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Documents authored by Shavit, Nir


Document
High Throughput Connectomics (Dagstuhl Seminar 18481)

Authors: Moritz Helmstaedter, Jeff Lichtman, and Nir Shavit

Published in: Dagstuhl Reports, Volume 8, Issue 11 (2019)


Abstract
The structure of the nervous system is extraordinarily complicated because individual neurons are interconnected to hundreds or even thousands of other cells in networks that can extend over large volumes. Mapping such networks at the level of synaptic connections, a field called connectomics, began in the 1970s and has recently garnered general interest thanks to technical and computational advances that offer the possibility of mapping mammalian brains. However, modern connectomics produces `big data' that must be analyzed at unprecedented rates, and will require, as with genomics at the time, breakthrough algorithmic and computational solutions. This workshop will bring together key researchers in the field, and experts from related fields, in order to understand the problems at hand and provide new approaches towards the design of high throughput systems for mapping the micro-connectivity of the brain.

Cite as

Moritz Helmstaedter, Jeff Lichtman, and Nir Shavit. High Throughput Connectomics (Dagstuhl Seminar 18481). In Dagstuhl Reports, Volume 8, Issue 11, pp. 112-138, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2019)


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@Article{helmstaedter_et_al:DagRep.8.11.112,
  author =	{Helmstaedter, Moritz and Lichtman, Jeff and Shavit, Nir},
  title =	{{High Throughput Connectomics (Dagstuhl Seminar 18481)}},
  pages =	{112--138},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2019},
  volume =	{8},
  number =	{11},
  editor =	{Helmstaedter, Moritz and Lichtman, Jeff and Shavit, Nir},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.8.11.112},
  URN =		{urn:nbn:de:0030-drops-103588},
  doi =		{10.4230/DagRep.8.11.112},
  annote =	{Keywords: Big Data, Connectomics, Distributed Computing, Machine Learning, Parallel Computing}
}
Document
Keynote Abstract
High Throughput Connectomics (Keynote Abstract)

Authors: Nir Shavit

Published in: LIPIcs, Volume 70, 20th International Conference on Principles of Distributed Systems (OPODIS 2016)


Abstract
Connectomics is an emerging field of neurobiology that uses cutting edge machine learning and image processing to extract brain connectivity graphs from electron microscopy images. It has long been assumed that the processing of connectomics data will require mass storage and farms of CPUs and GPUs and will take months if not years. This talk will discuss the feasibility of designing a high-throughput connectomics-on-demand system that runs on a multicore machine with less than 100 cores and extracts connectomes at the terabyte per hour pace of modern electron microscopes. Building this system required solving algorithmic and performance engineering issues related to scaling machine learning on multicore architectures, and may have important lessons for other problem spaces in the natural sciences, where until now large distributed server or GPU farms seemed to be the only way to go.

Cite as

Nir Shavit. High Throughput Connectomics (Keynote Abstract). In 20th International Conference on Principles of Distributed Systems (OPODIS 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 70, p. 1:1, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2017)


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@InProceedings{shavit:LIPIcs.OPODIS.2016.1,
  author =	{Shavit, Nir},
  title =	{{High Throughput Connectomics}},
  booktitle =	{20th International Conference on Principles of Distributed Systems (OPODIS 2016)},
  pages =	{1:1--1:1},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-031-6},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{70},
  editor =	{Fatourou, Panagiota and Jim\'{e}nez, Ernesto and Pedone, Fernando},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2016.1},
  URN =		{urn:nbn:de:0030-drops-70705},
  doi =		{10.4230/LIPIcs.OPODIS.2016.1},
  annote =	{Keywords: Machine learning, multicore architectures}
}
Document
08241 Abstracts Collection – Transactional Memory : From Implementation to Application

Authors: Christof Fetzer, Tim Harris, Maurice Herlihy, and Nir Shavit

Published in: Dagstuhl Seminar Proceedings, Volume 8241, Transactional Memory : From Implementation to Application (2008)


Abstract
From 08.06. to 13.06.2008, the Dagstuhl Seminar 08241 ``Transactional Memory: From Implementation to Application'' was held in Schloss Dagstuhl – Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.

Cite as

Christof Fetzer, Tim Harris, Maurice Herlihy, and Nir Shavit. 08241 Abstracts Collection – Transactional Memory : From Implementation to Application. In Transactional Memory : From Implementation to Application. Dagstuhl Seminar Proceedings, Volume 8241, pp. 1-13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2008)


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@InProceedings{fetzer_et_al:DagSemProc.08241.1,
  author =	{Fetzer, Christof and Harris, Tim and Herlihy, Maurice and Shavit, Nir},
  title =	{{08241 Abstracts Collection – Transactional Memory : From Implementation to Application}},
  booktitle =	{Transactional Memory : From Implementation to Application},
  pages =	{1--13},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8241},
  editor =	{Christof Fetzer and Tim Harris and Maurice Herlihy and Nir Shavit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08241.1},
  URN =		{urn:nbn:de:0030-drops-17757},
  doi =		{10.4230/DagSemProc.08241.1},
  annote =	{Keywords: Multiprocessors, Multi-core machines, Concurrent Programming, Parallel Programming, Synchronization, Transactional Memory}
}
Document
08241 Summary – Transactional Memory : From Implementation to Application

Authors: Christof Fetzer, Tim Harris, Maurice Herlihy, and Nir Shavit

Published in: Dagstuhl Seminar Proceedings, Volume 8241, Transactional Memory : From Implementation to Application (2008)


Abstract
A goal of current multiprocessor software design is to introduce parallelism into software applications by allowing operations that do not conflict in accessing memory to proceed concurrently. The key tool in designing concurrent data structures has been the use of locks. Unfortunately, course grained locking is easy to program with, but provides very poor performance because of limited parallelism. Fine-grained lock-based concurrent data structures perform exceptionally well, but designing them has long been recognized as a difficult task better left to experts. If concurrent programming is to become ubiquitous, researchers agree that one must develop alternative approaches that simplify code design and verification.

Cite as

Christof Fetzer, Tim Harris, Maurice Herlihy, and Nir Shavit. 08241 Summary – Transactional Memory : From Implementation to Application. In Transactional Memory : From Implementation to Application. Dagstuhl Seminar Proceedings, Volume 8241, pp. 1-3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2008)


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@InProceedings{fetzer_et_al:DagSemProc.08241.2,
  author =	{Fetzer, Christof and Harris, Tim and Herlihy, Maurice and Shavit, Nir},
  title =	{{08241 Summary – Transactional Memory : From Implementation to Application}},
  booktitle =	{Transactional Memory : From Implementation to Application},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8241},
  editor =	{Christof Fetzer and Tim Harris and Maurice Herlihy and Nir Shavit},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08241.2},
  URN =		{urn:nbn:de:0030-drops-17741},
  doi =		{10.4230/DagSemProc.08241.2},
  annote =	{Keywords: Multiprocessors, Multi-core machines, Concurrent Programming, Parallel Programming, Synchronization, Transactional Memory}
}
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