3 Search Results for "Hung, Chien-Wen"

Document
DOI: 10.4230/LIPIcs.SoCG.2025.78
Efficient Greedy Discrete Subtrajectory Clustering

Authors: Ivor van der Hoog, Lara Ost, Eva Rotenberg, and Daniel Rutschmann

Published in: LIPIcs, Volume 332, 41st International Symposium on Computational Geometry (SoCG 2025)

Abstract
We cluster a set of trajectories 𝒯 using subtrajectories of 𝒯. We require for a clustering C that any two subtrajectories (𝒯[a, b], 𝒯[c, d]) in a cluster have disjoint intervals [a,b] and [c, d]. Clustering quality may be measured by the number of clusters, the number of vertices of 𝒯 that are absent from the clustering, and by the Fréchet distance between subtrajectories in a cluster. A Δ-cluster of 𝒯 is a cluster 𝒫 of subtrajectories of 𝒯 with a centre P ∈ 𝒫, where all subtrajectories in 𝒫 have Fréchet distance at most Δ to P. Buchin, Buchin, Gudmundsson, Löffler and Luo present two O(n² + n m 𝓁)-time algorithms: SC(max, 𝓁, Δ, 𝒯) computes a single Δ-cluster where P has at least 𝓁 vertices and maximises the cardinality m of 𝒫. SC(m, max, Δ, 𝒯) computes a single Δ-cluster where 𝒫 has cardinality m and maximises the complexity 𝓁 of P. In this paper, which is a mixture of algorithms engineering and theoretical insights, we use such maximum-cardinality clusters in a greedy clustering algorithm. We first provide an efficient implementation of SC(max, 𝓁, Δ, 𝒯) and SC(m, max, Δ, 𝒯) that significantly outperforms previous implementations. Next, we use these functions as a subroutine in a greedy clustering algorithm, which performs well when compared to existing subtrajectory clustering algorithms on real-world data. Finally, we observe that, for fixed Δ and 𝒯, these two functions always output a point on the Pareto front of some bivariate function θ(𝓁, m). We design a new algorithm PSC(Δ, 𝒯) that in O(n² log⁴ n) time computes a 2-approximation of this Pareto front. This yields a broader set of candidate clusters, with comparable quality to the output of the previous functions. We show that using PSC(Δ, 𝒯) as a subroutine improves the clustering quality and performance even further.
Cite as

Ivor van der Hoog, Lara Ost, Eva Rotenberg, and Daniel Rutschmann. Efficient Greedy Discrete Subtrajectory Clustering. In 41st International Symposium on Computational Geometry (SoCG 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 332, pp. 78:1-78:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{vanderhoog_et_al:LIPIcs.SoCG.2025.78,
  author =	{van der Hoog, Ivor and Ost, Lara and Rotenberg, Eva and Rutschmann, Daniel},
  title =	{{Efficient Greedy Discrete Subtrajectory Clustering}},
  booktitle =	{41st International Symposium on Computational Geometry (SoCG 2025)},
  pages =	{78:1--78:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-370-6},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{332},
  editor =	{Aichholzer, Oswin and Wang, Haitao},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SoCG.2025.78},
  URN =		{urn:nbn:de:0030-drops-232308},
  doi =		{10.4230/LIPIcs.SoCG.2025.78},
  annote =	{Keywords: Algorithms engineering, Fr\'{e}chet distance, subtrajectory clustering}
}
Document
Position
DOI: 10.4230/TGDK.2.1.2
Grounding Stream Reasoning Research

Authors: Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
In the last decade, there has been a growing interest in applying AI technologies to implement complex data analytics over data streams. To this end, researchers in various fields have been organising a yearly event called the "Stream Reasoning Workshop" to share perspectives, challenges, and experiences around this topic. In this paper, the previous organisers of the workshops and other community members provide a summary of the main research results that have been discussed during the first six editions of the event. These results can be categorised into four main research areas: The first is concerned with the technological challenges related to handling large data streams. The second area aims at adapting and extending existing semantic technologies to data streams. The third and fourth areas focus on how to implement reasoning techniques, either considering deductive or inductive techniques, to extract new and valuable knowledge from the data in the stream. This summary is written not only to provide a crystallisation of the field, but also to point out distinctive traits of the stream reasoning community. Moreover, it also provides a foundation for future research by enumerating a list of use cases and open challenges, to stimulate others to join this exciting research area.
Cite as

Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer. Grounding Stream Reasoning Research. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 2:1-2:47, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{bonte_et_al:TGDK.2.1.2,
  author =	{Bonte, Pieter and Calbimonte, Jean-Paul and de Leng, Daniel and Dell'Aglio, Daniele and Della Valle, Emanuele and Eiter, Thomas and Giannini, Federico and Heintz, Fredrik and Schekotihin, Konstantin and Le-Phuoc, Danh and Mileo, Alessandra and Schneider, Patrik and Tommasini, Riccardo and Urbani, Jacopo and Ziffer, Giacomo},
  title =	{{Grounding Stream Reasoning Research}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:47},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.2},
  URN =		{urn:nbn:de:0030-drops-198597},
  doi =		{10.4230/TGDK.2.1.2},
  annote =	{Keywords: Stream Reasoning, Stream Processing, RDF streams, Streaming Linked Data, Continuous query processing, Temporal Logics, High-performance computing, Databases}
}
Document
DOI: 10.4230/OASIcs.GCB.2013.56
Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics

Authors: Anna Katharina Hildebrandt, Ernst Althaus, Hans-Peter Lenhof, Chien-Wen Hung, Andreas Tholey, and Andreas Hildebrandt

Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013

Abstract
Mass spectrometry is the major analytical tool for the identification and quantification of proteins in biological samples. In so-called top-down proteomics, separation and mass spectrometric analysis is performed at the level of intact proteins, without preparatory digestion steps. It has been shown that the tandem mass tag (TMT) labeling technology, which is often used for quantification based on digested proteins (bottom-up studies), can be applied in top-down proteomics as well. This, however, leads to a complex interpretation problem, where we need to annotate measured peaks with their respective generating protein, the number of charges, and the a priori unknown number of TMT-groups attached to this protein. In this work, we give an algorithm for the efficient enumeration of all valid annotations that fulfill available experimental constraints. Applying the algorithm to real-world data, we show that the annotation problem can indeed be efficiently solved. However, our experiments also demonstrate that reliable annotation in complex mixtures requires at least partial sequence information and high mass accuracy and resolution to go beyond the proof-of-concept stage.
Cite as

Anna Katharina Hildebrandt, Ernst Althaus, Hans-Peter Lenhof, Chien-Wen Hung, Andreas Tholey, and Andreas Hildebrandt. Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 56-67, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@InProceedings{hildebrandt_et_al:OASIcs.GCB.2013.56,
  author =	{Hildebrandt, Anna Katharina and Althaus, Ernst and Lenhof, Hans-Peter and Hung, Chien-Wen and Tholey, Andreas and Hildebrandt, Andreas},
  title =	{{Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics}},
  booktitle =	{German Conference on Bioinformatics 2013},
  pages =	{56--67},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-59-0},
  ISSN =	{2190-6807},
  year =	{2013},
  volume =	{34},
  editor =	{Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.56},
  URN =		{urn:nbn:de:0030-drops-42304},
  doi =		{10.4230/OASIcs.GCB.2013.56},
  annote =	{Keywords: Mass spectrometry, TMT labeling, Top-down Proteomics}
}
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