• My pages on Google Scholar and Mathematics Genealogy Project.
  • Peer review notice: in addition to peer-reviewed journals, I publish papers at machine learning conferences such as ICML and NeurIPS, which have double-blind peer reviews, and only accept about 20% of submitted papers.
  • Reproducible Research notice: a “Reproducible” link for each paper below provides source code and data that I used to perform the analysis and make the figures/tables.
  • Software notice: a “Software” link for each paper below provides a software package with a reference implementation of the algorithms described in our paper. See also my Software page.
  • Please download my TDH-refs.bib BibTeX citation database, and use it to cite my papers. This is the file that was used to generate the list of publications below.
Type count
journal paper 34
in progress 18
conference paper 12
book chapter 1
PHD thesis 1
Figure Published Authors Title Venue Links
In progress Gurney K, Aslam B, Dass P, Gawuc L, Hocking TD, Barber JJ, Kato A Assessment of the Climate Trace global powerplant CO2 emissions Accepted at Environmental Research Letters  
In progress Hocking TD Comparing binsegRcpp with other implementations of binary segmentation for changepoint detection In progress Reproducible, Software
In progress Hocking TD Teaching Hidden Markov Models Using Interactive Data Visualization In progress Reproducible, Slides
In progress Hocking TD mlr3resampling: an R implementation of cross-validation for comparing models learned using different train subsets In progress Software
In progress Sutherland V, Hocking TD, Lindly O Interpretable machine learning algorithms for understanding factors related to childhood autism In progress Reproducible
In progress Thibault G, Morin-Bernard A, Sylvain J-D, Drolet G, Roussel J-R, Hocking TD, Achim A Spatial characterization of burn severity in a boreal forest using high-resolution satellite imagery In progress  
In progress Truong C, Hocking TD Efficient change-point detection for multivariate circular data In progress Reproducible, Software
In progress Nguyen TL, Hocking TD Penalty Learning for Optimal Partitioning through Deep Learning Techniques Preprint arXiv:2408.00856, under review at Computational Statistics Preprint
In progress Fowler J, Hocking TD Efficient line search for optimizing Area Under the ROC Curve in gradient descent Preprint arXiv:2410.08635 Preprint, Talk announcement for JSM’23 Toronto, Video of talk at Université Laval July 2023, Slides PDF, source
In progress Bodine CS, Thibault G, Arellano PN, Shenkin AF, Lindly O, Hocking TD SOAK: Same/Other/All K-fold cross-validation for estimating similarity of patterns in data subsets Preprint arXiv:2410.08643 Preprint, Software, Reproducible
In progress Hocking TD Finite Sample Complexity Analysis of Binary Segmentation Preprint arXiv:2410.08654 Preprint, Reproducible, Software
In progress Hocking TD Why does functional pruning yield such fast algorithms for optimal changepoint detection? In progress Invited talk for TRIPODS seminar video, slides, IEEE NJACS, ASU West ML Day
In progress Rust KR, Hocking TD A Log-linear Gradient Descent Algorithm for Unbalanced Binary Classification using the All Pairs Squared Hinge Loss Preprint arXiv:2302.11062, under review at Journal of Machine Learning Research Preprint
In progress Agyapong D, Propster JR, Marks J, Hocking TD Cross-Validation for Training and Testing Co-occurrence Network Inference Algorithms Preprint arXiv:2309.15225, under review at BMC Bioinformatics Preprint
In progress Hocking TD, Killick R Introduction to optimal changepoint detection algorithms Tutorial at international useR 2017 conference, textbook in progress Conference, Book, Reproducible
In progress Hocking TD, Ekstrøm CT Understanding and Creating Interactive Graphics Tutorial at international useR 2016 conference, textbook in progress Conference, Manual, Reproducible
