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Research Output 1988 2019

2019

Adaptive online extreme learning machine by regulating forgetting factor by concept drift map

Yu, H. & Webb, G. I., 28 May 2019, In : Neurocomputing. p. 141-153 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework

Zhang, Y., Xie, R., Wang, J., Leier, A., Marquez-Lago, T. T., Akutsu, T., Webb, G. I., Chou, K-C. & Song, J., 2019, (Accepted/In press) In : Briefings in Bioinformatics. 15 p., bby079.

Research output: Contribution to journalArticleResearchpeer-review

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites

Li, P., Chen, J., Leier, A., Marquez-Lago, T., Liu, Q., Wang, Y., Revote, J., Smith, A. I., Akutsu, T., Webb, G. I., Kurgan, L. & Song, J., 30 Sep 2019, (Accepted/In press) In : Bioinformatics. 9 p., btz721.

Research output: Contribution to journalArticleResearchpeer-review

Elastic bands across the path: a new framework and method to lower bound DTW

Tan, C. W., Petitjean, F. & Webb, G. I., 2019, Proceedings of the 2019 SIAM International Conference on Data Mining. Berger-Wolf, T. & Chawla, N. (eds.). Philadelphia PA USA: Society for Industrial & Applied Mathematics (SIAM), p. 522-530 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data

Chen, Z., Zhao, P., Li, F., Marquez-Lago, T. T., Leier, A., Revote, J., Zhu, Y., Powell, D. R., Akutsu, T., Webb, G. I., Chou, K-C., Smith, A. I., Daly, R. J., Li, J. & Song, J., 24 Apr 2019, (Accepted/In press) In : Briefings in Bioinformatics. 11 p., bbz041.

Research output: Contribution to journalArticleResearchpeer-review

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

Song, J., Wang, Y., Li, F., Akutsu, T., Rawlings, N. D., Webb, G. I. & Chou, K-C., 25 Mar 2019, In : Briefings in Bioinformatics. 20, 2, p. 638-658 21 p.

Research output: Contribution to journalReview ArticleResearchpeer-review

Open Access
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Positive-unlabelled learning of glycosylation sites in the human proteome

Li, F., Zhang, Y., Purcell, A. W., Webb, G. I., Chou, K-C., Lithgow, T., Li, C. & Song, J., 6 Mar 2019, In : BMC Bioinformatics. 20, 1, 17 p., 112.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

Li, F., Fan, C., Marquez-Lago, T. T., Leier, A., Revote, J., Jia, C., Zhu, Y., Smith, A. I., Webb, G. I., Liu, Q., Wei, L., Li, J. & Song, J., 4 Jun 2019, (Accepted/In press) In : Briefings in Bioinformatics. 11 p., bbz050.

Research output: Contribution to journalArticleResearchpeer-review

Proximity Forest: an effective and scalable distance-based classifier for time series

Lucas, B., Shifaz, A., Pelletier, C., O’Neill, L., Zaidi, N., Goethals, B., Petitjean, F. & Webb, G. I., May 2019, In : Data Mining and Knowledge Discovery. 33, 3, p. 607-635 29 p.

Research output: Contribution to journalArticleResearchpeer-review

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches

Wang, J., Yang, B., An, Y., Marquez-Lago, T., Leier, A., Wilksch, J., Hong, Q., Zhang, Y., Hayashida, M., Akutsu, T., Webb, G. I., Strugnell, R. A., Song, J. & Lithgow, T., 21 May 2019, In : Briefings in Bioinformatics. 20, 3, p. 931-951 21 p.

Research output: Contribution to journalArticleResearchpeer-review

Temporal Convolutional Neural Network for the classification of satellite image time series

Pelletier, C., Webb, G. I. & Petitjean, F., 4 Mar 2019, In : Remote Sensing. 11, 5, 25 p., 523.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2018

Accurate parameter estimation for Bayesian network classifiers using hierarchical Dirichlet processes

Petitjean, F., Buntine, W., Webb, G. I. & Zaidi, N., Sep 2018, In : Machine Learning. 107, 8-10, p. 1303-1331 29 p.

