14 Search Results for "R�mer, Kay"


Document
Visualization of Biological Data - From Analysis to Communication (Dagstuhl Seminar 21401)

Authors: Karsten Klein, Georgeta Elisabeta Marai, Kay Katja Nieselt, and Blaz Zupan

Published in: Dagstuhl Reports, Volume 11, Issue 9 (2022)


Abstract
Technological advancements in biology allow us to collect and generate a large quantity of data and pose a significant challenge to data interpretation and understanding. Addressing this challenge requires a blend of methodology from data visualization, bioinformatics, and biology. This methodology encompasses perception and design knowledge, algorithm design, techniques for analyzing and visualizing big data, statistical approaches, and specific domain knowledge for different application problems. In particular, it is essential to develop robust and integrative visualization methods combined with computational analytical techniques and approaches to communicate the outcomes visually. The purpose of Dagstuhl Seminar 21401, "Visualization of Biological Data - From Analysis to Communication," was to bring together researchers from various fields to discuss the state of the art, to debate means of advancing science in the field of visualization of biological data, and to foster the development of our international community.

Cite as

Karsten Klein, Georgeta Elisabeta Marai, Kay Katja Nieselt, and Blaz Zupan. Visualization of Biological Data - From Analysis to Communication (Dagstuhl Seminar 21401). In Dagstuhl Reports, Volume 11, Issue 9, pp. 1-27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)


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@Article{klein_et_al:DagRep.11.9.1,
  author =	{Klein, Karsten and Marai, Georgeta Elisabeta and Nieselt, Kay Katja and Zupan, Blaz},
  title =	{{Visualization of Biological Data - From Analysis to Communication (Dagstuhl Seminar 21401)}},
  pages =	{1--27},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2022},
  volume =	{11},
  number =	{9},
  editor =	{Klein, Karsten and Marai, Georgeta Elisabeta and Nieselt, Kay Katja and Zupan, Blaz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.11.9.1},
  URN =		{urn:nbn:de:0030-drops-159158},
  doi =		{10.4230/DagRep.11.9.1},
  annote =	{Keywords: Bioinformatics, biology, Imaging, interdisciplinarity, Omics, Visual analytics, visualization}
}
Document
Transparency by Design (Dagstuhl Seminar 21231)

Authors: Judy Kay, Tsvi Kuflik, and Michael Rovatsos

Published in: Dagstuhl Reports, Volume 11, Issue 5 (2021)


Abstract
This report documents the program and outcomes of Dagstuhl Seminar 21231 on "Transparency by Design" held in June 2021. Despite extensive ongoing discussions surrounding fairness, accountability, and transparency in the context of ethical issues around AI systems that are having an increasing impact on society, the notion of transparency - closely linked to explainability and interpretability - has largely eluded systematic treatment within computer science to date. The purpose of this Dagstuhl Seminar was to initiate a debate around theoretical foundations and practical methodologies around transparency in data-driven AI systems, with the overall aim of laying the foundations for a "transparency by design" framework – a framework for systems development methodology that integrates transparency in all stages of the software development process. Addressing this long-term challenge requires bringing together researchers from Artificial Intelligence, Human-Computer Interaction, and Software Engineering, as well as ethics specialists from the humanities and social sciences, which was a key objective for the four-day seminar conducted online.

Cite as

Judy Kay, Tsvi Kuflik, and Michael Rovatsos. Transparency by Design (Dagstuhl Seminar 21231). In Dagstuhl Reports, Volume 11, Issue 5, pp. 1-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


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@Article{kay_et_al:DagRep.11.5.1,
  author =	{Kay, Judy and Kuflik, Tsvi and Rovatsos, Michael},
  title =	{{Transparency by Design (Dagstuhl Seminar 21231)}},
  pages =	{1--22},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2021},
  volume =	{11},
  number =	{5},
  editor =	{Kay, Judy and Kuflik, Tsvi and Rovatsos, Michael},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.11.5.1},
  URN =		{urn:nbn:de:0030-drops-155685},
  doi =		{10.4230/DagRep.11.5.1},
  annote =	{Keywords: Artificial Intelligence, Dagstuhl Seminar, Ethics, Human-ComputerInteraction, Software Engineering, Transparency}
}
Document
StoqMA Meets Distribution Testing

