3 Search Results for "Cristescu, Ioana"

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.CONCUR.2020.7
How Reversibility Can Solve Traditional Questions: The Example of Hereditary History-Preserving Bisimulation

Authors: Clément Aubert and Ioana Cristescu

Published in: LIPIcs, Volume 171, 31st International Conference on Concurrency Theory (CONCUR 2020)

Abstract
Reversible computation opens up the possibility of overcoming some of the hardware’s current physical limitations. It also offers theoretical insights, as it enriches multiple paradigms and models of computation, and sometimes retrospectively enlightens them. Concurrent reversible computation, for instance, offered interesting extensions to the Calculus of Communicating Systems, but was still lacking a natural and pertinent bisimulation to study processes equivalences. Our paper formulates an equivalence exploiting the two aspects of reversibility: backward moves and memory mechanisms. This bisimulation captures classical equivalences relations for denotational models of concurrency (history- and hereditary history-preserving bisimulation, (H)HPB), that were up to now only partially characterized by process algebras. This result gives an insight on the expressiveness of reversibility, as both backward moves and a memory mechanism - providing "backward determinism" - are needed to capture HHPB.
Cite as

Clément Aubert and Ioana Cristescu. How Reversibility Can Solve Traditional Questions: The Example of Hereditary History-Preserving Bisimulation. In 31st International Conference on Concurrency Theory (CONCUR 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 171, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{aubert_et_al:LIPIcs.CONCUR.2020.7,
  author =	{Aubert, Cl\'{e}ment and Cristescu, Ioana},
  title =	{{How Reversibility Can Solve Traditional Questions: The Example of Hereditary History-Preserving Bisimulation}},
  booktitle =	{31st International Conference on Concurrency Theory (CONCUR 2020)},
  pages =	{7:1--7:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-160-3},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{171},
  editor =	{Konnov, Igor and Kov\'{a}cs, Laura},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2020.7},
  URN =		{urn:nbn:de:0030-drops-128196},
  doi =		{10.4230/LIPIcs.CONCUR.2020.7},
  annote =	{Keywords: Formal semantics, Process algebras and calculi, Distributed and reversible computation, Configuration structures, Reversible CCS, Bisimulation}
}
Document
DOI: 10.4230/LIPIcs.CALCO.2019.9
Causal Unfoldings

Authors: Marc de Visme and Glynn Winskel

Published in: LIPIcs, Volume 139, 8th Conference on Algebra and Coalgebra in Computer Science (CALCO 2019)

Abstract
In the simplest form of event structure, a prime event structure, an event is associated with a unique causal history, its prime cause. However, it is quite common for an event to have disjunctive causes in that it can be enabled by any one of multiple sets of causes. Sometimes the sets of causes may be mutually exclusive, inconsistent one with another, and sometimes not, in which case they coexist consistently and constitute parallel causes of the event. The established model of general event structures can model parallel causes. On occasion however such a model abstracts too far away from the precise causal histories of events to be directly useful. For example, sometimes one needs to associate probabilities with different, possibly coexisting, causal histories of a common event. Ideally, the causal histories of a general event structure would correspond to the configurations of its causal unfolding to a prime event structure; and the causal unfolding would arise as a right adjoint to the embedding of prime in general event structures. But there is no such adjunction. However, a slight extension of prime event structures remedies this defect and provides a causal unfolding as a universal construction. Prime event structures are extended with an equivalence relation in order to dissociate the two roles, that of an event and its enabling; in effect, prime causes are labelled by a disjunctive event, an equivalence class of its prime causes. With this enrichment a suitable causal unfolding appears as a pseudo right adjoint. The adjunction relies critically on the central and subtle notion of extremal causal realisation as an embodiment of causal history.
Cite as

Marc de Visme and Glynn Winskel. Causal Unfoldings. In 8th Conference on Algebra and Coalgebra in Computer Science (CALCO 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 139, pp. 9:1-9:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

Copy BibTex To Clipboard

@InProceedings{devisme_et_al:LIPIcs.CALCO.2019.9,
  author =	{de Visme, Marc and Winskel, Glynn},
  title =	{{Causal Unfoldings}},
  booktitle =	{8th Conference on Algebra and Coalgebra in Computer Science (CALCO 2019)},
  pages =	{9:1--9:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-120-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{139},
  editor =	{Roggenbach, Markus and Sokolova, Ana},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CALCO.2019.9},
  URN =		{urn:nbn:de:0030-drops-114376},
  doi =		{10.4230/LIPIcs.CALCO.2019.9},
  annote =	{Keywords: Event Structures, Parallel Causes, Causal Unfolding, Probability}
}
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