Research output: Contribution to journalArticleResearchpeer-review

Analyzing concept drift and shift from sample data

Webb, G. I., Lee, L. K., Goethals, B. & Petitjean, F., Sep 2018, In : Data Mining and Knowledge Discovery. 32, 5, p. 1179-1199 21 p.

Research output: Contribution to journalArticleResearchpeer-review

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI

An, Y., Wang, J., Li, C., Leier, A., Marquez-Lago, T., Wilksch, J., Zhang, Y., Webb, G. I., Song, J. & Lithgow, T., 1 Jan 2018, In : Briefings in Bioinformatics. 19, 1, p. 148-161 14 p., bbw100.

Research output: Contribution to journalArticleResearchpeer-review

Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity

Wang, H., Feng, L., Webb, G. I., Kurgan, L., Song, J. & Lin, D., 28 Sep 2018, In : Briefings in Bioinformatics. 19, 5, p. 838-852 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Efficient and effective accelerated hierarchical higher-order logistic regression for large data quantities

Zaidi, N. A., Petitjean, F. & Webb, G. I., 2018, 2018 SIAM International Conference on Data Mining, SDM 2018: San Diego Marriott Mission Valley San Diego, California USA May 3-5, 2018. Ester, M. & Pedreschi, D. (eds.). Philadelphia PA USA: Society for Industrial & Applied Mathematics (SIAM), p. 459-467 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Efficient search of the best warping window for Dynamic time Warping

Tan, C. W., Herrmann, M., Forestier, G., Webb, G. I. & Petitjean, F., 2018, 2018 SIAM International Conference on Data Mining, SDM 2018: San Diego Marriott Mission Valley San Diego, California USA May 3-5, 2018. Ester, M. & Pedreschi, D. (eds.). Philadelphia PA USA: Society for Industrial & Applied Mathematics (SIAM), p. 225-233 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Extremely fast decision tree

Manapragada, C., Webb, G. I. & Salehi, M., 2018, KDD' 2018 - Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining : August 19-23, 2018, London, United Kingdom . Lin, C-J. & Xiong, H. (eds.). New York NY USA: Association for Computing Machinery (ACM), p. 1953-1962 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

iFeature: a python package and web server for features extraction and selection from protein and peptide sequences

Chen, Z., Zhao, P., Li, F., Leier, A., Marquez-Lago, T., Wang, Y., Webb, G. I., Smith, A. I., Daly, R. J., Chou, K-C. & Song, J., 15 Jul 2018, In : Bioinformatics. 34, 14, p. 2499-2502 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

Chen, Z., Liu, X., Li, F., Li, C., Marquez-Lago, T., Leier, A., Akutsu, T., Webb, G. I., Xu, D., Smith, A. I., Li, L., Chou, K-C. & Song, J., 4 Oct 2018, (Accepted/In press) In : Briefings in Bioinformatics. 24 p., bby089.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Mining significant crisp-fuzzy spatial association rules

Shi, W., Zhang, A. & Webb, G. I., 2018, In : International Journal of Geographical Information Science. 32, 6, p. 1247-1270 24 p.

Research output: Contribution to journalArticleResearchpeer-review

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework

Song, J., Li, F., Takemoto, K., Haffari, G., Akutsu, T., Chou, K. C. & Webb, G. I., 14 Apr 2018, In : Journal of Theoretical Biology. 443, p. 125-137 13 p.

Research output: Contribution to journalArticleResearchpeer-review

PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy

Song, J., Li, F., Leier, A., Marquez-Lago, T., Akutsu, T., Haffari, G., Chou, K-C., Webb, G. I. B. & Pike, R. N., 15 Feb 2018, In : Bioinformatics. 34, 4, p. 684-687 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Robust Bayesian kernel machine via Stein variational gradient descent for big data

Nguyen, K., Le, T., Nguyen, T. D., Phung, D. & Webb, G. I., 19 Jul 2018, KDD'18: Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. Lin, C-J. & Xiong, H. (eds.). New York NY USA: Association for Computing Machinery (ACM), p. 2003-2011 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Structural Capacitance in Protein Evolution and Human Diseases

Li, C., Clark, L. V. T., Zhang, R., Porebski, B. T., McCoey, J. M., Borg, N. A., Webb, G. I., Kass, I., Buckle, M., Song, J., Woolfson, A. & Buckle, A. M., 14 Sep 2018, In : Journal of Molecular Biology. 430, 18, p. 3200-3217 18 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Survey of distance measures for quantifying concept drift and shift in numeric data

Goldenberg, I. & Webb, G. I., 8 Sep 2018, (Accepted/In press) In : Knowledge and Information Systems. 25 p.