Authors: Yupan Liu

Published in: LIPIcs, Volume 197, 16th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2021)


Abstract
StoqMA captures the computational hardness of approximating the ground energy of local Hamiltonians that do not suffer the so-called sign problem. We provide a novel connection between StoqMA and distribution testing via reversible circuits. First, we prove that easy-witness StoqMA (viz. eStoqMA, a sub-class of StoqMA) is contained in MA. Easy witness is a generalization of a subset state such that the associated set’s membership can be efficiently verifiable, and all non-zero coordinates are not necessarily uniform. This sub-class eStoqMA contains StoqMA with perfect completeness (StoqMA₁), which further signifies a simplified proof for StoqMA₁ ⊆ MA [Bravyi et al., 2006; Bravyi and Terhal, 2010]. Second, by showing distinguishing reversible circuits with ancillary random bits is StoqMA-complete (as a comparison, distinguishing quantum circuits is QMA-complete [Janzing et al., 2005]), we construct soundness error reduction of StoqMA. Additionally, we show that both variants of StoqMA that without any ancillary random bit and with perfect soundness are contained in NP. Our results make a step towards collapsing the hierarchy MA ⊆ StoqMA ⊆ SBP [Bravyi et al., 2006], in which all classes are contained in AM and collapse to NP under derandomization assumptions.

Cite as

Yupan Liu. StoqMA Meets Distribution Testing. In 16th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 197, pp. 4:1-4:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


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@InProceedings{liu:LIPIcs.TQC.2021.4,
  author =	{Liu, Yupan},
  title =	{{StoqMA Meets Distribution Testing}},
  booktitle =	{16th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2021)},
  pages =	{4:1--4:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-198-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{197},
  editor =	{Hsieh, Min-Hsiu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2021.4},
  URN =		{urn:nbn:de:0030-drops-139995},
  doi =		{10.4230/LIPIcs.TQC.2021.4},
  annote =	{Keywords: StoqMA, distribution testing, error reduction, reversible circuits}
}
Document
Bounds on the QAC^0 Complexity of Approximating Parity

Authors: Gregory Rosenthal

Published in: LIPIcs, Volume 185, 12th Innovations in Theoretical Computer Science Conference (ITCS 2021)


Abstract
QAC circuits are quantum circuits with one-qubit gates and Toffoli gates of arbitrary arity. QAC^0 circuits are QAC circuits of constant depth, and are quantum analogues of AC^0 circuits. We prove the following: - For all d ≥ 7 and ε > 0 there is a depth-d QAC circuit of size exp(poly(n^{1/d}) log(n/ε)) that approximates the n-qubit parity function to within error ε on worst-case quantum inputs. Previously it was unknown whether QAC circuits of sublogarithmic depth could approximate parity regardless of size. - We introduce a class of "mostly classical" QAC circuits, including a major component of our circuit from the above upper bound, and prove a tight lower bound on the size of low-depth, mostly classical QAC circuits that approximate this component. - Arbitrary depth-d QAC circuits require at least Ω(n/d) multi-qubit gates to achieve a 1/2 + exp(-o(n/d)) approximation of parity. When d = Θ(log n) this nearly matches an easy O(n) size upper bound for computing parity exactly. - QAC circuits with at most two layers of multi-qubit gates cannot achieve a 1/2 + exp(-o(n)) approximation of parity, even non-cleanly. Previously it was known only that such circuits could not cleanly compute parity exactly for sufficiently large n. The proofs use a new normal form for quantum circuits which may be of independent interest, and are based on reductions to the problem of constructing certain generalizations of the cat state which we name "nekomata" after an analogous cat yōkai.

