6 Search Results for "Brown, Malcolm B."

Document
DOI: 10.4230/LIPIcs.WABI.2025.11
Mutational Signature Refitting on Sparse Pan-Cancer Data

Authors: Gal Gilad, Teresa M. Przytycka, and Roded Sharan

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the disease, improving patient stratification and the prediction of drug response. Thus, there is growing interest in developing refitting methods that decipher those exposures. Previous work in this domain was unsupervised in nature, employing algebraic decomposition and probabilistic inference methods. Here we provide a supervised approach to the problem of signature refitting and show its superiority over current methods. Our method, SuRe, leverages a neural network model to capture correlations between signature exposures in real data. We show that SuRe outperforms previous methods on sparse mutation data from tumor type specific data sets, as well as pan-cancer data sets, with an increasing advantage as the data become sparser. We further demonstrate its utility in clinical settings.
Cite as

Gal Gilad, Teresa M. Przytycka, and Roded Sharan. Mutational Signature Refitting on Sparse Pan-Cancer Data. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gilad_et_al:LIPIcs.WABI.2025.11,
  author =	{Gilad, Gal and Przytycka, Teresa M. and Sharan, Roded},
  title =	{{Mutational Signature Refitting on Sparse Pan-Cancer Data}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{11:1--11:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.11},
  URN =		{urn:nbn:de:0030-drops-239374},
  doi =		{10.4230/LIPIcs.WABI.2025.11},
  annote =	{Keywords: mutational signatures, signature refitting, cancer genomics, genomic data analysis, somatic mutations}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Cite as

Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
DOI: 10.4230/DagSemProc.09471.1
09471 Abstracts Collection – Computer-assisted proofs - tools, methods and applications

Authors: Malcolm B. Brown, Erich Kaltofen, Shin'ichi Oishi, and Siegfried M. Rump

Published in: Dagstuhl Seminar Proceedings, Volume 9471, Computer-assisted proofs - tools, methods and applications (2010)

Abstract
From 15.11. to 20.11.2009, the Dagstuhl Seminar 09471 ``Computer-assisted proofs - tools, methods and applications '' 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

Malcolm B. Brown, Erich Kaltofen, Shin'ichi Oishi, and Siegfried M. Rump. 09471 Abstracts Collection – Computer-assisted proofs - tools, methods and applications. In Computer-assisted proofs - tools, methods and applications. Dagstuhl Seminar Proceedings, Volume 9471, pp. 1-24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{brown_et_al:DagSemProc.09471.1,
  author =	{Brown, Malcolm B. and Kaltofen, Erich and Oishi, Shin'ichi and Rump, Siegfried M.},
  title =	{{09471 Abstracts Collection – Computer-assisted proofs - tools, methods and applications}},
  booktitle =	{Computer-assisted proofs - tools, methods and applications},
  pages =	{1--24},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{9471},
  editor =	{B. Malcolm Brown and Erich Kaltofen and Shin'ichi Oishi and Siegfried M. Rump},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09471.1},
  URN =		{urn:nbn:de:0030-drops-25328},
  doi =		{10.4230/DagSemProc.09471.1},
  annote =	{Keywords: Verification methods, computer algebra, computer-assisted proofs}
}
Document
DOI: 10.4230/DagSemProc.09471.2
09471 Executive Summary – Computer-assisted proofs - tools, methods and applications

Authors: Malcolm B. Brown, Erich Kaltofen, Shin'ichi Oishi, and Siegfried M. Rump

Published in: Dagstuhl Seminar Proceedings, Volume 9471, Computer-assisted proofs - tools, methods and applications (2010)

Abstract
From November 15-20, 2009, the Dagstuhl seminar on "Computer-assisted proofs - tools, methods and applications" continued a series of previous successful seminars. Participants from 10 different countries presented recent results in verification methods, computer algebra, and other computer-assisted-proof related areas. We had lively talks and discussions, during the regular times for talks, during meals and afterwards. In the following links to abstracts and/or the presentation are given were applicable.
Cite as

