Professor Mark Girolami
http://www.dcs.gla.ac.uk/~girolami
Email:	girolami@dcs.gla.ac.uk
Location:	Room 302, Sir Alwyn Williams Building
Research interests:	Statistical Inference, Machine Learning, Systems Biology

Projects

• Inference-based Modelling in Population and Systems Biology
• CLIMB - Classifiers in Medicine and Biology (Advancing Machine Learning Methodology for New Classes of Prediction Problems)
• The Synthesis of Probabilistic Prediction & Mechanistic Modelling within a Computational & Systems Biology Context
• The Molecular Nose
• Stochastic modelling and statistical inference of gene regulatory pathways: integrating multiple sources of data
• Data Mining Tools for Fraud Detection
• Bayesian Inference in Systems Biology: Modelling Organ Specificity of Circadian Control in Plants
• Bayesian System Identification for Biological Pathway Modelling
• Probabilistic Reconstruction of Signalling Pathways & Identification of Novel Transcription Factors
• Machine Learning Strategies for Document Recognition and Validation
• Mathematical & Statistical Modelling of Cytokine Receptor Cross-Regulation by Cyclic Amp
• Cross Disciplinary Account - Computational Statistics and Cognitive Neuroscience
• Bayesian modelling of transmission of Streptococcus agalactiae and its antimicrobial resistance determinants in networks of humans and animals

Publications

• On the Fully Bayesian Treatment of Latent Gaussian Models using Stochastic Simulations (2012) FILIPPONE M. ZHONG M. GIROLAMI M. - DCS Technical Report Series (Dept of Computing Science, University of Glasgow, 36) (google scholar)
• Protein Interaction Detection in Sentences via Gaussian Processes: A preliminary evaluation (2010) POLAJNAR T. ROGERS S.D. GIROLAMI M. - International Journal of Data Mining and Bioinformatics (google scholar)
• Analysis of SVM with Indefinite Kernels (2010) GIROLAMI M. - NIPS 2009 (MIT Press) (google scholar)
• Predictive response-relevant clustering of expression data provides insights into disease processes (2010) HOPCROFT L.E. HARRIS K. GIROLAMI M. - Nucleic Acids Research (google scholar)
• Semi-Parametric Analysis of Multi-Rater Data (2009) ROGERS S.D. GIROLAMI M. POLAJNAR T. - Statistics and Computing (Springer) (google scholar)
• Accelerating Bayesian Inference over Nonlinear Differential Equations with Gaussian Processes (2009) CALDERHEAD B. GIROLAMI M. - Advances in Neural Information Processing Systems 21 (2009) (MIT Press, 217-224) (google scholar)
• Probabilistic assignment of formulas to mass peaks in metabolomics experiments (2009) ROGERS S.D. GIROLAMI M. - Bioinformatics, 25(4) (Oxford University Press, 512--518) (google scholar)
• Reversible Jump MCMC for Non-Negative Matrix Factorization (2009) ZHONG M. GIROLAMI M. - In D. Dyk and M. Welling, editors, Proceedings of the 12th International Conference on Artificial Intelligence and Statistics, volume 5, pages 663-670, 2009 (google scholar)
• Combining Feature Spaces for Classification (2009) DAMOULAS T. GIROLAMI M. - Pattern Recognition, Volume 42, Issue 11 (Elsevier Science, 2671-2683) (google scholar)
• Riemannian Manifold Hamiltonian Monte Carlo (2009) GIROLAMI M. CALDERHEAD B. - DCS Technical Report Series (Dept of Computing Science, University of Glasgow, 35) (google scholar)
• Class Prediction from Disparate Biological Data Sources using an Iterative Multi-kernel Algorithm (2009) DAMOULAS T. GIROLAMI M. - Lecture Notes in Bioinformatics, Proceedings of the 4th IAPR International Conference, Pattern Recognition in Bioinformatics 2009 (PRIB 2009) (Springer Verlag, 427-438) (google scholar)
• Estimating Bayes Factors via Thermodynamic Integration and Population MCMC (2009) CALDERHEAD B. GIROLAMI M. - Computational Statistics and Data Analysis 53 (2009). DOI information: 10.1016/j.csda.2009.07.025 (Elsevier Science, 4028-4045) (google scholar)
• Definition of Valid Proteomic Biomarkers: A Bayesian Solution (2009) HARRIS K. GIROLAMI M. - Pattern Recognition In Bioinformatics 2009 (Springer Verlag) (google scholar)
• Inferring Meta-covariates in Classification (2009) HARRIS K. GIROLAMI M. HOPCROFT L.E. - Pattern Recognition In Bioinformatics 2009 (Springer Verlag) (google scholar)