Cite as

Gregory Rosenthal. Bounds on the QAC^0 Complexity of Approximating Parity. In 12th Innovations in Theoretical Computer Science Conference (ITCS 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 185, pp. 32:1-32:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


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@InProceedings{rosenthal:LIPIcs.ITCS.2021.32,
  author =	{Rosenthal, Gregory},
  title =	{{Bounds on the QAC^0 Complexity of Approximating Parity}},
  booktitle =	{12th Innovations in Theoretical Computer Science Conference (ITCS 2021)},
  pages =	{32:1--32:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-177-1},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{185},
  editor =	{Lee, James R.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2021.32},
  URN =		{urn:nbn:de:0030-drops-135713},
  doi =		{10.4230/LIPIcs.ITCS.2021.32},
  annote =	{Keywords: quantum circuit complexity, QAC^0, fanout, parity, nekomata}
}
Document
Exact Transcript Quantification Over Splice Graphs

Authors: Cong Ma, Hongyu Zheng, and Carl Kingsford

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)


Abstract
The probability of sequencing a set of RNA-seq reads can be directly modeled using the abundances of splice junctions in splice graphs instead of the abundances of a list of transcripts. We call this model graph quantification, which was first proposed by Bernard et al. (2014). The model can be viewed as a generalization of transcript expression quantification where every full path in the splice graph is a possible transcript. However, the previous graph quantification model assumes the length of single-end reads or paired-end fragments is fixed. We provide an improvement of this model to handle variable-length reads or fragments and incorporate bias correction. We prove that our model is equivalent to running a transcript quantifier with exactly the set of all compatible transcripts. The key to our method is constructing an extension of the splice graph based on Aho-Corasick automata. The proof of equivalence is based on a novel reparameterization of the read generation model of a state-of-art transcript quantification method. This new approach is useful for modeling scenarios where reference transcriptome is incomplete or not available and can be further used in transcriptome assembly or alternative splicing analysis.

Cite as

Cong Ma, Hongyu Zheng, and Carl Kingsford. Exact Transcript Quantification Over Splice Graphs. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 12:1-12:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)


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@InProceedings{ma_et_al:LIPIcs.WABI.2020.12,
  author =	{Ma, Cong and Zheng, Hongyu and Kingsford, Carl},
  title =	{{Exact Transcript Quantification Over Splice Graphs}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{12:1--12:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.12},
  URN =		{urn:nbn:de:0030-drops-128013},
  doi =		{10.4230/LIPIcs.WABI.2020.12},
  annote =	{Keywords: RNA-seq, alternative splicing, transcript quantification, splice graph, network flow}
}
Document
Control of Networked Cyber-Physical Systems (Dagstuhl Seminar 19222)

Authors: John S. Baras, Sandra Hirche, Kay Römer, and Klaus Wehrle

Published in: Dagstuhl Reports, Volume 9, Issue 5 (2019)


Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 19222 "Control of Networked Cyber-Physical Systems". Such systems typically operate under very tight timing constraints and at the same time witness an ever-increasing complexity in both size and the amount of information needed to main controllability. Yet, the development of control systems and of communication/computation infrastructures has traditionally been decoupled, so that valuable insights from the respective other domain could not be used towards the joint goal of keeping cyber-physical systems (CPS) controllable. In order to overcome this "black box" thinking, the seminar brought together researchers from the key communities involved in the development of CPS. In a series of impulse talks and plenary discussions, the seminar reviewed the current start-of-the-art in CPS research and identified promising research directions that may benefit from closer cooperation between the communication and control communities.

Cite as

John S. Baras, Sandra Hirche, Kay Römer, and Klaus Wehrle. Control of Networked Cyber-Physical Systems (Dagstuhl Seminar 19222). In Dagstuhl Reports, Volume 9, Issue 5, pp. 132-141, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@Article{baras_et_al:DagRep.9.5.132,
  author =	{Baras, John S. and Hirche, Sandra and R\"{o}mer, Kay and Wehrle, Klaus},
  title =	{{Control of Networked Cyber-Physical Systems (Dagstuhl Seminar 19222)}},
  pages =	{132--141},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2019},
  volume =	{9},
  number =	{5},
  editor =	{Baras, John S. and Hirche, Sandra and R\"{o}mer, Kay and Wehrle, Klaus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.9.5.132},
  URN =		{urn:nbn:de:0030-drops-113847},
  doi =		{10.4230/DagRep.9.5.132},
  annote =	{Keywords: Control Theory, Cyber-Physical Systems, Latency, Network Architecture}
}
Document
Context-Aware Seeds for Read Mapping

