KERMIT -- Research Unit Knowledge-based Systems

Michiel STOCK

michiel.stock@ugent.be
@KERMIT, office 110.54
(+32) 9 264.60.18

Stock Michiel
https://orcid.org/0000-0003-0903-6061
Biblio UGent
Google Scholar
#michielstock
https://michielstock.github.io/

Research Interests:

Machine learning methods for understanding, predicting and controlling community ecosystems.

Learning from networks

Journal papers Conference papers

Journal papers

All
2024 (9)
2023 (2)
2022 (10)
2021 (10)
2020 (6)
2019 (3)
2018 (2)
2017 (2)
2016 (2)
2015 (1)
2014 (2)
2013 (2)
2012 (1)

(52) Hyperdimensional computing: a fast, robust and interpretable paradigm for biological data
M. Stock, D. Boeckaerts, P. Dewulf, S. Taelman, M. Van Haeverbeke, W. Van Criekinge and B. De Baets
(2024) PLOS COMPUTATIONAL BIOLOGY. 20, e1012426 .

(51) DepoScope: accurate phage depolymerase annotation and domain delineation using large language models
R. Concha-Eloko, M. Stock, B. De Baets, Y. Briers, R. Sanjuan, P. Domingo-Calap and D. Boeckaerts
(2024) PLOS COMPUTATIONAL BIOLOGY. 20, e1011831.

(50) Link prediction in stagewise graphs
P. Dewulf, M. Stock and B. De Baets
(2024) IEEE TRANSACTIONS ON DATA AND KNOWLEDGE ENGINEERING. 36, 3252-3264.

(49) Prediction of Klebsiella phage-host specificity at the strain level
D. Boeckaerts, M. Stock, C. Ferriol-González, J. Oteo-Iglesias, R. Sanjuán, P. Domingo-Calap, B. De Baets and Y. Briers
(2024) NATURE COMMUNICATIONS. 15, 4355.

(48) Engineering is evolution : a perspective on design processes to engineer biology
S. D. Castle, M. Stock and T. E. Gorochowski
(2024) NATURE COMMUNICATIONS. 15, 3640.

(47) Plant science in the age of simulation intelligence
M. Stock, O. Pieters, T. De Swaef and F. wyffels
(2024) FRONTIERS IN PLANT SCIENCE. 14, 1299208.

(46) The role of Helicobacter suis, Fusobacterium gastrosuis, and the pars oesophageal microbiota in gastric ulceration in slaughter pigs receiving meal or pelleted feed
E. Taillieu, S. Taelman, S. De Bruyckere, E. Goossens, I. Chantziaras, C. Van Steenkiste, P. Yde, S. Hanssens, D. De Meyer, W. Van Criekinge, M. Stock, D. Maes, K. Chiers and F. Haesebrouck
(2024) VETERINARY RESEARCH. 55, 15.

(45) Open-endedness in synthetic biology: A route to continual innovation for biological design
M. Stock and T. E. Gorochowski
(2024) SCIENCE ADVANCES. 10, eadi3621.

(44) Impedimetric biofilm characterisation with microelectrode arrays using equivalent electrical circuit features and ensemble classifiers
M. Van Haeverbeke, C. Cums, T. Vackier, D. Braeken, M. Stock, H. Steenackers and B. De Baets
(2024) CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS. 244, 105048.

(43) Evaluating the potential of Distribution of Relaxation Times analysis for plant agriculture
M. Van Haeverbeke, B. De Baets and M. Stock
(2023) COMPUTERS AND ELECTRONICS IN AGRICULTURE. 213, 108249.

(42) Plant impedance spectroscopy: a review of modeling approaches and applications
M. Van Haeverbeke, B. De Baets and M. Stock
(2023) FRONTIERS IN PLANT SCIENCE. 14, 1187573.

(41) Optimising predictive models to prioritise viral discovery in zoonotic reservoirs
D.J. Becker, G.F. Albery, A.R. Sjodin, T. Poisot, L.M. Bergner, B. Chen, L.E. Cohen, T.A. Dallas, E.A. Eskew, A.C. Fagre, M.J. Farrell, S. Guth, B.A. Han, N.B. Simmons, M. Stock, E.C. Teeling and C.J. Carlson
(2022) THE LANCET MICROBE. 3, e625-e637.

(40) Leveraging plant physiological dynamics using physical reservoir computing
O. Pieters, T. De Swaef, M. Stock and F. wyffels
(2022) SCIENTIFIC REPORTS. 12, 12594.