• Semi-supervised Prediction of Protein Interaction Sentences Exploiting Semantically Encoded Metrics (2009) POLAJNAR T. GIROLAMI M. - Lecture Notes in Bioinformatics, Proceedings of the 4th IAPR International Conference, Pattern Recognition in Bioinformatics 2009 (Springer Verlag, 270–281) (google scholar)
• Classification of Protein Interaction Sentences via Gaussian Processes (2009) POLAJNAR T. ROGERS S.D. GIROLAMI M. - Lecture Notes in Bioinformatics, Proceedings of 4th IAPR International Conference, Pattern Recognition in Bioinformatics 2009 (Springer Verlag, 282–292) (google scholar)
• Using Higher-Order Dynamic Bayesian Networks to Model Periodic Data from the Circadian Clock of Arabidopsis Thaliana (2009) DALY R. GIROLAMI M. - Proceedings of the Fourth IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2009) (LNCS, Springer, 67--78) (google scholar)
• Infinite Factorization of Multiple Non-parametric Views (2009) ROGERS S.D. GIROLAMI M. - Machine Learning (Springer) (google scholar)
• Bayesian Methods to Detect Dye Labelled DNA Oligonucleotides in Multiplexed Raman Spectra (2009) ZHONG M. GIROLAMI M. (google scholar)
• vbmp: Variational Bayesian Multinomial Probit Regression for multi-class classification in R (2008) GIROLAMI M. - Bioinformatics (Oxford University Press) (google scholar)
• Bayesian Ranking of Biochemical System Models (2008) VYSHEMIRSKY V. GIROLAMI M. - Bioinformatics (Oxford University Press) (google scholar)
• Classifying EEG for Brain Computer Interfaces Using Gaussian Processes (2008) ZHONG M. GIROLAMI M. - Pattern Recognition Letters (google scholar)
• ParCrys: A Parzen Window Density Estimation Approach to Protein Crystallisation Propensity Prediction (2008) GIROLAMI M. - Bioinformatics (Oxford University Press) (google scholar)
• Probabilistic multi-class multi-kernel learning: On protein fold recognition and remote homology detection (2008) DAMOULAS T. GIROLAMI M. - Bioinformatics, 24(10) (Oxford University Press, 1264-70) (google scholar)
• An Evaluation of Gaussian Processes for Sentence Classification and Protein Interaction Detection (2008) POLAJNAR T. ROGERS S.D. GIROLAMI M. - DCS Technical Report Series (Dept of Computing Science, University of Glasgow) (google scholar)
• BRCA1 and BRCA2 Missense Variants of High and Low Clinical Significance Influence Lymphoblastoid Cell Line Post-Irradiation Gene Expression (2008) GIROLAMI M. - PLoS Genetics (google scholar)
• Bayesian Inference for Differential Equations (2008) GIROLAMI M. - Theoretical Computer Science (Elsevier Science) (google scholar)
• BioBayes: A Software Package for Bayesian Inference in Systems Biology (2008) VYSHEMIRSKY V. GIROLAMI M. - Bioinformatics (Oxford University Press) (google scholar)
• Pattern recognition with a Bayesian kernel combination machine (2008) DAMOULAS T. GIROLAMI M. - Pattern Recognition Letters, Volume 30, Issue 1, (Elsevier Science) (google scholar)
• Inferring Sparse Kernel Combinations and Relevance Vectors: An application to subcellular localization of proteins (2008) DAMOULAS T. GIROLAMI M. - International Conference on Machine Learning and Applications, (IEEE) (google scholar)
• Sloppy Parameters in Oscillatory Systems with Unobserved Species (2008) CALDERHEAD B. GIROLAMI M. - Proceedings of the Fifth International Workshop on Computational Systems Biology (google scholar)
• Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models (2008) ROGERS S.D. GIROLAMI M. - Bioinformatics, Volume 24, Number 24 (Oxford University Press, pages 2894–2900) (google scholar)
• Kernel Maximum Entropy Data Transformation and an Enhanced Spectral Clustering Algorithm (2007) GIROLAMI M. - Twentieth Annual Conference on Neural Information Processing Systems - NIPS 2006 (MIT Press) (google scholar)
• Data Integration for Classification Problems Employing Gaussian Process Priors (2007) GIROLAMI M. ZHONG M. - Twentieth Annual Conference on Neural Information Processing Systems - NIPS 2006 (MIT Press) (google scholar)
• Sparse Multinomial Logistic Regression via Bayesian Regularisation using a Laplace Prior (2007) GIROLAMI M. - Twentieth Annual Conference on Neural Information Processing Systems - NIPS 2006 (MIT Press) (google scholar)
