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Padraig Cunningham

dblp:c/PadraigCunningham · also Pádraig Cunningham · DBLP profile ↗
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102ranked-venue papers
11as first author
5since 2021 · last 2025
0000-0002-3499-0810ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 66 · 8 first-author · 4 since 2021Databases, data management, data science and information retrieval · 33 · 3 first-authorApplied, interdisciplinary, general and emerging computing · 19 · 1 since 2021Graphics, computer vision, multimedia, augmented reality and games · 15 · 2 first-authorHuman-computer interaction and ubiquitous computing · 14

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Artificial intelligence
9 papers
Probabilistic and Bayesian machine learning · 37% Trustworthy machine learning · 33% Knowledge representation and reasoning · 19%
Databases, data mining, and information retrieval
4 papers
Data mining · 42% Web and social media mining · 34% Knowledge graphs · 24%
Interdisciplinary, comprehensive, and emerging computing
5 papers
Bioinformatics and computational biology · 79% Computational science and engineering · 18% Environmental and earth informatics · 4%
Theoretical computer science
1 paper
Distributed computing theory · 100%

Topics — the 30 heaviest of 34, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Machine learning › Trustworthy machine learning › interpretability
counterfactual explanation
0.512021
Exploring the Efficacy of Automatically Generated Counterfactuals for Sentiment Analysis · ACL/IJCNLP (1) 2021
Machine learning › Trustworthy machine learning
interpretability
0.512021
Exploring the Efficacy of Automatically Generated Counterfactuals for Sentiment Analysis · ACL/IJCNLP (1) 2021
Knowledge, reasoning and agents › Knowledge representation and reasoning
case-based reasoning
0.532018
Marathon Race Planning: A Case-Based Reasoning Approach · IJCAI 2018
A Taxonomy of Similarity Mechanisms for Case-Based Reasoning · IEEE Trans. Knowl. Data Eng. 2009
Hierarchical Case-Based Reasoning Integrating Case-Based and Decompositional Problem-Solving Techniques for Plant-Control Software Design · IEEE Trans. Knowl. Data Eng. 2001
Machine learning › Probabilistic and Bayesian machine learning › statistical inference
bayesian inference
0.212016
Online Trans-dimensional von Mises-Fisher Mixture Models for User Profiles · J. Mach. Learn. Res. 2016
Machine learning › Probabilistic and Bayesian machine learning › structured models › latent variable model
mixture model
0.212016
Online Trans-dimensional von Mises-Fisher Mixture Models for User Profiles · J. Mach. Learn. Res. 2016
Machine learning › Probabilistic and Bayesian machine learning › monte carlo methods › markov chain monte carlo
reversible jump MCMC
0.212016
Online Trans-dimensional von Mises-Fisher Mixture Models for User Profiles · J. Mach. Learn. Res. 2016
Machine learning › Probabilistic and Bayesian machine learning › structured models › latent variable model › mixture model
von mises-fisher mixture
0.212016
Online Trans-dimensional von Mises-Fisher Mixture Models for User Profiles · J. Mach. Learn. Res. 2016
Knowledge graphs
link prediction
0.212013
Link prediction with social vector clocks · KDD 2013
Web and social media mining
social network analysis
0.212013
Link prediction with social vector clocks · KDD 2013
Distributed computing theory › logical clocks
vector clocks
0.212013
Link prediction with social vector clocks · KDD 2013
Natural language and speech › Information extraction and text analysis
sentiment analysis
0.112021
Exploring the Efficacy of Automatically Generated Counterfactuals for Sentiment Analysis · ACL/IJCNLP (1) 2021
Bioinformatics and computational biology › gene expression analysis
clustering validation
0.122005
A knowledge-driven approach to cluster validity assessment · Bioinform. 2005
An integrated tool for microarray data clustering and cluster validity assessment · Bioinform. 2005
Bioinformatics and computational biology
gene expression analysis
0.122005
A knowledge-driven approach to cluster validity assessment · Bioinform. 2005
An integrated tool for microarray data clustering and cluster validity assessment · Bioinform. 2005
Machine learning › Representation and self-supervised learning
similarity measure
0.112009
A Taxonomy of Similarity Mechanisms for Case-Based Reasoning · IEEE Trans. Knowl. Data Eng. 2009
Computational science and engineering › numerical linear algebra
matrix factorization
0.112008
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions · Bioinform. 2008
