2 Search Results for "Fontana, Walter"

Document
DOI: 10.4230/LIPIcs.DNA.31.4
Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems

Authors: Inhoo Lee, Salvador Buse, and Erik Winfree

Published in: LIPIcs, Volume 347, 31st International Conference on DNA Computing and Molecular Programming (DNA 31) (2025)

Abstract
Many molecular systems are best understood in terms of prototypical species and reactions. The central dogma and related biochemistry are rife with examples: gene i is transcribed into RNA i, which is translated into protein i; kinase n phosphorylates substrate m; protein p dimerizes with protein q. Engineered nucleic acid systems also often have this form: oligonucleotide i hybridizes to complementary oligonucleotide j; signal strand n displaces the output of seesaw gate m; hairpin p triggers the opening of target q. When there are many variants of a small number of prototypes, it can be conceptually cleaner and computationally more efficient to represent the full system in terms of indexed species (e.g. for dimerization, M_p, D_pq) and indexed reactions (M_p + M_q → D_pq). Here, we formalize the Indexed Chemical Reaction Network (ICRN) model and describe a Python software package designed to simulate such systems in the well-mixed and reaction-diffusion settings, using a differentiable programming framework originally developed for large-scale neural network models, taking advantage of GPU acceleration when available. Notably, this framework makes it straightforward to train the models’ initial conditions and rate constants to optimize a target behavior, such as matching experimental data, performing a computation, or exhibiting spatial pattern formation. The natural map of indexed chemical reaction networks onto neural network formalisms provides a tangible yet general perspective for translating concepts and techniques from the theory and practice of neural computation into the design of biomolecular systems.
Cite as

Inhoo Lee, Salvador Buse, and Erik Winfree. Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems. In 31st International Conference on DNA Computing and Molecular Programming (DNA 31). Leibniz International Proceedings in Informatics (LIPIcs), Volume 347, pp. 4:1-4:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{lee_et_al:LIPIcs.DNA.31.4,
  author =	{Lee, Inhoo and Buse, Salvador and Winfree, Erik},
  title =	{{Differentiable Programming of Indexed Chemical Reaction Networks and Reaction-Diffusion Systems}},
  booktitle =	{31st International Conference on DNA Computing and Molecular Programming (DNA 31)},
  pages =	{4:1--4:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-399-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{347},
  editor =	{Schaeffer, Josie and Zhang, Fei},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.31.4},
  URN =		{urn:nbn:de:0030-drops-238534},
  doi =		{10.4230/LIPIcs.DNA.31.4},
  annote =	{Keywords: Differentiable Programming, Chemical Reaction Networks, Reaction-Diffusion Systems}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2012.276
Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models

Authors: Vincent Danos, Jerome Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh, and Glynn Winskel

Published in: LIPIcs, Volume 18, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012)

Abstract
In this paper, we introduce a novel way of constructing concise causal histories (pathways) to represent how specified structures are formed during simulation of systems represented by rule-based models. This is founded on a new, clean, graph-based semantics introduced in the first part of this paper for Kappa, a rule-based modelling language that has emerged as a natural description of protein-protein interactions in molecular biology [Bachman 2011]. The semantics is capable of capturing the whole of Kappa, including subtle side-effects on deletion of structure, and its structured presentation provides the basis for the translation of techniques to other models. In particular, we give a notion of trajectory compression, which restricts a trace culminating in the production of a given structure to the actions necessary for the structure to occur. This is central to the reconstruction of biochemical pathways due to the failure of traditional techniques to provide adequately concise causal histories, and we expect it to be applicable in a range of other modelling situations.
Cite as

Vincent Danos, Jerome Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh, and Glynn Winskel. Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models. In IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012). Leibniz International Proceedings in Informatics (LIPIcs), Volume 18, pp. 276-288, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

Copy BibTex To Clipboard

@InProceedings{danos_et_al:LIPIcs.FSTTCS.2012.276,
  author =	{Danos, Vincent and Feret, Jerome and Fontana, Walter and Harmer, Russell and Hayman, Jonathan and Krivine, Jean and Thompson-Walsh, Chris and Winskel, Glynn},
  title =	{{Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models}},
  booktitle =	{IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012)},
  pages =	{276--288},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-47-7},
  ISSN =	{1868-8969},
  year =	{2012},
  volume =	{18},
  editor =	{D'Souza, Deepak and Radhakrishnan, Jaikumar and Telikepalli, Kavitha},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2012.276},
  URN =		{urn:nbn:de:0030-drops-38669},
  doi =		{10.4230/LIPIcs.FSTTCS.2012.276},
  annote =	{Keywords: concurrency, rule-based models, graph rewriting, pathways, causality}
}
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