• Multi-class semi-supervised learning with the e-truncated multinomial probit Gaussian process (2007) ROGERS S.D. GIROLAMI M. - Proceeding of the Gaussian Processes in Practice Workshop, 2006 (google scholar)
• An empirical analysis of the probabilistic k-nearest neighbour classifier (2007) GIROLAMI M. - Pattern Recognition Letters, Volume 28, Number 13 (Elsevier Science, 1818-1824) (google scholar)
• Bayesian model-based inference of transcription factor activity (2007) ROGERS S.D. GIROLAMI M. - BMC Bioinformatics (google scholar)
• Detecting Worm Variants using Machine Learning (2007) SHARMA O. GIROLAMI M. SVENTEK J.S. - Proceedings of the 3rd International Conference on emerging Networking EXperiments and Technologies (CoNEXT), New York, NY, USA, December 2007 (ACM) (google scholar)
• Clustering via Kernel Decomposition (2006) GIROLAMI M. - IEEE Transactions on Neural Networks, Vol. 17, No. 1, pp. 256-264 (IEEE) (google scholar)
• Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors (2006) GIROLAMI M. ROGERS S.D. - Neural Computation, Volume 18, Number 8, pages 1790 - 1817. (MIT Press, 28) (google scholar)
• Identification of Prognostic Signatures in Breast Cancer Microarray Data using Bayesian Techniques (2006) ROGERS S.D. GIROLAMI M. - Journal of the Royal Society Interface, Vol.3, No.8. (google scholar)
• Accurate Prediction of BRCA1 and BRCA2 heterozygous genotype using expression profiling after induced DNA damage (2006) GIROLAMI M. - Clinical Cancer Research, Vol. 12, No. 13, pp. 3896 - 3901 (google scholar)
• A Bayesian analysis of the ERK signalling pathway (2006) VYSHEMIRSKY V. GIROLAMI M. - Department of Computing Science Technical Reports (google scholar)
• Sequential Activity Profiling : Latent Dirichlet Allocation of Markov Chains (2005) GIROLAMI M. - Data Mining and Knowledge Discovery, Vol 10, pp 175 - 196. (Kluwer) (google scholar)
• The Latent Process Decomposition of cDNA Microarray Datasets (2005) ROGERS S.D. GIROLAMI M. - IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 2, Number 2. (IEEE Computer Society Press, 143-156) (google scholar)
• A Bayesian Regression Approach to the Inference of Regulatory Networks from Gene Expression Data (2005) ROGERS S.D. GIROLAMI M. - Bioinformatics, Vol 21, Nos 14, pp 313 - 3137. (Oxford University Press) (google scholar)
• Hierarchic Bayesian Models for Kernel Learning (2005) GIROLAMI M. ROGERS S.D. (google scholar)
• Hierarchic Bayesian Models for Kernel Learning (2005) GIROLAMI M. ROGERS S.D. - Proceedings of 22nd International Conference on Machine Learning (google scholar)
• Disease Classification with Capillary Electrophoresis:Mass Spectrometry (2005) ROGERS S.D. GIROLAMI M. - International Conference for Advances in Pattern Recognition, Bath 2005 (google scholar)
• Probabilistic Hyperspace Analogue to Language (2005) AZZOPARDI L. GIROLAMI M. - Proceedings of the 28th Annual ACM Conference on Research and Development in Infomration Retrieval (SIGIR 2005) (google scholar)
• Employing Optimised Combinations of One-Class Classifiers for Automated Currency Validation (2004) HE C. GIROLAMI M. ROSS G. - Pattern Recognition Vol 37, Nos 6 (Elsevier Science, 1085-1096) (google scholar)
• Novelty Detection Employing an L2 Optimal Nonparametric Density Estimator (2004) HE C. GIROLAMI M. - Pattern Recognition Letters, Vol 25, Nos 12, pp 1389-1397. (Elsevier Science) (google scholar)
• Simplicial Mixtures of Markov Chains: Distributed Modelling of Dynamic User Profiles (2004) GIROLAMI M. - Advances in Neural Information Processing Systems 16, eds Sebastian Thrun and Lawrence Saul and Bernhard Scholkopf, MIT Press (MIT Press, 9 - 16) (google scholar)
• Biologically Valid Linear Factor Models of Gene Expression (2004) GIROLAMI M. - Bioinformatics, Vol 20, Nos 17, pp 3021 - 3033. (Oxford University Press, 26) (google scholar)
• User Biased Document Language Modelling (2004) AZZOPARDI L. GIROLAMI M. VAN RIJSBERGEN C.J. - (google scholar)
• Topic Based Language Models for Ad Hoc Information Retrieval (2004) AZZOPARDI L. GIROLAMI M. VAN RIJSBERGEN C.J. - Proceedings of the International Joint Conference in Neural Networks (IJCNN 2004) (google scholar)
