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ARODZ BIOINFORMATICS & MACHINE LEARNING LAB
labpublications  
 
  • S. Saeedi, M. Serrano, D. Yang, P. Brooks, G. Buck, T. Arodz
    Real-valued group testing for quantitative molecular assays
    Conference on Research in Computational Molecular Biology RECOMB'22
     
  • S. Saeedi, M. Serrano, D. Yang, P. Brooks, G. Buck, T. Arodz
    Group testing matrix design for PCR screening with real-valued measurements
    Journal of Computational Biology, 29:1397-1411, 2022
     
  • S. Saeedi, A. Panahi T. Arodz
    Quantum semi-supervised kernel learning
    Quantum Machine Intelligence, 3:1-11, 2021
     
  • A. Panahi, S. Saeedi, T. Arodz
    Shapeshifter: a parameter-efficient Transformer using factorized reshaped matrices
    Conference on Neural Information Processing Systems NeurIPS'21
     
  • H. Zhang, T. Arodz
    Learning invariance in deep neural networks.
    International Conference on Computational Science ICCS'21
     
  • Y. Bokhari, T. Arodz
    PathMEx: Pathway-based mutual exclusivity for discovering rare cancer driver mutations.
    International Conference on Computational Science ICCS'21
     
  • H. Zhang, X. Gao, J. Unterman, T. Arodz
    Approximation capabilities of Neural ODEs and Invertible Residual Networks.
    International Conference on Machine Learning ICML'20
     
  • A. Panahi, S. Saeedi, T. Arodz
    word2ket: space-efficient word embeddings inspired by quantum entanglement.
    International Conference on Learning Representations ICLR'20
     
  • Y. Bokhari, A. Alhareeri, T. Arodz
    QuaDMutNetEx: a method for detecting cancer driver genes with low mutation frequency.
    BMC Bioinformatics, 21:122, 2020
     
  • T. Arodz
    Generalized quantum Deutsch-Jozsa algorithm.
    International Conference on Computational Science ICCS'20
     
  • T. Arodz
    Biological network visualization for targeted proteomics based on mean first-passage time in semi-lazy random walks
    International Conference on Computational Science ICCS'20
     
  • M. G. Serrano, H. I. Parikh, J. P. Brooks, D. J. Edwards, T. Arodz, L. Edupuganti, B. Huang, P. H. Girerd, Y. Bokhari, S. P. Bradley, J. L. Brooks, M. R. Dickinson, J. I. Drake, R. A. Duckworth III, S. S. Fong, A. L. Glascock, S. Jean, N. R. Jimenez, J. Khoury, V. N. Koparde, A. M. Lara, V. Lee, A. V. Matveyev, S. H. Milton, S. D. Mistry, S. K. Rozycki, N. U. Sheth, E. Smirnova, S. C. Vivadelli, N. R. Wijesooriya, J. Xu, P. Xu, D. O. Chaffin, A. L. Sexton, M. G. Gravett, C. E. Rubens, K. D. Hendricks-Munoz, K. K. Jefferson, J. F. Strauss III, J. M. Fettweis, G. A. Buck
    Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy
    Nature Medicine, 25: 1001-1011, 2019
     
  • J. M. Fettweis, M. G. Serrano, J. P. Brooks, D. J. Edwards, P. H. Girerd, H. I. Parikh, B. Huang, T. Arodz, L. Edupuganti, A. L. Glascock, J. Xu, N. R. Jimenez, S. C. Vivadelli, S. S. Fong, N. U. Sheth, S. Jean, V. Lee, Y. Bokhari, A. M. Lara, S. D. Mistry, R. A. Duckworth III, S. P. Bradley, V. N. Koparde, X. V. Orenda, S. H. Milton, S. K. Rozycki, A. V. Matveyev, M. L. Wright, S. V. Huzurbazar, E. M. Jackson, E. Smirnova, J. Korlach, Y.-Ch. Tsai, M. R. Dickinson, J. L. Brooks, J. I. Drake, D. O. Chaffin, A. L. Sexton, M. G. Gravett, C. E. Rubens, N. R. Wijesooriya, K. D. Hendricks-Munoz, K. K. Jefferson, J. F. Strauss III, G. A. Buck
    The vaginal microbiome and preterm birth.
    Nature Medicine, 25:1012-1021, 2019
     
  • A. Dhungana, T. Arodz , E. Bulut
    Exploiting peer-to-peer wireless energy sharing for mobile charging relief.
    Ad Hoc Networks, 91:101882, 2019
     
  • A. Dhungana, T. Arodz , E. Bulut
    Charging skip optimization with peer-to-peer wireless energy sharing in mobile networks.
    IEEE International Conference on Communications ICC'18,
     
  • X. Gao, E.F. Petricoin, K.R. Ward, S.R. Goldberg, T.M. Duane, D. Bonchev, T. Arodz, R.F. Diegelmann
    Network proteomics of human dermal wound healing.
    Physiological Measurement, 39:124002, 2018
     