Research output: Contribution to journalArticleResearchpeer-review

Tamping effectiveness prediction using supervised machine learning techniques

Tan, C. W., Webb, G. I., Petitjean, F. & Reichl, P., 2018, ICRT 2017 - Railway Development, Operations, and Maintenance: Proceedings of the First International Conference on Rail Transportation 2017 - July 10–12, 2017 Chengdu, Sichuan Province, China. Zhai, W. & Wang, K. C. P. (eds.). Reston Virginia USA: American Society of Civil Engineers, p. 1010-1023 14 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearch

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods

Li, F., Wang, Y., Li, C., Marquez-Lago, T. T., Leier, A., Rawlings, N. D., Haffari, G., Revote, J., Akutsu, T., Chou, K-C., Purcell, A. W., Pike, R. N., Webb, G. I., Smith, A. I., Lithgow, T., Daly, R. J., Whisstock, J. C. & Song, J., 2018, (Accepted/In press) In : Briefings in Bioinformatics. 17 p., bby077.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2017

A fast trust-region Newton method for softmax logistic regression

Zaidi, N. & Webb, G. I., 2017, Proceedings of the 17th SIAM International Conference on Data Mining: Houston, Texas, USA, 27 – 29 April , 2017. Chawla, N. & Wang, W. (eds.). Philadelphia, PA: Society for Industrial and Applied Mathematics SIAM Publications, p. 705-713 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Corrigendum: Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity [Briefings in Bioinformatics, (2017)] doi: 10.1093/bib/bbx018

Wang, H., Feng, L., Webb, G. I., Kurgan, L., Song, J. & Lin, D., 1 Nov 2017, In : Briefings in Bioinformatics. 18, 6, 1 p.

Research output: Contribution to journalComment / DebateOtherpeer-review

Designing a more efficient, effective and safe Medical Emergency Team (MET) service using data analysis

Bergmeir, C., Bilgrami, I., Bain, C., Webb, G. I., Orosz, J. & Pilcher, D., 1 Dec 2017, In : PLoS ONE. 12, 12, 13 p., e0188688.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Efficient parameter learning of Bayesian network classifiers

Zaidi, N. A., Webb, G. I., Carman, M., Petitjean, F., Buntine, W., Hynes, M. & De Sterck, H., 2017, In : Machine Learning. 106, 9-10, p. 1289-1329 41 p.

Research output: Contribution to journalArticleResearchpeer-review

Generating synthetic time series to augment sparse datasets

Forestier, G., Petitjean, F., Dau, H. A., Webb, G. I. & Keogh, E., 15 Dec 2017, Proceedings: 17th IEEE International Conference on Data Mining. Raghavan, V., Aluru, S., Karypis, G., Miele, L. & Wu, X. (eds.). Piscataway NJ USA: IEEE, Institute of Electrical and Electronics Engineers, p. 865-870 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Indexing and classifying gigabytes of time series under time warping

Tan, C. W., Webb, G. I. & Petitjean, F., 1 Jan 2017, Proceedings of the 17th SIAM International Conference on Data Mining: Houston, Texas, USA, 27 – 29 April , 2017. Chawla, N. & Wang, W. (eds.). Philadelphia, PA: Society for Industrial and Applied Mathematics SIAM Publications, p. 282-290 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Knowledge-Transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

Wang, Y., Song, J., Marquez-Lago, T., Leier, A., Li, C., Lithgow, T., Webb, G. I. & Shen, H-B., 1 Dec 2017, In : Scientific Reports. 7, 1, 5755.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Metalexplorer, a bioinformatics tool for the improved prediction of eight types of metal-binding sites using a random forest algorithm with two-step feature selection

Song, J., Li, C., Zheng, C., Revote, J., Zhang, Z. & Webb, G. I., 2017, In : Current Bioinformatics. 12, 6, p. 480-489 10 p.