• A Process for Automated Currency Validation (2003) GIROLAMI M. HE C. ROSS G. - (google scholar)
• Probability Density Estimation from Optimally Condensed Data Samples (2003) GIROLAMI M. HE C. - IEEE Transactions Pattern Analysis and Machine Intelligence (IEEE, v.25 no.10 1253-1264) (google scholar)
• On an Equivalence between PLSI and LDA (2003) GIROLAMI M. - 26th ACM Conference on Research and Development in Information Retrieval, SIGIR (google scholar)
• Investigating the Relationship between Language Model Perplexity and IR Precision-Recall Measures (2003) AZZOPARDI L. GIROLAMI M. VAN RIJSBERGEN C.J. - 26th ACM Conference on Research and Development in Ingormation Retrieval, SIGIR (google scholar)
• Orthogonal Series Density Estimation and the Kernel Eigenvalue Problem (2002) GIROLAMI M. - Neural Computation (MIT Press, v.13 No.4 669-668) (google scholar)
• Mercer Kernel Based Clustering in Feature Space (2002) GIROLAMI M. - IEEE Transactions on Neural Networks (IEEE, v.13, No.4, 780-784) (google scholar)
• A Dynamic Probabilistic Model to Visualise Topic Evolution in Text Streams (2002) GIROLAMI M. - Journal of Intelligent Information Systems (google scholar)
• A Probabilistic Framework for the Hierachic Organisation & Classification of Document Collections (2002) GIROLAMI M. - Journal of Intelligent Information Systems (google scholar)
• Fast extraction of Semantic features from a Latent Semantic Indexed Text Corpus (2002) GIROLAMI M. - Neural Processing Letters (google scholar)
• Topic Indentification in Chat line Discussions by Extracting Independent Minimum Complexity Time Components. (2002) GIROLAMI M. - Neural Processing Letters (google scholar)
• Advances in Infomration Retrieval (2002) GIROLAMI M. - 24th BCS-IRSG European Colloquium on IR Research, Glasgow, UK, 2002 (Springer Verlag) (google scholar)
• "Artificial Intelligence Systmes Techniques and Applications in Speech Processing" (2002) GIROLAMI M. - Intelligence Systems Technology and Applications, Vol.III Signal, Image and Speech processing, 1-48, Ed: C T Leondes (CRC Press, V.III 1-48) (google scholar)
• A General Framework for Principled Hierachical Visulisation of Multivariate Data (2002) GIROLAMI M. - Third International Conference on Intelligent Data Engineering and Automated Learnind (IDEAL`02) (google scholar)
• The Topographic Organisation and Visulisation of Binary Data using Mutivariate-Bernoulli Latent Variable Models (2001) GIROLAMI M. - IEEE Transactions on Neural Networks (IEE Publications, v.12, no.6, 1367-1374) (google scholar)
• Latent Variable Models for the Topographic Organisation of Discrete and Strictly Positive Data (2001) GIROLAMI M. - Neural Computation (MIT Press, v.48, no.1-4, 185-198) (google scholar)
• Kernel PCA for Feature Extraction and De-Noising in Non-Linear Regression (2001) GIROLAMI M. - Neural Computing and Applications (google scholar)
• A Combined Latent Class and Trait Model for the Analysis and Visualisation of Discrete Data (2001) GIROLAMI M. - IEEE Transactions on Pattern Analysis and Machine Intelligence (IEEE Computer Society Press, v.23, no.8 859-872) (google scholar)
• `ICA: Principles and Practice' (2001) GIROLAMI M. - Latent Class and Trait Models for Data Classification and Visulisation. Editors Stephen Roberts (Oxford University) & Richard Everson (Exeter University). (Cambridge University Press) (google scholar)
• A Variational Method for Learning Sparse and Overcomplete Representations (2001) GIROLAMI M. - Neural Computation (MIT Press, v.13, no.11, 2517-2532) (google scholar)
• An Expectation Maximisation Approach to Nonlinear Component Analysis (2001) GIROLAMI M. - Neural Computation (MIT Press) (google scholar)
• Document classification employing the Fisher kernel derived from probabilistic hierachic corpus representations (2001) GIROLAMI M. - (google scholar)
• Document classification employing the Fisher kernel derived from probabilistic hierachic corpus representations (2001) GIROLAMI M. - 23rd European Colloquium on IR Research (google scholar)
• Finding topics in dynamical text: application to chat line discussions (2001) GIROLAMI M. - 10th International World Wide Web Conference (WWW10) (google scholar)