  • Y. Bokhari, T. Arodz
    QuaDMutEx: quadratic driver mutation explorer.
    BMC Bioinformatics, 18:458, 2017
     
  • T. Arodz, D. Bonchev
    Identifying influential nodes in a wound healing-related network of biological processes using mean first-passage time.
    New Journal of Physics, 17:025002, 2015
     
  • J. Slawek, T. Arodz
    ENNET: Inferring Large Gene Regulatory Networks from Expression Data using Gradient Boosting
    BMC Systems Biology, 7:106, 2013
     
  • T. Arodz, D. Bonchev, R. F. Diegelmann
    Network Approach to Wound Healing
    Advances in Wound Care, 2:499-509, 2013
     
  • G. Federici, X. Gao, J. Slawek, T. Arodz, A. Shitaye, J. D. Wulfkuhle, R. de Maria, L. A. Liotta, E. F. Petricoin
    Systems Level Network Analysis of the NCI-60 Cancer Cell Lines by Alignment of Protein Pathway Activation Modules with Multiple "-omic" Data Fields and Therapeutic Response Signatures
    Molecular Cancer Research, 11:676-685, 2013
     
  • T. Arodz, P.M. Plonka
    Sequence and Structure Space Model of Protein Divergence driven by Point Mutations
    Journal of Theoretical Biology, 330:1-8, 2013
     
  • X. Gao, T. Arodz
    Detecting Differentially Co-expressed Genes for Drug Target Analysis
    International Conference on Computational Science ICCS'2013, Procedia Computer Science 18:1392-1401, Elsevier, 2013
     
  • X. Gao, T. Arodz
    Robust differential co-expression discovery: an insight into pharmacodynamics of tyrosine kinase inhibitor
    ACM Conference on Bioinformatics, Computational Biology and Biomedicine ACM-BCB'12, pp. 604-606, 2012
     
  • J. Slawek, T. Arodz
    ADANET: Inferring Gene Regulatory Networks using Ensemble Classifiers
    ACM Conference on Bioinformatics, Computational Biology and Biomedicine ACM-BCB'12, pp. 434-441, 2012
     
  • T. Arodz, P.M. Plonka
    Effects of point mutations on protein structure are nonexponentially distributed
    Proteins: Structure, Function and Bioinformatics, 80:1780-1790, 2012
     
  • W. Czech, W. Dzwinel, S. Goryczka, T. Arodz, A.Z. Dudek
    Exploring Complex Networks with Graph Investigator Research Application
    Computing and Informatics, 30:381-410, 2011
     
  • T. Arodz
    Conservation of edge essentiality profiles in metabolic networks across species
    International Conference on Complex Sciences, COMPLEX'09, LNICST, Vol. 5, pp. 1865-1976. Springer, 2009
     
  • T. Arodz
    Clustering Species using Topological Measures of Edge Essentiality in Metabolic Networks
    BioSysBio' 20'09
     
  • T. Arodz
    Clustering Organisms Using Metabolic Networks
    International Conference on Computational Science ICCS'08, Lecture Notes in Computer Science, Vol. 5102, pp. 527-534. Springer, 2008
     
  • T. Arodz, A. Z. Dudek
    Multivariate Modeling and Analysis in Drug Discovery
    Current Computer-Aided Drug Design, 3(4):240-247, 2007
     
  • T. Arodz, D. A. Yuen, A. Z. Dudek
    Ensemble of Linear Models for Predicting Drug Properties
    Journal of Chemical Information and Modeling, 46(1):416-423, 2006
     
  • A. Z. Dudek, T. Arodz, J. Galvez
    Computational Methods in Developing Quantitative Structure-Activity Relationships (QSAR): A Review
    Combinatorial Chemistry & High Throughput Screening, 9(3):213-228, 2006
     
  • T. Arodz, M. Kurdziel, T.J. Popiela, E.O.D. Sevre, D.A. Yuen
    Detection of Clustered Microcalcifications in Small Field Digital Mammography
    Computer Methods and Programs in Biomedicine, 81(1):56-65, 2006
     
  • S. Goryczka, T. Arodz
    Complex-network-based Methodology for Analysis of Biomedical Data
    Bio-Algorithms and Med-Systems, 2(3):19-26, 2006
     
  • T. Arodz
    Invariant Object Recognition Using Radon-based Transform
    Computing and Informatics, 24(2):183-199, 2005
     
  • T. Arodz, M. Kurdziel, E.O. D. Sevre, D.A. Yuen
    Pattern Recognition Techniques for Automatic Detection of Suspicious-looking Anomalies in Mammograms
    Computer Methods and Programs in Biomedicine, 79(2):135-149, 2005
     
  • T. Arodz
    Training Set Size in Ensemble Feature Selection for Clinical Proteomics
    Bio-Algorithms and Med-Systems, 1(1/2):107-110, 2005
     
