Theoretical Computer Science

Research Output 1993 2019

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2019

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk

Jansen, I. E., Savage, J. E., Watanabe, K., Bryois, J., Williams, D. M., Steinberg, S., Sealock, J., Karlsson, I. K., Hägg, S., Athanasiu, L., Voyle, N., Proitsi, P., Witoelar, A., Stringer, S., Aarsland, D., Almdahl, I. S., Andersen, F., Bergh, S., Bettella, F., Bjornsson, S. & 33 othersBrækhus, A., Bråthen, G., de Leeuw, C., Desikan, R. S., Djurovic, S., Dumitrescu, L., Fladby, T., Hohman, T. J., Jonsson, P. V., Kiddle, S. J., Rongve, A., Saltvedt, I., Sando, S. B., Selbæk, G., Shoai, M., Skene, N. G., Snaedal, J., Stordal, E., Ulstein, I. D., Wang, Y., White, L. R., Hardy, J., Hjerling-Leffler, J., Sullivan, P. F., van der Flier, W. M., Dobson, R., Davis, L. K., Stefansson, H., Stefansson, K., Pedersen, N. L., Ripke, S., Andreassen, O. A. & Posthuma, D., Mar 2019, In : Nature Genetics. 51, 3, p. 404-413 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Meta-Analysis
Alzheimer Disease
Genome
Proxy
Genes

L.E.J. Brouwer, fifty years later

van Dalen, D., Jongbloed, G., Klop, J. W. & van Mill, J., 11 Jan 2019, (Accepted/In press) In : Indagationes Mathematicae. p. 1-16 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Projections for infinitary rewriting (extended version)

Lombardi, C., Ríos, A. & de Vrijer, R., 16 Aug 2019, In : Theoretical Computer Science. 781, p. 92-110 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Rewriting
Projection
Term Rewriting
Term
Contraction

Reliable Restricted Process Theory

Ghassemi, F. & Fokkink, W., 14 Feb 2019, In : Fundamenta Informaticae. 165, 1, p. 1-41 41 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Communication
Network protocols
Network Protocols
Axiomatization
Multi-hop

Scalable Fine-Grained Proofs for Formula Processing

Barbosa, H., Blanchette, J. C., Fleury, M. & Fontaine, P., 4 Jan 2019, In : Journal of Automated Reasoning. p. 1-26 26 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Surface mount technology
Data structures
Processing

Syllogistic logic with Most

Endrullis, J. & Moss, L. S., 1 Jun 2019, In : Mathematical Structures in Computer Science. 29, 6, p. 763-782 20 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Computability and decidability
Polynomials
Logic
Soundness
Decidability
2018

A Formal Proof of the Expressiveness of Deep Learning

Bentkamp, A., Blanchette, J. C. & Klakow, D., 22 Sep 2018, (Accepted/In press) In : Journal of Automated Reasoning. p. 1-22 22 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Image recognition
Bioinformatics
Computer science
Tensors
Polynomials

A Verified SAT Solver Framework with Learn, Forget, Restart, and Incrementality

Blanchette, J. C., Fleury, M., Lammich, P. & Weidenbach, C., 12 Mar 2018, In : Journal of Automated Reasoning. 2018, p. 1-33 33 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Functional programming
Computer programming languages
Data structures
Concretes
Experiments

Braids via term rewriting

Endrullis, J. & Klop, J. W., 6 Dec 2018, In : Theoretical Computer Science. p. 1-36 36 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Term Rewriting
Braid
Notation
Diamonds
Diagram

Coinductive foundations of infinitary rewriting and infinitary equational logic

Endrullis, J., Hansen, H. H., Hendriks, D., Polonsky, A. & Silva, A., 10 Jan 2018, In : Logical Methods in Computer Science. 14, 1, p. 1-44 44 p., 3.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Infinitary Logic
Equational Logic
Rewriting
Term Rewriting
Equational Theory

Degrees of Infinite Words, Polynomials and Atoms

Endrullis, J., Karhumäki, J., Klop, J. W. & Saarela, A., Aug 2018, In : International Journal of Foundations of Computer Science. 29, 5, p. 825-843 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Transducers
Polynomials
Atoms
Turing machines
Equivalence classes