(39) Machine learning techniques to characterize functional traits of plankton from image data
E. Orenstein, S.-D. Ayata, F. Maps, T. Biard, E. Becker, F. Benedetti, T. de Garidel-Thoron, J.S. Ellen, F. Ferrario, S.L.C. Giering, T. Guy-Haim, L. Hoebeke, M. Iversen, T. Kiørboe, J.-F. Lalonde, A. Lana, M. Laviale, F. Lombard, T. Lorimer, S. Martini, A. Meyer, K.O. Möller, B. Niehoff, M. Ohman, C. Pradalier, J.-B. Romagnan, S.-M. Schröder, V. Sonnet, H.M. Sosik, L. Stemmann, M. Stock, T. Terbiyik-Kurt, N. Valcàrcel-Pérez, L. Vilgrain, G. Wacquet, A. Waite and J.-O. Irisson
(2022) LIMNOLOGY AND OCEANOGRAPHY. 67, 1647-1669.

(38) Machine learning to assist in large-scale, activity-based synthetic cannabinoid receptor agonist screening of serum samples
L. Janssens, D. Boeckaerts, S. Hudson, D. Morozova, A. Cannaert, D.M. Wood, C. Wolfe, B. De Baets, M. Stock, P.I. Dargan and C.P. Stove
(2022) CLINICAL CHEMISTRY. 68, 906-916.

(37) Covering the combinatorial design space of multiplex CRISPR/Cas experiments in plants
K. Van Huffel, M. Stock, T. Ruttink and B. De Baets
(2022) FRONTIERS IN PLANT SCIENCE. 13, 907095.

(36) Identification of phage receptor-binding protein sequences with hidden Markov models and an extreme gradient boosting classifier
D. Boeckaerts, M. Stock, B. De Baets and Y. Briers
(2022) VIRUSES. 14, 1329.

(35) Equivalent electrical circuits and their use across electrochemical impedance spectroscopy application domains
M. Van Haeverbeke, M. Stock and B. De Baets
(2022) IEEE ACCESS. 10, 51363-51379.

(34) Hydraulics and beyond: a review on water potential as pivotal driver of physiological processes in plant models
T. De Swaef, O. Pieters, S. Appeltans, I. Borra-Serrano, W. Coudron, V. Couvreur, S. Garré, P. Lootens, B. Nicolaï, L. Pols, C. Saint Cast, J. Šalagovič, M. Van Haeverbeke, M. Stock and F. wyffels
(2022) IN SILICO PLANTS. 4, 1-28.

(33) BioCCP.jl: Collecting Coupons in combinatorial biotechnology
K. Van Huffel, M. Stock and B. De Baets
(2022) BIOINFORMATICS. 38, 1144-1145.

(32) Digital phagograms: predicting phage infectivity through a multi-layer machine learning approach
C. Lood, D. Boeckaerts, M. Stock, B. De Baets, R. Lavigne, V. Van Noort and Y. Briers
(2022) CURRENT OPINION IN VIROLOGY. 52, 174-181.

(31) Practical equivalent electrical circuit identification for electrochemical impedance spectroscopy analysis with gene expression programming
M. Van Haeverbeke, M. Stock and B. De Baets
(2021) IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT. 70, 2514612.

(30) Crowdsourced mapping of unexplored target space of kinase inhibitors
A. Cichonska, B. Ravikumar, R. J. Allaway, F. Wan, S. Park, O. Isayev, S. Li, M. Mason, A. Lamb, Z. Tanoli, M. Jeon, S. Kim, M. Popova, S. Capuzzi, J. Zeng, K. Dang, G. Koytiger, J. Kang, C. I. Wells, T. M. Willson, M. Tan, C.-H. Huang, E. S. C. Shih, T.-M. Chen, C.-H. Wu, W.-Q. Fang, J.-Y. Chen, M.-J. Hwang, X. Wang, M. B. Guebila, B. Shamsaei, S. Singh, T. Nguyen, M. Karimi, D. Wu, Z. Wang, Y. Shen, H. Öztürk, E. Ozkirimli, A. Özgür, H. Lim, L. Xie, G. K. Kanev, A. J. Kooistra, B. A. Westerman, P. Terzopoulos, K. Ntagiantas, C. Fotis, L. Alexopoulos, D. Boeckaerts, M. Stock, B. De Baets, Y. Briers, F. Wan, S. Li, Y. Luo, H. Hu, J. Peng, J. Zeng, T. Dogan, A. S. Rifaioglu, H. Atas, R. C. Atalay, V. Atalay, M. J. Martin, S. Park, M. Jeon, S. Kim, J. Lee, S. Yun, B. Kim, B. Chang, J. Kang, M. Popova, S. Capuzzi, O. Isayev, G. Turu, Á. Misák, B. Szalai, L. Hunyady, M. Lienhard, P. Prasse, I. Bachmann, J. Ganzlin, G. Barel, R. Herwig, D. Oršolić, B. Lučić, V. Stepanić, T. Šmuc, T. I. Oprea, A. Schlessinger, D. H. Drewry, G. Stolovitzky, K. Wennerberg, J. Guinney, T. Aittokallio
(2021) NATURE COMMUNICATIONS. 12, 3307.