Bioinformatics and computational biology › protein analysis
protein-protein interaction
0.112008
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions · Bioinform. 2008
Data mining
clustering
0.122006
Practical solutions to the problem of diagonal dominance in kernel document clustering · ICML 2006
An integrated tool for microarray data clustering and cluster validity assessment · Bioinform. 2005
Data mining › predictive analytics
churn prediction
0.112016
Online Trans-dimensional von Mises-Fisher Mixture Models for User Profiles · J. Mach. Learn. Res. 2016
Web and social media mining › user behavior analysis
user behavior modeling
0.112016
Online Trans-dimensional von Mises-Fisher Mixture Models for User Profiles · J. Mach. Learn. Res. 2016
Data mining › clustering
document clustering
0.112006
Practical solutions to the problem of diagonal dominance in kernel document clustering · ICML 2006
Data mining › clustering
kernel clustering
0.112006
Practical solutions to the problem of diagonal dominance in kernel document clustering · ICML 2006
Machine learning › Probabilistic and Bayesian machine learning › statistical inference
density estimation
0.112005
Predicting probability distributions for surf height using an ensemble of mixture density networks · ICML 2005
Machine learning › Kernel, tree and ensemble methods
ensemble learning
0.112005
Sequential Genetic Search for Ensemble Feature Selection · IJCAI 2005
Machine learning › Probabilistic and Bayesian machine learning › structured models › latent variable model › mixture model
mixture density network
0.112005
Predicting probability distributions for surf height using an ensemble of mixture density networks · ICML 2005
Bioinformatics and computational biology › gene expression analysis › gene expression clustering
microarray data clustering
0.112005
An integrated tool for microarray data clustering and cluster validity assessment · Bioinform. 2005
Machine learning › Kernel, tree and ensemble methods › kernel methods
kernel learning
0.012009
A Taxonomy of Similarity Mechanisms for Case-Based Reasoning · IEEE Trans. Knowl. Data Eng. 2009
Bioinformatics and computational biology › knowledge representation in biology › biomedical ontology
gene ontology semantic similarity
0.012005
A knowledge-driven approach to cluster validity assessment · Bioinform. 2005
Environmental and earth informatics
meteorology
0.012005
Predicting probability distributions for surf height using an ensemble of mixture density networks · ICML 2005
Data mining › clustering › clustering evaluation
cluster number estimation
0.012005
An integrated tool for microarray data clustering and cluster validity assessment · Bioinform. 2005
Knowledge, reasoning and agents › Knowledge representation and reasoning
qualitative reasoning
0.011987
Qualitative Reasoning in Electronic Fault Diagnosis · IJCAI 1987

Methods — techniques the papers use, named apart from their topics

case-based reasoning · 0.7reversible jump MCMC · 0.5counterfactual generation · 0.5collapsed gibbs sampling · 0.5ensemble learning · 0.1clustering · 0.1cluster validation · 0.1taxonomy construction · 0.1kernel function · 0.1hierarchical clustering · 0.1ensemble non-negative matrix factorization · 0.1kernel methods · 0.1SVM · 0.1sequential search · 0.1semantic similarity · 0.1mixture density networks · 0.1mixture density network · 0.1genetic search · 0.1
YearPublicationVenuePosition
2025 Fade: fairness-aware deep ensemble for quantifying uncertainty
William Blanzeisky, Padraig Cunningham
Neural Comput. Appl.2
2023 Towards Globalised Models for Exercise Classification using Inertial Measurement Units
abstract
Wearable sensors are becoming a popular method of objectively evaluating motor performance in various exercise tasks. A challenge in working with this motion capture data is the personalised nature of the data where one individual’s data may be different to that of others due to factors such as differences in exercise form. Hence global models generally perform poorly in this domain. The aim of this study is to investigate a technique to push personalised classification models into global models. In this research, a dataset of Inertial Measurement Unit data consisting of fatigued and non-fatigued running is used to employ a clustering strategy where participants are grouped together using a hierarchical clustering methodology. These clusters are used to form semi-globalised models. The investigation shows that this strategy can improve the global model performance by up to 20%.