Authors: Hongyi Xin, Mingfu Shao, and Carl Kingsford

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Motivation: Most modern seed-and-extend NGS read mappers employ a seeding scheme that requires extracting t non-overlapping seeds in each read in order to find all valid mappings under an edit distance threshold of t. As t grows (such as in long reads with high error rate), this seeding scheme forces mappers to use more and shorter seeds, which increases the seed hits (seed frequencies) and therefore reduces the efficiency of mappers. Results: We propose a novel seeding framework, context-aware seeds (CAS). CAS guarantees finding all valid mapping but uses fewer (and longer) seeds, which reduces seed frequencies and increases efficiency of mappers. CAS achieves this improvement by attaching a confidence radius to each seed in the reference. We prove that all valid mappings can be found if the sum of confidence radii of seeds are greater than t. CAS generalizes the existing pigeonhole-principle-based seeding scheme in which this confidence radius is implicitly always 1. Moreover, we design an efficient algorithm that constructs the confidence radius database in linear time. We experiment CAS with E. coli genome and show that CAS reduces seed frequencies by up to 20.3% when compared with the state-of-the-art pigeonhole-principle-based seeding algorithm, the Optimal Seed Solver. Availability: https://github.com/Kingsford-Group/CAS_code

Cite as

Hongyi Xin, Mingfu Shao, and Carl Kingsford. Context-Aware Seeds for Read Mapping. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 15:1-15:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{xin_et_al:LIPIcs.WABI.2019.15,
  author =	{Xin, Hongyi and Shao, Mingfu and Kingsford, Carl},
  title =	{{Context-Aware Seeds for Read Mapping}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{15:1--15:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.15},
  URN =		{urn:nbn:de:0030-drops-110452},
  doi =		{10.4230/LIPIcs.WABI.2019.15},
  annote =	{Keywords: Read Mapping, Seed and Extend, Edit Distance, Suffix Trie}
}
Document
Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem

Authors: Yutong Qiu, Cong Ma, Han Xie, and Carl Kingsford

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Transcriptomic structural variants (TSVs) - large-scale transcriptome sequence change due to structural variation - are common, especially in cancer. Detecting TSVs is a challenging computational problem. Sample heterogeneity (including differences between alleles in diploid organisms) is a critical confounding factor when identifying TSVs. To improve TSV detection in heterogeneous RNA-seq samples, we introduce the Multiple Compatible Arrangement Problem (MCAP), which seeks k genome rearrangements to maximize the number of reads that are concordant with at least one rearrangement. This directly models the situation of a heterogeneous or diploid sample. We prove that MCAP is NP-hard and provide a 1/4-approximation algorithm for k=1 and a 3/4-approximation algorithm for the diploid case (k=2) assuming an oracle for k=1. Combining these, we obtain a 3/16-approximation algorithm for MCAP when k=2 (without an oracle). We also present an integer linear programming formulation for general k. We characterize the graph structures that require k>1 to satisfy all edges and show such structures are prevalent in cancer samples. We evaluate our algorithms on 381 TCGA samples and 2 cancer cell lines and show improved performance compared to the state-of-the-art TSV-calling tool, SQUID.

Cite as

Yutong Qiu, Cong Ma, Han Xie, and Carl Kingsford. Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 18:1-18:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{qiu_et_al:LIPIcs.WABI.2019.18,
  author =	{Qiu, Yutong and Ma, Cong and Xie, Han and Kingsford, Carl},
  title =	{{Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{18:1--18:5},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.18},
  URN =		{urn:nbn:de:0030-drops-110483},
  doi =		{10.4230/LIPIcs.WABI.2019.18},
  annote =	{Keywords: transcriptomic structural variation, integer linear programming, heterogeneity}
}
Document
Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation

Authors: Natalie Sauerwald, Yihang Shen, and Carl Kingsford

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Topological data analysis (TDA) is a mathematically well-founded set of methods to derive robust information about the structure and topology of data. It has been applied successfully in several biological contexts. Derived primarily from algebraic topology, TDA rigorously identifies persistent features in complex data, making it well-suited to better understand the key features of three-dimensional chromosome structure. Chromosome structure has a significant influence in many diverse genomic processes and has recently been shown to relate to cellular differentiation. While there exist many methods to study specific substructures of chromosomes, we are still missing a global view of all geometric features of chromosomes. By applying TDA to the study of chromosome structure through differentiation across three cell lines, we provide insight into principles of chromosome folding and looping. We identify persistent connected components and one-dimensional topological features of chromosomes and characterize them across cell types and stages of differentiation. Availability: Scripts to reproduce the results from this study can be found at https://github.com/Kingsford-Group/hictda

Cite as

Natalie Sauerwald, Yihang Shen, and Carl Kingsford. Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 23:1-23:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{sauerwald_et_al:LIPIcs.WABI.2019.23,
  author =	{Sauerwald, Natalie and Shen, Yihang and Kingsford, Carl},
  title =	{{Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{23:1--23:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.23},
  URN =		{urn:nbn:de:0030-drops-110537},
  doi =		{10.4230/LIPIcs.WABI.2019.23},
  annote =	{Keywords: topological data analysis, chromosome structure, Hi-C, topologically associating domains}
}
Document
Visualization of Biological Data - Crossroads (Dagstuhl Seminar 18161)

Authors: Jan Aerts, Nils Gehlenborg, Georgeta Elisabeta Marai, and Kay Katja Nieselt

Published in: Dagstuhl Reports, Volume 8, Issue 4 (2018)


Abstract
Our ability to generate and collect biological data has accelerated significantly in the past two decades. In response, many novel computational and statistical analysis techniques have been developed to process and integrate biological data sets. However, in addition to computational and statistical approaches, visualization techniques are needed to enable the interpretation of data as well as the communication of results. The design and implementation of such techniques lies at the intersection of the biology, bioinformatics, and data visualization fields. The purpose of Dagstuhl Seminar 18161 "Visualization of Biological Data - Crossroads" was to bring together researchers from all three fields, to identify opportunities and challenges, and to develop a path forward for biological data visualization research.

Cite as

Jan Aerts, Nils Gehlenborg, Georgeta Elisabeta Marai, and Kay Katja Nieselt. Visualization of Biological Data - Crossroads (Dagstuhl Seminar 18161). In Dagstuhl Reports, Volume 8, Issue 4, pp. 32-71, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


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@Article{aerts_et_al:DagRep.8.4.32,
  author =	{Aerts, Jan and Gehlenborg, Nils and Marai, Georgeta Elisabeta and Nieselt, Kay Katja},
  title =	{{Visualization of Biological Data - Crossroads (Dagstuhl Seminar 18161)}},
  pages =	{32--71},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2018},
  volume =	{8},
  number =	{4},
  editor =	{Aerts, Jan and Gehlenborg, Nils and Marai, Georgeta Elisabeta and Nieselt, Kay Katja},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.8.4.32},
  URN =		{urn:nbn:de:0030-drops-97600},
  doi =		{10.4230/DagRep.8.4.32},
  annote =	{Keywords: imaging, omics, sequence analysis, visual analytics, visualisation}
}
Document
Ambient Notification Environments (Dagstuhl Seminar 17161)

Authors: Lewis Chuang, Sven Gehring, Judy Kay, and Albrecht Schmidt

Published in: Dagstuhl Reports, Volume 7, Issue 4 (2018)


Abstract
Direct notifications are on the exponential rise. In our time, numerous personal computing devices and applications vie for limited attention, racing to deliver large amounts of information to us. This often results in users being overwhelmed by notifications and interruptions to their regular schedule, to whom a complete avoidance of technology seems to be the only viable option. In other words, the current approach for notification delivery is unsustainable and will not scale. In the Dagstuhl Seminar 17161 ``Ambient Notification Environments'' we brought together experts from different fields related to smart homes, ambient intelligence, human-computer interaction, activity recognition, and psychology to discuss a potential alternative approach: ambient notifications. We explored how ambient notifications can support people in their daily activities, by providing relevant information that are contextually embedded in the environment. The objective is to facilitate unobtrusive access to information at the right time and in the right place, hence reducing the disruptions and annoyances that are commonly associated with direct notifications. In this report, we present the numerous ideas and concepts of how the research community could strive toward towards realising ambient notifications. This is based on the presentations and activities conducted during the seminar. Overall, the community is in agreement that current approaches to notifications will not scale and that ambient notifications are a potential solution.