(29) PhaLP: A database for the study of phage lytic proteins and their evolution
B. Criel, S. Taelman, W. Van Criekinge, M. Stock and Y. Briers
(2021) VIRUSES. 13, 1240.

(28) Disentangling the information in species interaction networks
M. Stock, L. Hoebeke and B. De Baets
(2021) ENTROPY. 23, 703.

(27) Optimal transportation theory for species interaction networks
M. Stock, T. Poisot and B. De Baets
(2021) ECOLOGY AND EVOLUTION. 11, 3841-3855.

(26) Cold-start problems in data-driven prediction of drug-drug interaction effects
P. Dewulf, M. Stock and B. De Baets
(2021) PHARMACEUTICALS. 14, 429.

(25) Pairwise learning for predicting pollination interactions based on traits and phylogeny
M. Stock, N. Piot, S. Vanbesien, J. Meys, G. Smagghe and B. De Baets
(2021) ECOLOGICAL MODELLING. 451, 109508.

(24) Rapid and high-throughput evaluation of diverse configurations of engineered lysins using the VersaTile technique
L. Duyvejonck, H. Gerstmans, M. Stock, D. Grimon, R. Lavigne and Y. Briers
(2021) ANTIBIOTICS. 10, 293.

(23) Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins
D. Boeckaerts, M. Stock, B. Criel, H. Gerstmans, B. De Baets and Y. Briers
(2021) SCIENTIFIC REPORTS. 11, 1467.

(22) Otolith identification using a deep hierarchical classification model
M. Stock, B. Nguyen, W. Courtens, H. Verstraete, E. Stienen and B. De Baets
(2021) COMPUTERS AND ELECTRONICS IN AGRICULTURE. 180, 105883.

(21) Predictive design of sigma factor-specific promoters
M. Van Brempt, J. Clauwaert, F. Mey, M. Stock, J. Maertens, W. Waegeman and M. De Mey
(2020) NATURE COMMUNICATIONS. 11, 5822.

(20) Limitations of snapshot hyperspectral cameras to monitor plant response dynamics in stress-free conditions
O. Pieters, T. De Swaef, P. Lootens, M. Stock, I. Roldán-Ruiz and F. wyffels
(2020) COMPUTERS AND ELECTRONICS IN AGRICULTURE. 179, 105825.

(19) Information content in pollination network reveals missing interactions
M. Stock, N. Piot, S. Vanbesien, B. Vaissière, C. Coiffait-Gombault, G. Smagghe and B. De Baets
(2020) ECOLOGICAL MODELLING. 431, 109161.

(18) Gloxinia - An open-source sensing platform to monitor the dynamic responses of plants
O. Pieters, T. De Swaef, P. Lootens, M. Stock, I. Roldán-Ruiz and F. wyffels
(2020) SENSORS. 20, 3055.

(17) Predicting pharmaceutical particle size distributions using kernel mean embedding
D. Van Hauwermeiren, M. Stock, T. De Beer and I. Nopens
(2020) PHARMACEUTICS. 12, 271.

(16) Algebraic shortcuts for leave-one-out cross-validation in supervised network inference
M. Stock, T. Pahikkala, A. Airola, W. Waegeman and B. De Baets
(2020) BRIEFINGS IN BIOINFORMATICS. 21, 262-271.

(15) X-ray microtomography and linear discriminant analysis enable extraction of embolism-related acoustic emissions
N.J.F. De Baerdemaker, M. Stock, J. Van Den Bulcke, B. De Baets, L. Van Hoorebeke and K. Steppe
(2019) PLANT METHODS. 15, 153.

(14) Guiding mineralization co-culture discovery using Bayesian optimization
A.J. Daly, M. Stock, J.M. Baetens and B. De Baets
(2019) ENVIRONMENTAL SCIENCE AND TECHNOLOGY. 53, 14459-14469.

(13) EcologicalNetworks.jl: analysing ecological networks of species interactions
T. Poisot, Z. Bélisle, L. Hoebeke, M. Stock and P. Szefer
(2019) ECOGRAPHY. 42, 1850-1861.