Introduction to the STAF 2015 special section

Blanchette, J., Bordeleau, F., Pierantonio, A., Kosmatov, N., Taentzer, G. & Wimmer, M., 7 Jul 2018, (Accepted/In press) In : Software and Systems Modeling. p. 1-3 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Motif-Aware PRALINE: Improving the alignment of motif regions: Improving the alignment of motif regions

Dijkstra, M., Bawono, P., Abeln, S., Feenstra, K. A., Fokkink, W. & Heringa, J., 1 Nov 2018, In : PLoS Computational Biology. 14, 11, p. 1-19 19 p., e1006547.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Sequence Alignment
sequence alignment
Alignment
Multiple Sequence Alignment
Benchmarking

SOS-based modal decomposition on nondeterministic probabilistic processes

Castiglioni, V., Gebler, D. & Tini, S., 25 Jun 2018, In : Logical Methods in Computer Science. 14, 2, p. 1-51 51 p., 18.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Decomposition
Decompose
Structural Operational Semantics
Nondeterminism
Congruence

SOS specifications for uniformly continuous operators

Gebler, D. & Tini, S., Mar 2018, In : Journal of Computer and System Sciences. 92, March, p. 113-151 39 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Uniformly continuous
Semantics
Specification
Specifications
Operator

The characteristics of molten globule states and folding pathways strongly depend on the sequence of a protein

Dijkstra, M. J. J., Fokkink, W. J., Heringa, J., van Dijk, E. & Abeln, S., 17 Nov 2018, In : Molecular Physics. 116, 21-22, p. 3173-3180 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
globules
folding
Molten materials
Hot Temperature
proteins
2017

Clocked lambda calculus

Endrullis, J., Hendriks, D., Klop, J. W. & Polonsky, A., 1 Jun 2017, In : Mathematical Structures in Computer Science (MSCS). 27, 5, p. 782-806 25 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Lambda Calculus
Term
Normal Form
Fixed point
Unary

Divide and congruence II: From decomposition of modal formulas to preservation of delay and weak bisimilarity

Fokkink, W. & van Glabbeek, R., 1 Dec 2017, In : Information and Computation. 257, p. 79-113 35 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Preservation
Congruence
Divides
Decomposition Method
Decomposition

Language and Proofs for Higher-Order SMT (Work in Progress)

Barbosa, H., Blanchette, J. C., Cruanes, S., El Ouraoui, D. & Fontaine, P., 2017, In : Electronic Proceedings in Theoretical Computer Science. 262, p. 15-22

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Maximally permissive controlled system synthesis for non-determinism and modal logic

van Hulst, A. C., Reniers, M. A. & Fokkink, W. J., 1 Mar 2017, In : Discrete Event Dynamic Systems. 27, 1, p. 109-142 34 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Nondeterminism
Modal Logic
Synthesis
Supervisory Control
Requirements

Model-based design of supervisory controllers for baggage handling systems

Swartjes, L., van Beek, D. A., Fokkink, W. J. & van Eekelen, J. A. W. M., 1 Nov 2017, In : Simulation Modelling Practice and Theory. 78, p. 28-50 23 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Baggage handling
Model-based Design
Controller
Controllers
Formal Model

Multi-valued simulation and abstraction using lattice operations

Vijzelaar, S. & Fokkink, W. J., 1 Jan 2017, In : ACM Transactions on Embedded Computing Systems. 16, 2, 42.

Research output: Contribution to JournalArticleAcademicpeer-review

Projections for Infinitary Rewriting

Lombardi, C., Ríos, A. & de Vrijer, R., 11 Jun 2017, In : Electronic Notes in Theoretical Computer Science. 332, p. 131-148 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Rewriting
Projection
Computer science
Term Rewriting
Term

Soundness and Completeness Proofs by Coinductive Methods

Blanchette, J. C., Popescu, A. & Traytel, D., Jan 2017, In : Journal of Automated Reasoning. 58, 1, p. 149-179

Research output: Contribution to JournalArticleAcademicpeer-review

2016

Combining User Reputation and Provenance Analysis for Trust Assessment

Ceolin, D., Groth, P. T., Maccatrozzo, V., Fokkink, W. J., van Hage, W. R. & Nottamkandath, A., 2016, In : ACM Journal of Data and Information Quality. 7, 1-2, p. 1-28 28 p., 6.

