3 Search Results for "Irving, Samuel"

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/OASIcs.PARMA-DITAM.2021.2
BifurKTM: Approximately Consistent Distributed Transactional Memory for GPUs

Authors: Samuel Irving, Lu Peng, Costas Busch, and Jih-Kwon Peir

Published in: OASIcs, Volume 88, 12th Workshop on Parallel Programming and Run-Time Management Techniques for Many-core Architectures and 10th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2021)

Abstract
We present BifurKTM, the first read-optimized Distributed Transactional Memory system for GPU clusters. The BifurKTM design includes: GPU KoSTM, a new software transactional memory conflict detection scheme that exploits relaxed consistency to increase throughput; and KoDTM, a Distributed Transactional Memory model that combines the Data- and Control- flow models to greatly reduce communication overheads. Despite the allure of huge speedups, GPUs are limited in use due to their programmability and extreme sensitivity to workload characteristics. These become daunting concerns when considering a distributed GPU cluster, wherein a programmer must design algorithms to hide communication latency by exploiting data regularity, high compute intensity, etc. The BifurKTM design allows GPU programmers to exploit a new workload characteristic: the percentage of the workload that is Read-Only (e.g. reads but does not modify shared memory), even when this percentage is not known in advance. Programmers designate transactions that are suitable for Approximate Consistency, in which transactions "appear" to execute at the most convenient time for preventing conflicts. By leveraging Approximate Consistency for Read-Only transactions, the BifurKTM runtime system offers improved performance, application flexibility, and programmability without introducing any errors into shared memory. Our experiments show that Approximate Consistency can improve BkTM performance by up to 34x in applications with moderate network communication utilization and a read-intensive workload. Using Approximate Consistency, BkTM can reduce GPU-to-GPU network communication by 99%, reduce the number of aborts by up to 100%, and achieve an average speedup of 18x over a similarly sized CPU cluster while requiring minimal effort from the programmer.
Cite as

Samuel Irving, Lu Peng, Costas Busch, and Jih-Kwon Peir. BifurKTM: Approximately Consistent Distributed Transactional Memory for GPUs. In 12th Workshop on Parallel Programming and Run-Time Management Techniques for Many-core Architectures and 10th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2021). Open Access Series in Informatics (OASIcs), Volume 88, pp. 2:1-2:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{irving_et_al:OASIcs.PARMA-DITAM.2021.2,
  author =	{Irving, Samuel and Peng, Lu and Busch, Costas and Peir, Jih-Kwon},
  title =	{{BifurKTM: Approximately Consistent Distributed Transactional Memory for GPUs}},
  booktitle =	{12th Workshop on Parallel Programming and Run-Time Management Techniques for Many-core Architectures and 10th Workshop on Design Tools and Architectures for Multicore Embedded Computing Platforms (PARMA-DITAM 2021)},
  pages =	{2:1--2:15},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-181-8},
  ISSN =	{2190-6807},
  year =	{2021},
  volume =	{88},
  editor =	{Bispo, Jo\~{a}o and Cherubin, Stefano and Flich, Jos\'{e}},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.PARMA-DITAM.2021.2},
  URN =		{urn:nbn:de:0030-drops-136386},
  doi =		{10.4230/OASIcs.PARMA-DITAM.2021.2},
  annote =	{Keywords: GPU, Distributed Transactional Memory, Approximate Consistency}
}
Document
DOI: 10.4230/LITES-v003-i001-a005
A Survey on Static Cache Analysis for Real-Time Systems

Authors: Mingsong Lv, Nan Guan, Jan Reineke, Reinhard Wilhelm, and Wang Yi

Published in: LITES, Volume 3, Issue 1 (2016). Leibniz Transactions on Embedded Systems, Volume 3, Issue 1

Abstract
Real-time systems are reactive computer systems that must produce their reaction to a stimulus within given time bounds. A vital verification requirement is to estimate the Worst-Case Execution Time (WCET) of programs. These estimates are then used to predict the timing behavior of the overall system. The execution time of a program heavily depends on the underlying hardware, among which cache has the biggest influence. Analyzing cache behavior is very challenging due to the versatile cache features and complex execution environment. This article provides a survey on static cache analysis for real-time systems. We first present the challenges and static analysis techniques for independent programs with respect to different cache features. Then, the discussion is extended to cache analysis in complex execution environment, followed by a survey of existing tools based on static techniques for cache analysis. An outlook for future research is provided at last.
Cite as

Mingsong Lv, Nan Guan, Jan Reineke, Reinhard Wilhelm, and Wang Yi. A Survey on Static Cache Analysis for Real-Time Systems. In LITES, Volume 3, Issue 1 (2016). Leibniz Transactions on Embedded Systems, Volume 3, Issue 1, pp. 05:1-05:48, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@Article{lv_et_al:LITES-v003-i001-a005,
  author =	{Lv, Mingsong and Guan, Nan and Reineke, Jan and Wilhelm, Reinhard and Yi, Wang},
  title =	{{A Survey on Static Cache Analysis for Real-Time Systems}},
  journal =	{Leibniz Transactions on Embedded Systems},
  pages =	{05:1--05:48},
  ISSN =	{2199-2002},
  year =	{2016},
  volume =	{3},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LITES-v003-i001-a005},
  URN =		{urn:nbn:de:0030-drops-192603},
  doi =		{10.4230/LITES-v003-i001-a005},
  annote =	{Keywords: Hard real-time, Cache analysis, Worst-case execution time}
}
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