Cite as

Lewis Chuang, Sven Gehring, Judy Kay, and Albrecht Schmidt. Ambient Notification Environments (Dagstuhl Seminar 17161). In Dagstuhl Reports, Volume 7, Issue 4, pp. 38-82, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)


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@Article{chuang_et_al:DagRep.7.4.38,
  author =	{Chuang, Lewis and Gehring, Sven and Kay, Judy and Schmidt, Albrecht},
  title =	{{Ambient Notification Environments (Dagstuhl Seminar 17161)}},
  pages =	{38--82},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2017},
  volume =	{7},
  number =	{4},
  editor =	{Chuang, Lewis and Gehring, Sven and Kay, Judy and Schmidt, Albrecht},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.7.4.38},
  URN =		{urn:nbn:de:0030-drops-75475},
  doi =		{10.4230/DagRep.7.4.38},
  annote =	{Keywords: Ambient Notifications, Dagstuhl Seminar, Skill Transfer}
}
Document
Algorithmic Foundations of Programmable Matter (Dagstuhl Seminar 16271)

Authors: Sándor Fekete, Andréa W. Richa, Kay Römer, and Christian Scheideler

Published in: Dagstuhl Reports, Volume 6, Issue 7 (2016)


Abstract
his report documents the program and the outcomes of Dagstuhl Seminar 16271 "Algorithmic Foundations of Programmable Matter", a new and emerging field that combines theoretical work on algorithms with a wide spectrum of practical applications that reach all the way from small-scale embedded systems to cyber-physical structures at nano-scale. The aim of the Dagstuhl seminar was to bring together researchers from the algorithms community with selected experts from robotics and distributed systems in order to set a solid base for the development of models, technical solutions, and algorithms that can control programmable matter. Both communities benefited from such a meeting for the following reasons: - Meeting experts from other fields provided additional insights, challenges and focus when considering work on programmable matter. - Interacting with colleagues in a close and social manner gave many starting points for continuing collaboration. - Getting together in a strong, large and enthusiastic group provided the opportunity to plan a number of followup activities. In the following, we provide details and activities of this successful week.

Cite as

Sándor Fekete, Andréa W. Richa, Kay Römer, and Christian Scheideler. Algorithmic Foundations of Programmable Matter (Dagstuhl Seminar 16271). In Dagstuhl Reports, Volume 6, Issue 7, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)


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@Article{fekete_et_al:DagRep.6.7.1,
  author =	{Fekete, S\'{a}ndor and Richa, Andr\'{e}a W. and R\"{o}mer, Kay and Scheideler, Christian},
  title =	{{Algorithmic Foundations of Programmable Matter (Dagstuhl Seminar 16271)}},
  pages =	{1--14},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2016},
  volume =	{6},
  number =	{7},
  editor =	{Fekete, S\'{a}ndor and Richa, Andr\'{e}a W. and R\"{o}mer, Kay and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.6.7.1},
  URN =		{urn:nbn:de:0030-drops-67599},
  doi =		{10.4230/DagRep.6.7.1},
  annote =	{Keywords: distributed algorithms, distributed systems, programmable matter, robotics, self-organization}
}
Document
Genomic Privacy (Dagstuhl Seminar 13412)

Authors: Kay Hamacher, Jean Pierre Hubaux, and Gene Tsudik

Published in: Dagstuhl Reports, Volume 3, Issue 10 (2014)