Malcolm B. Brown, Erich Kaltofen, Shin'ichi Oishi, and Siegfried M. Rump. 09471 Executive Summary – Computer-assisted proofs - tools, methods and applications. In Computer-assisted proofs - tools, methods and applications. Dagstuhl Seminar Proceedings, Volume 9471, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{brown_et_al:DagSemProc.09471.2,
  author =	{Brown, Malcolm B. and Kaltofen, Erich and Oishi, Shin'ichi and Rump, Siegfried M.},
  title =	{{09471 Executive Summary – Computer-assisted proofs - tools, methods and applications}},
  booktitle =	{Computer-assisted proofs - tools, methods and applications},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{9471},
  editor =	{B. Malcolm Brown and Erich Kaltofen and Shin'ichi Oishi and Siegfried M. Rump},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09471.2},
  URN =		{urn:nbn:de:0030-drops-25316},
  doi =		{10.4230/DagSemProc.09471.2},
  annote =	{Keywords: Verification methods, computer algebra, computer-assisted proofs}
}
Document
DOI: 10.4230/DagSemProc.09471.3
Interval Approaches to Reliable Control of Dynamical Systems

Authors: Andreas Rauh and Ekaterina Auer

Published in: Dagstuhl Seminar Proceedings, Volume 9471, Computer-assisted proofs - tools, methods and applications (2010)

Abstract
Recently, we presented an implementation of interval-based algorithms which can be applied in real-time to control dynamical processes and to estimate internal states and disturbances. The approach is based on verified methods for sets of algebraic equations, ordinary differential equations as well as differential-algebraic equations. Due to this fact, the same program code can be used for two different tasks. On the one hand, we can use it online to estimate non-measurable internal system states which are necessary for nonlinear model-based control strategies. On the other hand, we can verify the admissibility and feasibility of these control strategies offline. Although we use the same code for the online and offline tasks, there is an important difference between them. While the computing time is of minor importance in offline applications, we have to guarantee that the necessary online computations are completed successfully in a predefined time interval. For that reason, the role of verification is slightly different depending on the task. In offline applications, our goal is to compute tightest possible bounds for the sets of all solutions to the control problem under consideration. In contrast to that, we restrict the online mode to a search for a single solution that matches all demands on feasibility of control inputs and admissibility of the trajectories of the state variables in a reliable way. To highlight the practical applicability of the underlying computational routines, we present the following cases for the use of verified solvers in real-time [1-3]. Case 1: Direct computation of feedforward control strategies with the help of differential-algebraic equation solvers. In this application, both verified and non-verified solvers can be used to determine open-loop control strategies for a dynamical system such that its output coincides with a predefined time response within given tolerances. This procedure corresponds to a numerical inversion of the dynamics of the system to be controlled. In this case, verified solvers are used to prove the existence of a control law within given physical bounds for the admissible range of the system inputs. Case 2: If measured data and their time derivatives are available, the same procedures as in case 1 can be used to estimate non-measured state variables as well as non-measurable disturbances. Since the verified algorithms used in this context are capable of propagating bounded measurement uncertainties, the quality of the state and disturbance estimates can be expressed in terms of the resulting interval widths. Moreover, assumptions about the parameters and the structure of the underlying model can be verified. Case 3: Routines for verified sensitivity analysis provide further information on the influence of variations of control inputs on the trajectories of the state variables. We present novel procedures implementing a sensitivity-based framework for model-predictive control. These procedures can be integrated directly in a feedback control structure. Sometimes it is necessary to combine verified and non-verified algorithms to solve a given control problem. In this case, it is important to certify the results of the algorithm appropriately. Based on the four-tier hierarchy presented in earlier works [4], we develop a measure for characterizing such mixed approaches. The presentation is concluded with simulation and experimental results for the example of temperature control of a distributed heating system. [1] Rauh, Andreas; Auer, Ekaterina: Applications of Verified DAE Solvers in Engineering, Intl. Workshop on Verified Computations and Related Topics, COE Lecture Note Vol. 15: Kyushu University, pp. 88-96, Karlsruhe, Germany, 2009. [2] Rauh, Andreas; Menn, Ingolf; Aschemann, Harald: Robust Control with State and Disturbance Estimation for Distributed Parameter Systems, Proc. of 15th Intl. Workshop on Dynamics and Control 2009, pp. 135-142, Tossa de Mar, Spain, 2009. [3] Rauh, Andreas; Auer, Ekaterina; Aschemann, Harald: Real-Time Application of Interval Methods for Robust Control of Dynamical Systems, CD-Proc. of IEEE Intl. Conference on Methods and Models in Automation and Robotics MMAR 2009, Miedzyzdroje, Poland, 2009. [4] Auer, Ekaterina; Luther, Wolfram: Numerical Verification Assessment in Computational Biomechanics, in A. Cuyt, W. Krämer, W. Luther, P. Markstein: Numerical Validation in Current Hardware Architectures, LNCS 5492, pp. 145-160, Springer-Verlag, Berlin, Heidelberg, 2009.
Cite as