(12) Liquid-to-solid ratio control as an advanced process control solution for continuous twin-screw wet granulation
N. Nicolaï, F. De Leersnyder, D. Copot, M. Stock, C.-M. Ionescu, K.V. Gernaey, I. Nopens and T. De Beer
(2018) AICHE JOURNAL. 64, 2500-2514.

(11) A comparative study of pairwise learning methods based on Kernel Ridge Regression
M. Stock, T. Pahikkala, A. Airola, B. De Baets and W. Waegeman
(2018) NEURAL COMPUTATION. 30, 2245-2283.

(10) miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure
G. Van Peer, A. De Paepe, M. Stock, J. Anckaert, P-J. Volders, J. Vandesompele, B. De Baets and W. Waegeman
(2017) NUCLEIC ACIDS RESEARCH. 45, e51.

(9) Linear filtering reveals false negatives in species interaction data
M. Stock, T. Poisot, W. Waegeman and B. De Baets
(2017) SCIENTIFIC REPORTS. 7, 45908.

(8) Exact and efficient top-K inference for multi-target prediction by querying separable linear relational models
M. Stock, K. Dembczyński, B. De Baets and W. Waegeman
(2016) DATA MINING AND KNOWLEDGE DISCOVERY. 30, 1370-1394.

(7) Data-driven recipe completion using machine learning methods
M. De Clercq, M. Stock, B. De Baets and W. Waegeman
(2016) TRENDS IN FOOD SCIENCE & TECHNOLOGY. 49, 1-13.

(6) A decoy-free approach to the identification of peptides
G. Gonnelli, M. Stock, J. Verwaeren, D. Maddelein, B. De Baets, L. Martens and S. Degroeve
(2015) JOURNAL OF PROTEOME RESEARCH. 14, 1792-1798.

(5) A community effort to assess and improve drug sensitivity prediction algorithms
J.C. Costello, L.M. Heiser, E. Georgii, M. Gönen, M.P. Menden, N.J. Wang, M. Bansal, M. Ammad-ud-din, P. Hintsanen, S.A. Khan, J.-P. Mpindi, O. Kallioniemi, A. Honkela, T. Aittokallio, K. Wennerberg, J.-P. Abbuehl, J. Allen, R.B. Altman, S. Balcome, A. Battle, A. Bender, B. Berger, J. Bernard, M. Bhattacharjee, K. Bhuvaneshwar, A.A. Bieberich, F. Boehm, A. Califano, C. Chan, B. Chen, T.-H. Chen, J. Choi, L.P. Coelho, T. Cokelaer, C.J. Creighton, J. Cui, W. Dampier, V.J. Davisson, B. De Baets, R. Deshpande, B. DiCamillo, M. Dundar, Z. Duren, A. Ertel, H. Fan, H. Fang, R. Gauba, A. Gottlieb, M. Grau, Y. Gusev, M.J. Ha, L. Han, M. Harris, N. Henderson, H.A. Hejase, K. Homicsko, J.P. Hou, W. Hwang, A.P. Ijzerman, B. Karacali, S. Keles, C. Kendziorski, J. Kim, M. Kim, Y. Kim, D.A. Knowles, D. Koller, J. Lee, J.K. Lee, E.B. Lenselink, B. Li, B. Li, J. Li, H. Liang, J. Ma, S. Madhavan, S. Mooney, C.L. Myers, M.A Newton, J.P. Overington, R. Pal, J. Peng, R. Pestell, R.J. Prill, P. Qiu, B. Rajwa, A. Sadanandam, F. Sambo, H. Shin, J. Song, L. Song, A. Sridhar, M. Stock, W. Sun, T. Ta, M. Tadesse, M. Tan, H. Tang, D. Theodorescu, G.M. Toffolo, A. Tozeren, W. Trepicchio, N. Varoquaux, J.-P. Vert, W. Waegeman, T. Walter, Q. Wan, D. Wang, W. Wang, Y. Wang, Z. Wang, J.K. Wegner, T. Wu, T. Xia, G. Xiao, Y. Xie, Y. Xu, J. Yang, Y. Yuan, S. Zhang, X.-S. Zhang, J. Zhao, C. Zuo, H.W.T. van Vlijmen, G.J.P. van Westen, J.J. Collins, D. Gallahan, D. Singer, J. Saez-Rodriguez, S. Kaski, J.W. Gray and G. Stolovitzky
(2014) NATURE BIOTECHNOLOGY. 32, 1202-1212.

(4) Identification of functionally-related enzymes by learning-to-rank methods and cavity-based similarity measures
M. Stock, T. Fober, E. Hüllermeier, S. Glinca, G. Klebe, T. Pahikkala, A. Airola, B. De Baets and W. Waegeman
(2014) IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 11, 1157-1169.

