2 Search Results for "Polishko, Anton"

Document
DOI: 10.4230/DagMan.11.1.19
Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352)

Authors: Christine Bauer, Li Chen, Nicola Ferro, Norbert Fuhr, Avishek Anand, Timo Breuer, Guglielmo Faggioli, Ophir Frieder, Hideo Joho, Jussi Karlgren, Johannes Kiesel, Bart P. Knijnenburg, Aldo Lipani, Lien Michiels, Andrea Papenmeier, Maria Soledad Pera, Mark Sanderson, Scott Sanner, Benno Stein, Johanne R. Trippas, Karin Verspoor, and Martijn C. Willemsen

Published in: Dagstuhl Manifestos, Volume 11, Issue 1 (2025)

Abstract
During the workshop, we deeply discussed what CONversational Information ACcess (CONIAC) is and its unique features, proposing a world model abstracting it, and defined the Conversational Agents Framework for Evaluation (CAFE) for the evaluation of CONIAC systems, consisting of six major components: 1) goals of the system’s stakeholders, 2) user tasks to be studied in the evaluation, 3) aspects of the users carrying out the tasks, 4) evaluation criteria to be considered, 5) evaluation methodology to be applied, and 6) measures for the quantitative criteria chosen.
Cite as

Christine Bauer, Li Chen, Nicola Ferro, Norbert Fuhr, Avishek Anand, Timo Breuer, Guglielmo Faggioli, Ophir Frieder, Hideo Joho, Jussi Karlgren, Johannes Kiesel, Bart P. Knijnenburg, Aldo Lipani, Lien Michiels, Andrea Papenmeier, Maria Soledad Pera, Mark Sanderson, Scott Sanner, Benno Stein, Johanne R. Trippas, Karin Verspoor, and Martijn C. Willemsen. Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352). In Dagstuhl Manifestos, Volume 11, Issue 1, pp. 19-67, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{bauer_et_al:DagMan.11.1.19,
  author =	{Bauer, Christine and Chen, Li and Ferro, Nicola and Fuhr, Norbert and Anand, Avishek and Breuer, Timo and Faggioli, Guglielmo and Frieder, Ophir and Joho, Hideo and Karlgren, Jussi and Kiesel, Johannes and Knijnenburg, Bart P. and Lipani, Aldo and Michiels, Lien and Papenmeier, Andrea and Pera, Maria Soledad and Sanderson, Mark and Sanner, Scott and Stein, Benno and Trippas, Johanne R. and Verspoor, Karin and Willemsen, Martijn C.},
  title =	{{Conversational Agents: A Framework for Evaluation (CAFE) (Dagstuhl Perspectives Workshop 24352)}},
  pages =	{19--67},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2025},
  volume =	{11},
  number =	{1},
  editor =	{Bauer, Christine and Chen, Li and Ferro, Nicola and Fuhr, Norbert and Anand, Avishek and Breuer, Timo and Faggioli, Guglielmo and Frieder, Ophir and Joho, Hideo and Karlgren, Jussi and Kiesel, Johannes and Knijnenburg, Bart P. and Lipani, Aldo and Michiels, Lien and Papenmeier, Andrea and Pera, Maria Soledad and Sanderson, Mark and Sanner, Scott and Stein, Benno and Trippas, Johanne R. and Verspoor, Karin and Willemsen, Martijn C.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagMan.11.1.19},
  URN =		{urn:nbn:de:0030-drops-252722},
  doi =		{10.4230/DagMan.11.1.19},
  annote =	{Keywords: Conversational Agents, Evaluation, Information Access}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.19
ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks

Authors: Anton Polishko, Md. Abid Hasan, Weihua Pan, Evelien M. Bunnik, Karine Le Roch, and Stefano Lonardi

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
We address the problem of comparing multiple genome-wide maps representing nucleosome positions or specific histone marks. These maps can originate from the comparative analysis of ChIP-Seq/MNase-Seq/FAIRE-Seq data for different cell types/tissues or multiple time points. The input to the problem is a set of maps, each of which is a list of genomics locations for nucleosomes or histone marks. The output is an alignment of nucleosomes/histone marks across time points (that we call trajectories), allowing small movements and gaps in some of the maps. We present a tool called ThIEF (TrackIng of Epigenetic Features) that can efficiently compute these trajectories. ThIEF comes into two "flavors": ThIEF:Iterative finds the trajectories progressively using bipartite matching, while ThIEF:LP solves a k-partite matching problem on a hyper graph using linear programming. ThIEF:LP is guaranteed to find the optimal solution, but it is slower than ThIEF:Iterative. We demonstrate the utility of ThIEF by providing an example of applications on the analysis of temporal nucleosome maps for the human malaria parasite. As a surprisingly remarkable result, we show that the output of ThIEF can be used to produce a supervised classifier that can accurately predict the position of stable nucleosomes (i.e., nucleosomes present in all time points) and unstable nucleosomes (i.e., present in at most half of the time points) from the primary DNA sequence. To the best of our knowledge, this is the first result on the prediction of the dynamics of nucleosomes solely based on their DNA binding preference. Software is available at https://github.com/ucrbioinfo/ThIEF.
Cite as

Anton Polishko, Md. Abid Hasan, Weihua Pan, Evelien M. Bunnik, Karine Le Roch, and Stefano Lonardi. ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 19:1-19:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{polishko_et_al:LIPIcs.WABI.2017.19,
  author =	{Polishko, Anton and Hasan, Md. Abid and Pan, Weihua and Bunnik, Evelien M. and Le Roch, Karine and Lonardi, Stefano},
  title =	{{ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{19:1--19:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.19},
  URN =		{urn:nbn:de:0030-drops-76375},
  doi =		{10.4230/LIPIcs.WABI.2017.19},
  annote =	{Keywords: Nucleosomes, Histone Marks, Histone Tail Modifications, Epigenetics, Genomics}
}
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