  • W. Dzwinel, K. Boryczko, T. Arodz, M. Kurdziel
    Computer-based Methods for Breast Cancer Detection in Mammograms
    Bio-Algorithms and Med-Systems, 1(1/2):287-290, 2005
     
  • T. Arodz
    Boosting the Fisher Linear Discriminant with Random Feature Subsets
    International Conference on Computer Recognition Systems - CORES'05, Advances in Soft Computing, pp. 79-86. Springer, 2005
     
  • T. Arodz
    Margin-based Diversity Measures for Ensemble Classifiers
    International Conference on Computer Recognition Systems - CORES'05, Advances in Soft Computing, pp. 71-78. Springer, 2005
     
  • T. Arodz, K. Boryczko, W. Dzwinel, M. Kurdziel, D. A. Yuen
    Visual Exploration of Multidimensional Feature Space of Biological Data
    abstract in: IEEE Visualization 2005 - (VIS'05), p. 90, 2005
     
  • B. Balis, M. Bubak, W. Funika, R. Wismueller, M. Radecki, T. Szepieniec, T. Arodz, M. Kurdziel
    Grid Environment for On-line Application Monitoring and Performance Analysis
    Scientific Programming, 12(4):239-251, 2004
     
  • T. Arodz
    On New Radon-based Translation, Rotation and Scaling Invariant Transform International Conference on Computational Science ICCS'04, Lecture Notes in Computer Science, Vol. 3039, pp. 9-17, Springer, 2004
     
  • B. Balis, M. Bubak, W. Funika, R. Wismueller, M. Radecki, T. Szepieniec, T. Arodz, M. Kurdziel
    Performance Evaluation and Monitoring of Interactive Grid Applications
    in: Kranzmuller, D., Kacsuk, P., Dongarra, J. (Editors) "Recent Advances in Parallel Virtual Machine and Message Passing Interface", Lecture Notes in Computer Science, Vol. 3241, pp. 345-352, Springer, 2004
     
  • M. Bubak, W. Funika, R. Wismueller, T. Arodz, M. Kurdziel
    Performance measurement model in the G-PM tool
    in: Bubak, M., van Albada, G.D., Sloot, P.M.A., Dongarra. J. (Editors) "Computational Science - ICCS'2004", Lecture Notes in Computer Science, Vol. 3036, pp. 462-465, Springer, 2004
     
  • R. Wismuller, M. Bubak, W. Funika, T. Arodz, M. Kurdziel
    Support for User-Defined Metrics in the On-line Performance Analysis Tool G-PM
    in: Dikaiakos, M.D. (Editor) "Grid Computing", Lecture Notes in Computer Science, Vol. 3165, pp. 159-168, Springer, 2004
     
  • M. Bubak, W. Funika, R. Wismueller, T. Arodz, M. Kurdziel
    The G-PM Tool for Grid-oriented Performance Analysis
    in: Fernandez Rivera, F., Bubak, M., Gomez Tato, A., Doallo, R. (Editors) "Grid Computing. First European Across Grids Conference", Lecture Notes in Computer Science, Vol. 2970, pp. 240-248, Springer, 2004
     
  • T.J. Popiela, A. Urbanik, T. Arodz, M. Kurdziel
    Computer-aid system for the detection of clustered microcalcifications in digital mammography
    in: Proc. XXXVII Polish Congress of Radiology, Polish Journal of Radiology, 69(S1):67-68, 2004
     
  • M. Bubak, W. Funika, R. Wismuller, T. Arodz, M. Kurdziel
    Performance Measurement for Interactive Applications in CrossGrid
    in: Bubak, M., Turala, M., Wiatr, K. (Editors) "Proc. Cracow Grid Workshop '04", pp. 169-175, ACC Cyfronet AGH, Krakow, 2005
     
  • B. Balis, M. Bubak, W. Funika, M. Radecki, T. Szepieniec, R. Wismueller, T. Arodz, M. Kurdziel
    A Concept of a Monitoring Infrastructure for Workflow-Based Grid Applications
    in: Bubak, M., Noga, M., Turala, M. (Editors) "Proc. Cracow Grid Workshop '03", pp. 136-141, ACC Cyfronet AGH, Krakow, 2004
     
  • M. Bubak, W. Funika, R. Wismuller, T. Arodz, M. Kurdziel
    The G-PM Performance Measurement Tool for Interactive Grid Applications
    in: Bubak, M., Noga, M., Turala, M. (Editors) "Proc. Cracow Grid Workshop '03", pp. 227-234, ACC Cyfronet AGH, Krakow, 2004
     
  • M. Bubak, W. Funika, R. Wismuller, T. Arodz, M. Kurdziel
    Performance Analysis of Grid Interactive Applications with G-PM Tool
    in: Bubak, M., Noga, M., Turala, M. (Editors) "Proc. 2nd Cracow Grid Workshop", ACC Cyfronet AGH, Krakow, 2003