(3) Exploration and prediction of interactions between methanotrophs and heterotrophs
M. Stock, S. Hoefman, F.-M. Kerckhof, N. Boon, P. De Vos, B. De Baets, K. Heylen and W. Waegeman
(2013) RESEARCH IN MICROBIOLOGY. 10, 1045-1054.

(2) Efficient regularized least-squares algorithms for conditional ranking on relational data
T. Pahikkala, A. Airola, M. Stock, B. De Baets and W. Waegeman
(2013) MACHINE LEARNING. 93, 321-356.

(1) A kernel-based framework for learning graded relations from data
W. Waegeman, T. Pahikkala, A. Airola, T. Salakoski, M. Stock and B. De Baets
(2012) IEEE TRANSACTIONS ON FUZZY SYSTEMS. 20, 1090-1101.

Conference papers

All
2015 (1)
2014 (1)
2012 (1)

(3) Recipe Completion using Machine Learning Techniques
M. De Clercq, M. Stock, B. De Baets and W. Waegeman
(2015) ICML 2015 WORKSHOP ON CONSTRUCTIVE MACHINE LEARNING.
Lille, France, 4 pages. .

(2) A two-step learning approach for solving full and almost full cold start problems in dyadic prediction
T. Pahikkala, M. Stock, A. Airola, T. Aittokallio, B. De Baets and W. Waegeman
(2014) MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES.
Nancy, France, 517-532. .

(1) Learning Monadic and Dyadic Relations: Three Case Studies in Systems Biology
M. Stock, T. Pahikkala, A. Airola, T. Salakoski, B. De Baets and W. Waegeman
(2012) ECML WORKSHOP ON LEARNING AND DISCOVERY IN SYMBOLIC SYSTEMS BIOLOGY.
Bristol, UK, 12 pages. .

Date	Title
19/01/2019	EOS-prize 2018 goes to Sarah Vanbesien
26/10/2018	Michiel Stock wins public prize TEDxGhent PhD contest
08/03/2018	Best Poster Presentation Award for Michiel Stock
02/10/2017	Michiel Stock reaches the Flemish PhD Cup Final
12/12/2016	Gold medal for student entry at the iGEM competition in Boston
18/08/2014	2015 IEEE CIS Outstanding TFS Paper Award

Name	Title	Date
S. Taelman	Beyond correlations: a causal perspective on host-microbiome interactions	29/08/2024
P. Dewulf	Exploiting data compositionality using tensor products and hyperdimensional computing	13/12/2023
D. Boeckaerts	Predicting and understanding phage-host interactions with machine learning tools based on phage receptor-binding proteins	19/10/2023
M. Van Haeverbeke	Advances in impedimetric modelling of electrochemical systems in engineering and the life sciences	07/07/2023
O. Pieters	Reservoir computing with plants	08/02/2022

Name	Title	Date
H. B. Karaaslan	Leveraging probabilistic programming in causal inference for precision medicine	2022 - 2024
M. Fatjanov	The potential of hyperdimensional computing for protein sequence representation	2022 - 2023
Y. Bae	Drug-drug interaction prediction for side effects, diseases, and cell lines using three-step kernel ridge regression	2021 - 2022
S. Van Parys	BIOBOTS: a new type of multicellularity	2021 - 2022
S. Van Hoye	Evolution and design of metabolic networks using quality-diversity optimization algorithms	2021 - 2022
J. De Landsheere	Data-driven prediction of pharmaceutical granules' size	2021 - 2022
W. Decrop	Computational prediction of bacteria-phage interactions of Escherichia coli through omics data analysis and machine learning	2021 - 2022
D. Snoeck	A data-based view for brewing	2021 - 2022
B. Spanoghe	Probabilistic programming for Bayesian modeling and its applications in biology	2021 - 2022
W. Van Belle	Automating the design of biological robots using MAP-Elites	2021 - 2022
Q. Q. Li	Applications of differentiable dynamic programming in biology	2020 - 2021
T. Vanneste	Predicting interactions between bacteria and their prophages based on genomic sequence data	2019 - 2020
T. Ntumba	Prediction of water quality parameters of Flemish surface waters using machine learning techniques	2019 - 2020
J. Vermout	A data-driven approach to the design of new cocktail recipes	2019 - 2020
A. Deloose	Acoustic monitoring of bats with self-organizing maps	2018 - 2019
S. Taelman	A dual computational approach to map domain architecture in phage lytic proteins	2018 - 2019
L. Hoebeke	Automated recognition of people and identification of animal species in camera trap images	2017 - 2018

Michiel STOCK

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