Bahavathy Kathirgamanathan, Brian Caulfield 0001, Padraig Cunningham
BSN3
2023 Addressing Underestimation Bias in CBR Through Case-Base Maintenance
William Blanzeisky, Padraig Cunningham
ICCBR2
2022 Algorithmic Bias and Fairness in Case-Based Reasoning
William Blanzeisky, Barry Smyth, Padraig Cunningham
ICCBR3
2021 Exploring the Efficacy of Automatically Generated Counterfactuals for Sentiment Analysis
abstract
Linyi Yang, Jiazheng Li, Padraig Cunningham, Yue Zhang, Barry Smyth, Ruihai Dong. Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2021.
Linyi Yang, Jiazheng Li 0002, Padraig Cunningham, Yue Zhang 0004, Barry Smyth, Ruihai Dong
ACL/IJCNLP (1)3
2019 Scoring Performance on the Y-Balance Test
Vivek Mahato, William Johnston, Padraig Cunningham
ICCBR3
2018 An Analysis of Case Representations for Marathon Race Prediction and Planning
Barry Smyth, Padraig Cunningham
ICCBR2
2018 Marathon Race Planning: A Case-Based Reasoning Approach
abstract
We describe and evaluate a novel application of case-based reasoning to help marathon runners to achieve a personal best by: (a) predicting a challenging, but realistic race-time; and (b) recommending a race-plan to achieve this time.
Barry Smyth, Padraig Cunningham
IJCAI2
2017 Running with Cases: A CBR Approach to Running Your Best Marathon
Barry Smyth, Padraig Cunningham
ICCBR2
2017 A Novel Recommender System for Helping Marathoners to Achieve a New Personal-Best
abstract
We describe a novel application for recommender systems -- helping marathon runners to run a new personal-best race-time -- by predicting a challenging, but achievable target-time, and by recommending a tailored race-plan to achieve this time. A comprehensive evaluation of prediction accuracy and race-plan quality is provided using a large-scale dataset with almost 400,000 runners from the last 12 years of the Chicago marathon.
Barry Smyth, Padraig Cunningham
RecSys2
2016 Time Series Analysis of VLE Activity Data
Ewa Mlynarska, Padraig Cunningham, Derek Greene
EDM2
2016 Online Trans-dimensional von Mises-Fisher Mixture Models for User Profiles
abstract
The proliferation of online communities has attracted much attention to modelling user behaviour in terms of social interaction, language adoption and contribution activity. Nevertheless, when applied to large-scale and cross-platform behavioural data, existing approaches generally suffer from expressiveness, scalability and generality issues. This paper proposes trans-dimensional von Mises-Fisher (TvMF) mixture models for $\mathcal{L}_{2}$ normalised behavioural data, which encapsulate: (1) a Bayesian framework for vMF mixtures that enables prior knowledge and information sharing among clusters, (2) an extended version of reversible jump MCMC algorithm that allows adaptive changes in the number of clusters for vMF mixtures when the model parameters are updated, and (3) an online TvMF mixture model that accommodates the dynamics of clusters for time-varying user behavioural data. We develop efficient collapsed Gibbs sampling techniques for posterior inference, which facilitates parallelism for parameter updates. Empirical results on simulated and real-world data show that the proposed TvMF mixture models can discover more interpretable and intuitive clusters than other widely-used models, such as k-means, non-negative matrix factorization (NMF), Dirichlet process Gaussian mixture models (DP-GMM), and dynamic topic models (DTM). We further evaluate the performance of proposed models in real-world applications, such as the churn prediction task, that shows the usefulness of the features generated.