In progress Hocking TD A breakpoint detection error function for segmentation model selection and validation Preprint arXiv:1509.00368 Preprint, Software, Reproducible
In progress Venuto D, Hocking TD, Sphanurattana L, Sugiyama M Support vector comparison machines Preprint arXiv:1401.8008 Preprint, Software, Reproducible
2024 Kaufman JM, Stenberg AJ, Hocking TD Functional Labeled Optimal Partitioning Journal of Computational and Graphical Statistics, DOI: 10 . 1080/10618600 . 2023 . 2293216 DOI, Preprint, Software, Reproducible, Preliminary code
2024 Bodine CS, Buscombe D, Hocking TD Automated River Substrate Mapping From Sonar Imagery With Machine Learning Journal of Geophysical Research: Machine Learning and Computation 1(3) DOI, Preprint, Software
2024 Tao F, Houlton BZ, Frey SD, Lehmann J, Manzoni S, Huang Y, Jiang L, Mishra U, Hungate BA, Schmidt MWI, Reichstein M, Carvalhais N, Ciais P, Wang Y-P, Ahrens B, Hugelius G, Hocking TD, Lu X, Shi Z, Viatkin K, Vargas R, Yigini Y, Omuto C, Malik AA, Peralta G, Cuevas-Corona R, Paolo LED, Luotto I, Liao C, Liang Y-S, Saynes VS, Huang X, Luo Y Reply to: Model uncertainty obscures major driver of soil carbon Nature 627(8002) Publisher, Preprint, Local PDF
2023 Sweeney N, Xu C, Shaw JA, Hocking TD, Whitaker BM Insect Identification in Pulsed Lidar Images Using Changepoint Detection Algorithms 2023 Intermountain Engineering, Technology and Computing (IETC) Publisher, Local PDF
2023 Hocking TD, Srivastava A Labeled optimal partitioning Computational Statistics 38 Publisher, Preprint, Video, Software, Reproducible
2023 Harshe K, Williams JR, Hocking TD, Lerner ZF Predicting Neuromuscular Engagement to Improve Gait Training With a Robotic Ankle Exoskeleton IEEE Robotics and Automation Letters 8(8) Publisher, Local PDF
2023 Hillman J, Hocking TD Optimizing ROC Curves with a Sort-Based Surrogate Loss for Binary Classification and Changepoint Detection Journal of Machine Learning Research 24(70) Publisher, Preprint, Software, Reproducible, Video, Local PDF
2023 Runge V, Hocking TD, Romano G, Afghah F, Fearnhead P, Rigaill G gfpop: An R Package for Univariate Graph-Constrained Change-Point Detection Journal of Statistical Software 106(6) Publisher, Preprint, Software, GUI, Reproducible, Local PDF
2023 Tao F, Huang Y, Hungate BA, Manzoni S, Frey SD, Schmidt MWI, Reichstein M, Carvalhais N, Ciais P, Jiang L, Lehmann J, Mishra U, Hugelius G, Hocking TD, Lu X, Shi Z, Viatkin K, Vargas R, Yigini Y, Omuto C, Malik AA, Perualta G, Cuevas-Corona R, Paolo LED, Luotto I, Liao C, Liang Y-S, Saynes VS, Huang X, Luo Y Microbial carbon use efficiency promotes global soil carbon storage Nature 618 Publisher, Local PDF
2022 Barr JR, Hocking TD, Morton G, Thatcher T, Shaw P Classifying Imbalanced Data with AUM Loss 2022 Fourth International Conference on Transdisciplinary AI (TransAI) Publisher, Local PDF
2022 Hocking TD, Barr JR, Thatcher T Interpretable linear models for predicting security vulnerabilities in source code 2022 Fourth International Conference on Transdisciplinary AI (TransAI) Publisher, Local PDF
2022 Barr JR, Shaw P, Abu-Khzam FN, Thatcher T, Hocking TD Graph embedding: A methodological survey 2022 fourth international conference on transdisciplinary AI (TransAI) Publisher, Local PDF
2022 Chaves AP, Egbert J, Hocking T, Doerry E, Gerosa MA Chatbots Language Design: The Influence of Language Variation on User Experience with Tourist Assistant Chatbots ACM Trans. Comput.-Hum. Interact. 29(2) Publisher, Preprint, Local PDF
2022 Mihaljevic JR, Borkovec S, Ratnavale S, Hocking TD, Banister KE, Eppinger JE, Hepp C, Doerry E SPARSEMODr: Rapidly simulate spatially explicit and stochastic models of COVID-19 and other infectious diseases Biology Methods and Protocols 7(1) Publisher, Preprint, Software