Abstract
Recent advances in genomics prompt a formidable privacy challenge: As the price of a complete genome profile has plummeted to as low as 99 USD for genome-wide genotyping, wide-spread usage of genomic information is about to become reality. Substantial progress is expected in the near future in terms of improved diagnoses and better preventive medicine. The impact of the increased availability of genomic information on privacy, however, is unprecedented, for obvious reasons: First, genetic conditions and the predisposition to specific diseases (such as Alzheimer's) can be revealed. Second, a person's genomic information leaks substantial information about his relatives. Third, complex privacy issues can arise if DNA analysis is used for criminal investigations, epidemiological research, and personalized medicine purposes. This report documents the program and the outcomes of the Dagstuhl Seminar 13412 "Genomic Privacy". The goal of the seminar was to bring together leading researchers, from different areas of academia and industry. The seminar welcomed participants from computer science, bioinformatics, genetics, ethics and medical fields. Through a series of presentations, discussions, and working groups, the seminar attempted to provide a coherent picture of the field, which transcends the borders of disciplines. The participants discussed many aspects of genomic privacy and jointly identified the main requirements and the possible technical solutions for protecting genomic data.

Cite as

Kay Hamacher, Jean Pierre Hubaux, and Gene Tsudik. Genomic Privacy (Dagstuhl Seminar 13412). In Dagstuhl Reports, Volume 3, Issue 10, pp. 25-35, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)


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@Article{hamacher_et_al:DagRep.3.10.25,
  author =	{Hamacher, Kay and Hubaux, Jean Pierre and Tsudik, Gene},
  title =	{{Genomic Privacy (Dagstuhl Seminar 13412)}},
  pages =	{25--35},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2014},
  volume =	{3},
  number =	{10},
  editor =	{Hamacher, Kay and Hubaux, Jean Pierre and Tsudik, Gene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.3.10.25},
  URN =		{urn:nbn:de:0030-drops-44267},
  doi =		{10.4230/DagRep.3.10.25},
  annote =	{Keywords: Genomics, Genetics, Health Data, Privacy Protection, Differential Privacy, Privacy by Design, Information Security, Cryptography, Secure Computation}
}
Document
06431 Working Group Report on Managing and Integrating Data in P2P Databases

Authors: Peter A. Boncz, Angela Bonifati, Arantza Illarramendi, Peter Janacik, Birgitta König-Ries, Wolfgang Lehner, Pedro Jose Marrón, Wolfgang May, Aris Ouksel, Kay Römer, Brahmananda Sapkota, Kai-Uwe Sattler, Heinz Schweppe, Rita Steinmetz, and Can Türker

Published in: Dagstuhl Seminar Proceedings, Volume 6431, Scalable Data Management in Evolving Networks (2007)


Abstract
In this report, to our best recollection, we provide a summary of the working group "Managing and Integrating Data in P2P Databases" of the Dagstuhl Seminar nr. 6431 on "Scalable Data Management in Evolving Neworks", held on October 23-27 in Dagstuhl (Germany).

Cite as

Peter A. Boncz, Angela Bonifati, Arantza Illarramendi, Peter Janacik, Birgitta König-Ries, Wolfgang Lehner, Pedro Jose Marrón, Wolfgang May, Aris Ouksel, Kay Römer, Brahmananda Sapkota, Kai-Uwe Sattler, Heinz Schweppe, Rita Steinmetz, and Can Türker. 06431 Working Group Report on Managing and Integrating Data in P2P Databases. In Scalable Data Management in Evolving Networks. Dagstuhl Seminar Proceedings, Volume 6431, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2007)


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@InProceedings{boncz_et_al:DagSemProc.06431.3,
  author =	{Boncz, Peter A. and Bonifati, Angela and Illarramendi, Arantza and Janacik, Peter and K\"{o}nig-Ries, Birgitta and Lehner, Wolfgang and Marr\'{o}n, Pedro Jose and May, Wolfgang and Ouksel, Aris and R\"{o}mer, Kay and Sapkota, Brahmananda and Sattler, Kai-Uwe and Schweppe, Heinz and Steinmetz, Rita and T\"{u}rker, Can},
  title =	{{06431 Working Group Report on Managing and Integrating Data in P2P Databases}},
  booktitle =	{Scalable Data Management in Evolving Networks},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2007},
  volume =	{6431},
  editor =	{Stefan B\"{o}ttcher and Le Gruenwald and Pedro Jose Marr\'{o}n and Evaggelia Pitoura},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06431.3},
  URN =		{urn:nbn:de:0030-drops-9505},
  doi =		{10.4230/DagSemProc.06431.3},
  annote =	{Keywords: P2P database, data integration}
}
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