Xiangju Qin, Padraig Cunningham, Michael Salter-Townshend
J. Mach. Learn. Res.2
2015 An analysis of the coherence of descriptors in topic modeling
Derek O'Callaghan, Derek Greene, Joe Carthy, Padraig Cunningham
Expert Syst. Appl.4
2015 Integration of multiple network views in Wikipedia
Padraig Cunningham
Knowl. Inf. Syst.2
2014 Online social media in the Syria conflict: Encompassing the extremes and the in-betweens
abstract
The Syria conflict has been described as the most socially mediated in history, with online social media playing a particularly important role. At the same time, the ever-changing landscape of the conflict leads to difficulties in applying analytical approaches taken by other studies of online political activism. Therefore, in this paper, we use an approach that does not require strong prior assumptions or the proposal of an advance hypothesis to analyze Twitter and YouTube activity of a range of protagonists to the conflict, in an attempt to reveal additional insights into the relationships between them. By means of a network representation that combines multiple data views, we uncover communities of accounts falling into four categories that broadly reflect the situation on the ground in Syria. A detailed analysis of selected communities within the anti-regime categories is provided, focusing on their central actors, preferred online platforms, and activity surrounding “real world” events. Our findings indicate that social media activity in Syria is considerably more convoluted than reported in many other studies of online political activism, suggesting that alternative analytical approaches can play an important role in this type of scenario.
Derek O'Callaghan, Nico Prucha, Derek Greene, Maura Conway, Joe Carthy, Padraig Cunningham
ASONAM6
2014 The Contribution of Morphological Features in the Classification of Prostate Carcinoma in Digital Pathology Images
abstract
In this paper we present work on the development of a system for automated classification of digitized H&E histopathology images of prostate carcinoma (PCa). In our system, images are transformed into a tiled grid from which various texture and morphological features are extracted. We evaluate the contribution of high-level morphological features such as those derived from tissue segmentation algorithms as they relate to the accuracy of our classifier models. We also present work on an algorithm for tissue segmentation in image tiles, and introduce a novel feature vector representation of tissue classes in same. Finally, we present the classification accuracy, sensitivity and specificity results of our system when performing three tasks: distinguishing between cancer and non-cancer tiles, between low and high-grade cancer and between Gleason grades 3, 4 and 5. Our results show that the novel tissue representation outperforms the morphological features derived from tissue segmentation by a significant margin, but that neither feature sets improve on the accuracy gained by features from low-level texture methods.
Nicholas McCarthy, Padraig Cunningham, Gillian O'Hurley
ICPR2
2014 Exploring the Relationship between Membership Turnover and Productivity in Online Communities
Xiangju Qin, Michael Salter-Townshend, Padraig Cunningham
ICWSM3
2014 How Many Topics? Stability Analysis for Topic Models
Derek Greene, Derek O'Callaghan, Padraig Cunningham
ECML/PKDD (1)3
2013 Simmelian backbones: amplifying hidden homophily in Facebook networks
abstract
Empirical social networks are often aggregate proxies for several heterogeneous relations. In online social networks, for instance, interactions related to friendship, kinship, business, interests, and other relationships may all be represented as catchall "friendships." Because several relations are mingled into one, the resulting networks exhibit relatively high and uniform density. As a consequence, the variation in positional differences and local cohesion may be too small for reliable analysis.
Bobo Nick, Conrad Lee, Padraig Cunningham, Ulrik Brandes
ASONAM3
2013 Temporal subgraph isomorphism
abstract
Temporal information is increasingly available with network data sets. This information can expose underlying processes in the data via sequences of link activations. Examples range from the propagation of ideas through a scientific collaboration network, to the spread of disease via contacts between infected and susceptible individuals. We focus on the flow of funds through an online financial transaction network, in which given patterns might signify suspicious behaviour. The search for these patterns may be formulated as a temporally constrained subgraph isomorphism problem. We compare two algorithms which use temporal data at different stages during the search, and empirically demonstrate one to be significantly more efficient.