Research output: Contribution to JournalArticleAcademicpeer-review

Pipelines
Museums
Acoustic waves
Stereotypes
Trustworthiness

Formal specification and verification of TCP extended with the Window Scale Option

Lockefeer, L., Williams, D. M. & Fokkink, W., 1 Mar 2016, In : Science of Computer Programming. 118, p. 3-23 21 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Specifications
Data transfer
Formal specification
Formal verification

Majority digraphs

Lai, T., Endrullis, J. & Moss, L. S., 2016, In : Proceedings of the American Mathematical Society. 144, 9, p. 3701-3715 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Digraph
If and only if
Propositional Logic
Reversal
Assertion

Model checking mobile ad hoc networks

Ghassemi, F. & Fokkink, W., 1 Dec 2016, In : Formal Methods in System Design. 49, 3, p. 159-189 31 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Model checking
Mobile ad hoc networks
Mobile Ad Hoc Networks
Model Checking
Multi-hop

Non-Termination of cycle rewriting by finite automata

Endrullis, J., 10 Sep 2016, In : Electronic Proceedings in Theoretical Computer Science. 225, p. 3-4 2 p.

Research output: Contribution to JournalArticleAcademicpeer-review

2015

Executable Behaviour and the pi-Calculus

Luttik, B. & Yang, F., 2015, In : Electronic Proceedings in Theoretical Computer Science. 189, p. 37-52

Research output: Contribution to JournalArticleAcademicpeer-review

Turing machines
Semantics
Specifications

Infinitary Term Rewriting for Weakly Orthogonal Systems: Properties and Counterexamples

Endrullis, J., Grabmayer, C. A., Hendriks, R. D. A. & van Oostrom, V., 2015, In : Logical Methods in Computer Science.

Research output: Contribution to JournalArticleAcademicpeer-review

Term Rewriting
Rewriting
Normal Form
Counterexample
Trivial

Maximal synthesis for Hennessy-Milner logic

van Hulst, A., Reniers, M. A. & Fokkink, W. J., 2015, In : ACM Transactions on Embedded Computing Systems. 14, 1, p. 1-21

Research output: Contribution to JournalArticleAcademicpeer-review

Discrete event simulation
Computational complexity
Controllers

On the axiomatizability of impossible futures

Chen, T., Fokkink, W. J. & van Glabbeek, R. J., 2015, In : Logical Methods in Computer Science. 11, 3

Research output: Contribution to JournalArticleAcademicpeer-review

Axiomatization
Semantics
Concretes
Acoustic waves
Preorder

SOS rule formats for convex and abstract probabilistic bisimulations

D'Argenio, P. R., Lee, M. D. & Gebler, D., 2015, In : Electronic Proceedings in Theoretical Computer Science. 190, p. 31-45

Research output: Contribution to JournalArticleAcademicpeer-review

Semantics
Specifications
2014

Analyzing user demographics and user behavior for trust assessment

Ceolin, D., Groth, P. T., Nottamkandath, A., Fokkink, W. J. & van Hage, W. R., 2014, In : Lecture Notes in Computer Science. 8816, p. 219-241

Research output: Contribution to JournalArticleAcademicpeer-review

User Behavior
Merging
Provenance
Acoustic waves
Chemical analysis

Automated evaluation of crowdsourced annotations in the cultural heritage domain

Nottamkandath, A., Oosterman, J., Ceolin, D. & Fokkink, W. J., 2014, In : CEUR Workshop Proceedings. 1259, p. 25-36

Research output: Contribution to JournalArticleAcademicpeer-review

Bridging gaps between subjective logic and semantic Web

Ceolin, D., Nottamkandath, A. & Fokkink, W. J., 2014, In : Lecture Notes in Computer Science. 8816, 8816, p. 242-264