2022 Hocking TD Introduction to machine learning and neural networks Chapter in Land Carbon Cycle Modeling: Matrix Approach, Data Assimilation, and Ecological Forecasting, edited by Yiqi Luo, published by CRC Press Publisher, My chapter, Reproducible, Video
2022 Vargovich J, Hocking TD Linear time dynamic programming for computing breakpoints in the regularization path of models selected from a finite set Journal of Computational and Graphical Statistics 31(2) Publisher, Preprint, Software, Reproducible, Local PDF
2022 Barnwal A, Cho H, Hocking T Survival Regression with Accelerated Failure Time Model in XGBoost Journal of Computational and Graphical Statistics 31(4) Publisher, Preprint, Software, Documentation, Video, Reproducible, Local PDF
2022 Hocking TD, Rigaill G, Fearnhead P, Bourque G Generalized Functional Pruning Optimal Partitioning (GFPOP) for Constrained Changepoint Detection in Genomic Data Journal of Statistical Software 101(10) Publisher, Software, Reproducible, Slides, Video
2021 Kolla AC, Groce A, Hocking TD Fuzz Testing the Compiled Code in R Packages 2021 IEEE 32nd International Symposium on Software Reliability Engineering (ISSRE) Publisher, Software, GitHub Action, Abstract, Video, Blog, Results, Local PDF
2021 Liehrmann A, Rigaill G, Hocking TD Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models BMC Bioinformatics 22(323) Publisher, Reproducible, Software
2021 Fotoohinasab A, Hocking T, Afghah F A greedy graph search algorithm based on changepoint analysis for automatic QRS complex detection Computers in Biology and Medicine 130 Publisher, Preprint
2021 Abraham AJ, Prys-Jones TO, De Cuyper A, Ridenour C, Hempson GP, Hocking T, Clauss M, Doughty CE Improved estimation of gut passage time considerably affects trait-based dispersal models Functional Ecology 35(4) Publisher
2021 Hocking TD Wide-to-tall Data Reshaping Using Regular Expressions and the nc Package The R Journal 13(1) Publisher, Software, Reproducible
2020 Fotoohinasab A, Hocking T, Afghah F A Graph-constrained Changepoint Detection Approach for ECG Segmentation 2020 42nd Annual International Conference of the IEEE Engineering in Medicine Biology Society (EMBC) Publisher, Local PDF
2020 Fotoohinasab A, Hocking T, Afghah F A Graph-Constrained Changepoint Learning Approach for Automatic QRS-Complex Detection 2020 54th Asilomar Conference on Signals, Systems, and Computers Publisher, Abstract, Preprint, Local PDF
2020 Hocking TD, Rigaill G, Fearnhead P, Bourque G Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection in Genomic Data Journal of Machine Learning Research 21(87) Publisher, Preprint, Software, Reproducible, Local PDF
2020 Hocking TD, Bourque G Machine Learning Algorithms for Simultaneous Supervised Detection of Peaks in Multiple Samples and Cell Types Proc. Pacific Symposium on Biocomputing Publisher, Software, Preprint, Reproducible
2019 Jewell SW, Hocking TD, Fearnhead P, Witten DM Fast nonconvex deconvolution of calcium imaging data Biostatistics 21(4) Pubmed
2019 Sievert C, VanderPlas S, Cai J, Ferris K, Khan FUF, Hocking TD Extending ggplot2 for Linked and Animated Web Graphics Journal of Computational and Graphical Statistics 28(2) Publisher, Software, Reproducible, Interactive Figures, Local PDF
2019 Hocking TD Comparing namedCapture with other R packages for regular expressions The R Journal 11(2) Publisher, Software, Reproducible
2018 Depuydt P, Boeva V, Hocking TD, Cannoodt R, Ambros IM, Ambros PF, Asgharzadeh S, Attiyeh EF, Combaret Vé, Defferrari R, Fischer M, Hero B, Hogarty MD, Irwin MS, Koster J, Kreissman S, Ladenstein R, Lapouble E, Laureys Gè, London WB, Mazzocco K, Nakagawara A, Noguera R, Ohira M, Park JR, Pötschger U, Theissen J, Tonini GP, Valteau-Couanet D, Varesio L, Versteeg R, Speleman F, Maris JM, Schleiermacher G, Preter KD Genomic amplifications and distal 6q loss: novel markers for poor survival in high-risk neuroblastoma patients JNCI: Journal of the National Cancer Institute 110(10) Publisher