Ursula Redmond, Padraig Cunningham
ASONAM2
2013 Link prediction with social vector clocks
abstract
State-of-the-art link prediction utilizes combinations of complex features derived from network panel data. We here show that computationally less expensive features can achieve the same performance in the common scenario in which the data is available as a sequence of interactions. Our features are based on social vector clocks, an adaptation of the vector-clock concept introduced in distributed computing to social interaction networks. In fact, our experiments suggest that by taking into account the order and spacing of interactions, social vector clocks exploit different aspects of link formation so that their combination with previous approaches yields the most accurate predictor to date.
Conrad Lee, Bobo Nick, Ulrik Brandes, Padraig Cunningham
KDD4
2013 A temporal network analysis reveals the unprofitability of arbitrage in The Prosper Marketplace
Ursula Redmond, Padraig Cunningham
Expert Syst. Appl.2
2012 The Geographic Flow of Music
abstract
The social media website last.fm provides a detailed snapshot of what its users in hundreds of cities listen to each week. After suitably normalizing this data, we use it to test one hypothesis related to the geographic flow of music: that some cities are consistently early adopters of new music (and early to snub stale music). To test this hypothesis, we adapt a method previously used to detect the leadership networks present in flocks of birds. We find empirical support for the claim that a similar leadership network exists among cities.
Conrad Lee, Padraig Cunningham
ASONAM2
2012 EgoNav: exploring networks through egocentric spatializations
abstract
EgoNav is a visual analytics system that characterizes egos based on the relationship structure of their egocentric networks and presents the results as a spatialization. An ego, or individual node in a network, is most closely related to its neighbors, and to a lesser degree, to its neighbor's neighbors. For example, in social networks, people are closely related to their friends and family. In financial networks, the affairs of borrowers and lenders are more closely tied to each other. In fact, the relationship structure surrounding an ego, or an egocentric network, can provide characteristic information about the ego itself. Using network motif analysis and dimensionality reduction techniques, the system places egos in similar areas of a spatialization if their egocentric networks are structurally similar. This view of a network discriminates between the various classes of typical and exceptional egos. We demonstrate its effectiveness using appropriate synthetic datasets, real-world mobile phone call and peer-to-peer lending datasets. We subsequently elicit user feedback from experts involved in the investigation of financial fraud to assess the tool's applicability in this domain.
Martin Harrigan, Daniel Archambault, Padraig Cunningham, Neil J. Hurley
AVI3
2012 Network Analysis of Recurring YouTube Spam Campaigns
Derek O'Callaghan, Martin Harrigan, Joe Carthy, Padraig Cunningham
ICWSM4
2012 A system for twitter user list curation
abstract
With increased adoption of social networking tools, it is becoming more difficult to extract useful information from the mass of data generated daily by users. Curation of content and sources is an important filter in separating the signal from noise. A good set of credible sources often requires painstaking manual curation, which often yields incomplete coverage of a topic. In this demo, we present a recommender system to aid this process, improving the quality and quantity of sources. The system is highly-adaptable to the goals of the curator, enabling some novel uses for curating and monitoring lists of users.
Igor Brigadir, Derek Greene, Padraig Cunningham
RecSys3
2011 Identifying Representative Textual Sources in Blog Networks
Karen Wade, Derek Greene, Conrad Lee, Daniel Archambault, Padraig Cunningham
ICWSM5
2010 Tracking the Evolution of Communities in Dynamic Social Networks
abstract
Real-world social networks from a variety of domains can naturally be modelled as dynamic graphs. However, approaches to detecting communities have largely focused on identifying communities in static graphs. Recently, researchers have begun to consider the problem of tracking the evolution of groups of users in dynamic scenarios. Here we describe a model for tracking the progress of communities over time in a dynamic network, where each community is characterised by a series of significant evolutionary events. This model is used to motivate a community-matching strategy for efficiently identifying and tracking dynamic communities. Evaluations on synthetic graphs containing embedded events demonstrate that this strategy can successfully track communities over time in volatile networks. In addition, we describe experiments exploring the dynamic communities detected in a real mobile operator network containing millions of users.