Andreas Rauh and Ekaterina Auer. Interval Approaches to Reliable Control of Dynamical Systems. In Computer-assisted proofs - tools, methods and applications. Dagstuhl Seminar Proceedings, Volume 9471, pp. 1-28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{rauh_et_al:DagSemProc.09471.3,
  author =	{Rauh, Andreas and Auer, Ekaterina},
  title =	{{Interval Approaches to Reliable Control of Dynamical Systems}},
  booktitle =	{Computer-assisted proofs - tools, methods and applications},
  pages =	{1--28},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{9471},
  editor =	{B. Malcolm Brown and Erich Kaltofen and Shin'ichi Oishi and Siegfried M. Rump},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09471.3},
  URN =		{urn:nbn:de:0030-drops-25120},
  doi =		{10.4230/DagSemProc.09471.3},
  annote =	{Keywords: Robust control, Ordinary differential equations, Differential-algebraic equations}
}
Document
DOI: 10.4230/DagSemProc.09471.4
Verification and Validation for Femur Prosthesis Surgery

Authors: Ekaterina Auer, Roger Cuypers, Eva Dyllong, Stefan Kiel, and Wolfram Luther

Published in: Dagstuhl Seminar Proceedings, Volume 9471, Computer-assisted proofs - tools, methods and applications (2010)

Abstract
In this paper, we describe how verified methods we are developing in the course of the project TellHim&S (Interval Based Methods For Adaptive Hierarchical Models In Modeling And Simulation Systems) can be applied in the context of the biomechanical project PROREOP (Development of a new prognosis system to optimize patient-specific pre- operative surgical planning for the human skeletal system). On the one hand, it includes the use of verified hierarchical structures for reliable geometric modeling, object decomposition, distance computation and path planning. On the other hand, we cover such tasks as verification and validation assessment and propagation of differently described uncertainties through system models in engineering or mechanics.
Cite as

Ekaterina Auer, Roger Cuypers, Eva Dyllong, Stefan Kiel, and Wolfram Luther. Verification and Validation for Femur Prosthesis Surgery. In Computer-assisted proofs - tools, methods and applications. Dagstuhl Seminar Proceedings, Volume 9471, pp. 1-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{auer_et_al:DagSemProc.09471.4,
  author =	{Auer, Ekaterina and Cuypers, Roger and Dyllong, Eva and Kiel, Stefan and Luther, Wolfram},
  title =	{{Verification and Validation for Femur Prosthesis Surgery}},
  booktitle =	{Computer-assisted proofs - tools, methods and applications},
  pages =	{1--22},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{9471},
  editor =	{B. Malcolm Brown and Erich Kaltofen and Shin'ichi Oishi and Siegfried M. Rump},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09471.4},
  URN =		{urn:nbn:de:0030-drops-25133},
  doi =		{10.4230/DagSemProc.09471.4},
  annote =	{Keywords: Graphical interface construction, superquadrics, 3D modeling, biomedical engineering}
}
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