Research output: Contribution to journalArticleResearchpeer-review

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

Song, J., Wang, H., Wang, J., Leier, A., Marquez-Lago, T., Yang, B., Zhang, Z., Akutsu, T., Webb, G. I. & Daly, R. J., 1 Dec 2017, In : Scientific Reports. 7, 1, 19 p., 6862.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles

Wang, J., Yang, B., Revote, J., Leier, A., Marquez-Lago, T. T., Webb, G., Song, J., Chou, K-C. & Lithgow, T., 1 Jan 2017, In : Bioinformatics. 33, 17, p. 2756-2758 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Sample-based attribute selective An DE for large data

Chen, S., Martinez, A. M., Webb, G. I. & Wang, L., 1 Jan 2017, In : IEEE Transactions on Knowledge and Data Engineering. 29, 1, p. 172-185 14 p., 7565579.

Research output: Contribution to journalArticleResearchpeer-review

SecretEPDB: A comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems

An, Y., Wang, J., Li, C., Revote, J., Zhang, Y., Naderer, T., Hayashida, M., Akutsu, T., Webb, G. I., Lithgow, T. & Song, J., 23 Jan 2017, In : Scientific Reports. 7, 10 p., 41031.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Selective AnDE for large data learning: A low-bias memory constrained approach

Chen, S., Martínez, A. M., Webb, G. I. & Wang, L., Feb 2017, In : Knowledge and Information Systems. 50, 2, p. 475-503 29 p.

Research output: Contribution to journalArticleResearchpeer-review

SimUSF: An efficient and effective similarity measure that is invariant to violations of the interval scale assumption

Fernando, T. L. & Webb, G. I., Jan 2017, In : Data Mining and Knowledge Discovery. 31, 1, p. 264-286 23 p.

Research output: Contribution to journalArticleResearchpeer-review

Specious rules: An efficient and effective unifying method for removing misleading and uninformative patterns in association rule mining

Hämäläinen, W. & Webb, G. I., 2017, Proceedings of the 17th SIAM International Conference on Data Mining: Houston, Texas, USA, 27 – 29 April , 2017. Chawla, N. & Wang, W. (eds.). Philadelphia, PA: Society for Industrial and Applied Mathematics SIAM Publications, p. 309-317 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

2016

ALRn: Accelerated higher-order logistic regression

Zaidi, N. A., Webb, G. I., Carman, M. J., Petitjean, F. & Cerquides, J., 1 Sep 2016, In : Machine Learning. 104, 2-3, p. 151-194 44 p.

Research output: Contribution to journalArticleResearchpeer-review

A multiple test correction for streams and cascades of statistical hypothesis tests

Webb, G. I. & Petitjean, F., 13 Aug 2016, KDD'16 / KDD 2016: Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, August 13-17, 2016, San Francisco, CA, USA. Smola, A. & Aggarwal, C. (eds.). New York, NY, USA: Association for Computing Machinery (ACM), p. 1255-1264 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

Characterizing concept drift

Webb, G. I., Hyde, R., Cao, H., Nguyen, H-L. & Petitjean, F., 1 Jul 2016, In : Data Mining and Knowledge Discovery. 30, 4, p. 964-994 31 p.

Research output: Contribution to journalArticleResearchpeer-review

Crysalis: An integrated server for computational analysis and design of protein crystallization

Wang, H., Feng, L., Zhang, Z., Webb, G. I., Lin, D. & Song, J., 24 Feb 2016, In : Scientific Reports. 6, 14 p., 21383.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Data Preparation

Abdallah, Z. S., Du, L. & Webb, G. I., 2016, Encyclopedia of Machine Learning and Data Mining. Sammut, C. & Webb, G. I. (eds.). Boston, MA: Humana Press, p. 318-327 10 p.

Research output: Chapter in Book/Report/Conference proceedingEncyclopaedia / Dictionary EntryOther

Open Access

Faster and more accurate classification of time series by exploiting a novel dynamic time warping averaging algorithm

Petitjean, F., Forestier, G., Webb, G. I., Nicholson, A. E., Chen, Y. & Keogh, E., 2016, In : Knowledge and Information Systems. 47, 1, p. 1 - 26 26 p.

Research output: Contribution to journalArticleResearchpeer-review