• A Unifying Information Theoretic Framework for Independent Component Anylasis (2000) GIROLAMI M. - International Journal on Mathematical and Computer Modellling (google scholar)
• Perspective in Neural Computation (2000) GIROLAMI M. - Advances in Independent Component Analysis. Editor J.Taylor (Springer Verlag) (google scholar)
• A Unifying Information Theoretic Framework for Independent Component Analysis (2000) GIROLAMI M. - International Journal on Mathematical and Computer Modelling (google scholar)
• The Organisation and Visualisation of Document Corpoar: A Probabilistic Approach (2000) GIROLAMI M. - Invited paper, DEXA, 2000. 11'th International Conference and Workshop on Database and Expert Systems Applications (google scholar)
• Implementing Decisions in Binary Decision Trees Using Independent Component Analysis (2000) GIROLAMI M. - 2'nd International Workshop on Independent Component Analysis and Blind Source Separation, ICA'2000, Helsinki (google scholar)
• Clustering of Text Documents by Skewness Maximisation (2000) GIROLAMI M. - 2'nd International Workshop on Independent Component Analysis and Blind Source Separation, ICA'2000, Helsinki (google scholar)
• Kernel PCA Feature Extracton of Event-Related Potentials for Human Signal Detection Performance (2000) GIROLAMI M. - In proceedings of International Conference on Artificial Neural Networks in Medicine Biology. Editors Malmgen, Borga and Niklasson (google scholar)
• Extraction of Sleep-Spindles from the Electroencephalogram (2000) GIROLAMI M. - In proceedings of International Conference on Artificial Neural Networks in Medicine and Biology. Editors Malmgren, Borga and Niklasson (google scholar)
• A Generative Model for Sparse Discrete Binary Data with Non-Uniform Categorical Priors (2000) GIROLAMI M. - In proceedings of ESANN'00, European Symposium on Artificial Neural Networks (google scholar)
• Stochastic ICA Contrast Maximisation Using Oja's Nonlinear PCA Algorithm (1999) GIROLAMI M. - International Journal of Neural Systems (google scholar)
• Independent Component Analysis using an Extended Infomax Algorithm for Mixed Sub-Gaussian and Super-Gaussian Sources (1999) GIROLAMI M. - Neural Computation (google scholar)
• Blind Source Separation of More Sources Using Overcomplete Representations (1999) GIROLAMI M. - IEEE Signal Processing Letters (IEE, v.1, no.4 87-90) (google scholar)
• Self-Organising Neural Networks: Independent Component Analysis and Blind Signal Separation (1999) GIROLAMI M. - Perspectives in Neural Computatation, Editor J.Taylor (Springer Verlag) (google scholar)
• An Alternative Perspective on Adaptive Independent Component Analysis Algorithms (1998) GIROLAMI M. - Neural Computation (google scholar)
• A Common Neural Network Model for Exploratory Data Analysis and Independent Component Analysis (1998) GIROLAMI M. - IEEE Transactions on Neural Networks (IEEE, V 9, No.6 1495 -1501) (google scholar)
• The Latent Variable Data Model for Expolartory Data Analysis and Visualisation: A Generalisation of the Nonlinear Infomax Algorithm (1998) GIROLAMI M. - Neural Processing Letters (google scholar)
• A Nonlinear Model of the Binaural Cocktail Party Effect (1998) GIROLAMI M. - Neurocomputing (google scholar)
• Symmetric Adaptive Maximum Likelihood Estimation for Noise Cancellation and Signal Separation (1997) GIROLAMI M. - Electronics Letters (google scholar)
• Extraction of Independent Signal Sources using a Deflationary Exploratory Projection Persuit Network with Lateral Inhibition (1997) GIROLAMI M. - I.E.E. Proceedings on Vision, Image and Signal Processing (google scholar)
• An Extended Exploratory Projection Persuit Network with Linear and Nonlinear Anti-Hebbian Connections Applied to the Cocktail Party Problem (1997) GIROLAMI M. - Neural Networks (google scholar)
• Adaptive Processing Schemes Inspired by Binaural Unmasking for Enhancement of Speech Corrupted with Noise and Reverberation (1997) GIROLAMI M. - Neuromorphic Systems: Engineering Silicon for Neurobiology, Editors L.S.Smith and A.Hamilton (World Scientific, 61-74) (google scholar)
• A Temporal Model of Linear Anti-Hebbian Learning (1996) GIROLAMI M. - Neural Processing Letters (google scholar)

Posters

• Inference and Modelling in Systems Biology