2018 Depuydt P, Koster J, Boeva V, Hocking TD, Speleman F, Schleiermacher G, De Preter K Meta-mining of copy number profiles of high-risk neuroblastoma tumors Scientific data 5(1) Publisher
2018 Alirezaie N, Kernohan KD, Hartley T, Majewski J, Hocking TD ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants The American Journal of Human Genetics 103(4) DOI, Software, used in dbNSFP
2017 Drouin A, Hocking T, Laviolette F Maximum Margin Interval Trees Advances in Neural Information Processing Systems 30 Publisher, Software, Reproducible, Preprint, Video
2017 Hocking TD, Goerner-Potvin P, Morin A, Shao X, Pastinen T, Bourque G Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning Bioinformatics 33(4) Pubmed, Software, Reproducible, Data
2017 Maidstone R, Hocking T, Rigaill G, Fearnhead P On optimal multiple changepoint algorithms for large data Statistics and Computing 27 Publisher, Software, Reproducible
2016 Chicard M, Boyault S, Colmet Daage L, Richer W, Gentien D, Pierron G, Lapouble E, Bellini A, Clement N, Iacono I, Bréjon Sé, Carrere M, Reyes Cé, Hocking T, Bernard V, Peuchmaur M, Corradini Nè, Faure-Conter Cé, Coze C, Plantaz D, Defachelles AS, Thebaud E, Gambart M, Millot Féé, Valteau-Couanet D, Michon J, Puisieux A, Delattre O, Combaret Vé, Schleiermacher G Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma Clinical Cancer Research 22(22) Publisher
2016 Shimada K, Shimada S, Sugimoto K, Nakatochi M, Suguro M, Hirakawa A, Hocking TD, Takeuchi I, Tokunaga T, Takagi Y, Sakamoto A, Aoki T, Naoe T, Nakamura S, Hayakawa F, Seto M, Tomita A, Kiyoi H Development and analysis of patient-derived xenograft mouse models in intravascular large B-cell lymphoma Leukemia 30(7) Pubmed, Local PDF
2015 Hocking TD, Rigaill G, Bourque G PeakSeg: constrained optimal segmentation and supervised penalty learning for peak detection in count data Proc. 32nd ICML Publisher, Video, Software, Reproducible
2014 Hocking TD, Boeva V, Rigaill G, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Richer W, Bourdeaut F, Suguro M, Seto M, Bach F, Vert JP SegAnnDB: interactive Web-based genomic segmentation Bioinformatics 30(11) Pubmed, Software, Reproducible, Preprint, Package, Reproducible
2014 Suguro M, Yoshida N, Umino A, Kato H, Tagawa H, Nakagawa M, Fukuhara N, Karnan S, Takeuchi I, Hocking TD, Arita K, Karube K, Tsuzuki S, Nakamura S, Kinoshita T, Seto M Clonal heterogeneity of lymphoid malignancies correlates with poor prognosis Cancer Sci 105(7) Pubmed
2013 Hocking TD, Schleiermacher G, Janoueix-Lerosey I, Boeva V, Cappo J, Delattre O, Bach F, Vert J-P Learning smoothing models of copy number profiles using breakpoint annotations BMC Bioinformatics 14(164) Publisher, Software, Reproducible
2013 Hocking TD, Wutzler T, Ponting K, Grosjean P Sustainable, Extensible Documentation Generation using inlinedocs Journal of Statistical Software 54 Publisher, Software, Reproducible
2013 Rigaill G, Hocking T, Vert J-P, Bach F Learning sparse penalties for change-point detection using max margin interval regression Proc. 30th ICML Publisher, Video, Software, Reproducible
2012 Hocking TD Learning algorithms and statistical software, with applications to bioinformatics PHD thesis, Ecole normale supérieure de Cachan Publisher, Reproducible
2011 Hocking TD, Joulin A, Bach F, Vert J-P Clusterpath an algorithm for clustering using convex fusion penalties 28th international conference on machine learning Publisher, Video, Software, Reproducible, Cited in Ihaka lecture
2010 Gautier M, Hocking TD, Foulley J-L A Bayesian outlier criterion to detect SNPs under selection in large data sets PLoS one 5(8) Publisher
2008 Doyon Y, McCammon JM, Miller JC, Faraji F, Ngo C, Katibah GE, Amora R, Hocking TD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Amacher SL Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases Nature biotechnology 26(6) Pubmed 
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