation Constraints and State Mapping
2.6 Analysis and Benchmarks
3 Results
3.1 Basic Electrophysiology
3.2 Spiraling
3.3 APD Stability
4 Discussion
5 Conclusion
References
Fridge Compiler: Optimal Circuits from Molecular Inventories
1 Introduction
1.1 Relation to Previous Work
2 Preliminaries
2.1 Molecular Circuit Synthesis from an Inventory
2.2 Modelling Molecular Inventories
2.3 Desired Features of a (DSD) Fridge Compiler
2.4 A Naive Solution
3 The ``Fridge'' Compiler
3.1 General Overview
3.2 Inputs
3.3 Implementation
3.4 Flexibility of Architecture Choice
4 One-Shot Cyclic Circuit Synthesis
5 Case Studies and Empirical Evaluation
5.1 Case Study: Synthesizing All k-Bit Predicates
5.2 Case Study: Inventory for All 4-Bit Predicates
5.3 Case Study: Cyclic vs Acyclic
5.4 Runtime Performance
6 Conclusion
References
Joint Distribution of Protein Concentration and Cell Volume Coupled by Feedback in Dilution
1 Introduction
2 Model Formulation
2.1 Single Cell Model: A Bivariate Markov Process
2.2 Population Model: A Measure-Valued Markov Process
3 Chapman–Kolmogorov Equation
4 Population Balance Equation
5 Conclusions
References
Author Index