Research output: Contribution to JournalArticleAcademicpeer-review

CIF 3: Model-based engineering of supervisory controllers

van Beek, D. A., Fokkink, W. J., Hendriks, D., Hofkamp, A., Markovski, J., van de Mortel-Fronczak, J. M. & Reniers, M. A., 2014, In : Lecture Notes in Computer Science. 8413, 8413, p. 575-580

Research output: Contribution to JournalArticleAcademicpeer-review

Efficient semi-automated assessment of annotations trustworthiness

Ceolin, D., Nottamkandath, A. & Fokkink, W. J., 2014, In : Journal of Trust Management. 1, 1, 31 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Formal specification and verification of TCP extended with the window scale option

Lockefeer, L., Williams, D. M. & Fokkink, W. J., 2014, In : Lecture Notes in Computer Science. 8718, p. 63-77

Research output: Contribution to JournalArticleAcademicpeer-review

Liveness Analysis for Parameterised Boolean Equation Systems

Keiren, J. J. A., Wesselink, J. W. & Willemse, T. A. C., 2014, In : Lecture Notes in Computer Science. 8837, p. 219-234

Research output: Contribution to JournalArticleAcademicpeer-review

Flow graphs
Liveness
Flow Graphs
Static analysis
Explosions

On the Complexity of Stream Equality

Endrullis, J., Hendriks, R. D. A., Bakhshi, R. R. & Rosu, G., 2014, (Accepted/In press) In : Journal of Functional Programming.

Research output: Contribution to JournalArticleAcademicpeer-review

Semantics

Towards the definition of an ontology for trust in (Web) data

Ceolin, D., Nottamkandath, A., Fokkink, W. J. & Maccatrozzo, V., 2014, In : CEUR Workshop Proceedings. 1259, p. 73-78

Research output: Contribution to JournalArticleAcademicpeer-review

Two procedures for analyzing the reliability of open government data

Ceolin, D., Moreau, L., O'Hara, K., Fokkink, W. J., van Hage, W. R., Maccatrozzo, V., Sackley, A., Schreiber, A. T. & Shadbolt, N., 2014, In : Communications in Computer and Information Science. 442, p. 15-24

Research output: Contribution to JournalArticleAcademicpeer-review

Uncertainty estimation and analysis of categorical Web data

Ceolin, D., van Hage, W. R., Fokkink, W. J. & Schreiber, A. T., 2014, In : Lecture Notes in Computer Science. 8816, p. 265-288

Research output: Contribution to JournalArticleAcademicpeer-review

2013

Gratis kennis voor de wereld: Wetenschappelijke uitgeverijen onder druk

Apt, K. & Fokkink, W. J., 20 Nov 2013, In : De Groene Amsterdammer.

Research output: Contribution to JournalArticlePopular

Model checking MANETs with arbitrary mobility

Fokkink, W. J., Ghassemi, F., Ahmadi, S. & Movaghar, A., 2013, In : Lecture Notes in Computer Science. 8161, p. 217-232

Research output: Contribution to JournalArticleAcademicpeer-review

Reliability analyses of open government data

Ceolin, D., Moreau, L., O'Hara, K., Schreiber, A. T., Sackley, A., Fokkink, W. J., van Hage, W. R. & Shadbolt, N., 2013, In : CEUR Workshop Proceedings. 1079, p. 34-39

Research output: Contribution to JournalArticleAcademicpeer-review

Turning GSOS into equations for linear time-branching time semantics

Gazda, M. & Fokkink, W. J., 2013, In : Computer Journal. 56, 1, p. 34-44

Research output: Contribution to JournalArticleAcademicpeer-review

Semantics
Algebra
2012

Analysis of DIRAC's behavior using model checking with process algebra

Remenska, D., Templon, J. A., Willemse, T. A. C., Bal, H. E., Verstoep, K., Fokkink, W. J., Charpentier, P., Graciana Diaz, R., Lanciotti, E., Roiser, S. & Ciba, K., 2012, In : Journal of Physics: Conference Series. 396, 5, 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

algebra
grids
space exploration
management systems
tracing