Derek Greene, Dónal Doyle, Padraig Cunningham
ASONAM3
2010 Using Crowdsourcing and Active Learning to Track Sentiment in Online Media
Anthony Brew, Derek Greene, Padraig Cunningham
ECAI3
2010 Vector Quantization Mappings for Speaker Verification
abstract
In speaker verification several techniques have emerged to map variable length utterances into a fixed dimensional space for classification. One popular approach uses Maximum A-Posteriori (MAP) adaptation of a Gaussian Mixture Model (GMM) to create a super-vector. This paper investigates using Vector Quantisation (VQ) as the global model to provide a similar mapping. This less computationally complex mapping gives comparable results to its GMM counterpart while also providing the ability for an efficient iterative update enabling media files to be scanned with a fixed length window.
Anthony Brew, Padraig Cunningham
ICPR2
2010 Merging multiple criteria to identify suspicious reviews
abstract
Assessing the trustworthiness of reviews is a key issue for the maintainers of opinion sites such as TripAdvisor, given the rewards that can be derived from posting false or biased reviews. In this paper we present a number of criteria that might be indicative of suspicious reviews and evaluate alternative methods for integrating these criteria to produce a unified "suspiciousness" ranking. The criteria derive from characteristics of the network of reviewers and also from analysis of the content and impact of reviews and ratings. The integration methods that are evaluated are singular value decomposition and the unsupervised hedge algorithm. These alternatives are evaluated in a user study on TripAdvisor reviews, where volunteers were asked to rate the suspiciousness of reviews that have been highlighted by the criteria.
Derek Greene, Padraig Cunningham
RecSys3
2010 Missing value imputation for epistatic MAPs
abstract
BACKGROUND: Epistatic miniarray profiling (E-MAPs) is a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typically take the form of a symmetric pairwise matrix of interaction scores. These datasets have a significant number of missing values - up to 35% - that can reduce the effectiveness of some data analysis techniques and prevent the use of others. An effective method for imputing interactions would therefore increase the types of possible analysis, as well as increase the potential to identify novel functional interactions between gene pairs. Several methods have been developed to handle missing values in microarray data, but it is unclear how applicable these methods are to E-MAP data because of their pairwise nature and the significantly larger number of missing values. Here we evaluate four alternative imputation strategies, three local (Nearest neighbor-based) and one global (PCA-based), that have been modified to work with symmetric pairwise data. RESULTS: We identify different categories for the missing data based on their underlying cause, and show that values from the largest category can be imputed effectively. We compare local and global imputation approaches across a variety of distinct E-MAP datasets, showing that both are competitive and preferable to filling in with zeros. In addition we show that these methods are effective in an E-MAP from a different species, suggesting that pairwise imputation techniques will be increasingly useful as analogous epistasis mapping techniques are developed in different species. We show that strongly alleviating interactions are significantly more difficult to predict than strongly aggravating interactions. Finally we show that imputed interactions, generated using nearest neighbor methods, are enriched for annotations in the same manner as measured interactions. Therefore our method potentially expands the number of mapped epistatic interactions. In addition we make implementations of our algorithms available for use by other researchers. CONCLUSIONS: We address the problem of missing value imputation for E-MAPs, and suggest the use of symmetric nearest neighbor based approaches as they offer consistently accurate imputations across multiple datasets in a tractable manner.
Colm J. Ryan, Derek Greene, Gerard Cagney, Padraig Cunningham
BMC Bioinform.4
2010 Noise reduction for instance-based learning with a local maximal margin approach
Nicola Segata, Enrico Blanzieri, Sarah Jane Delany, Padraig Cunningham
J. Intell. Inf. Syst.4
2010 Partitioning large networks without breaking communities
Anand Narasimhamurthy, Derek Greene, Neil J. Hurley, Padraig Cunningham
Knowl. Inf. Syst.4
2010 Combining cohort and UBM models in open set speaker detection
Anthony Brew, Padraig Cunningham
Multim. Tools Appl.2
2009 A Scalable Noise Reduction Technique for Large Case-Based Systems
Nicola Segata, Enrico Blanzieri, Padraig Cunningham
ICCBR3
2009 A Matrix Factorization Approach for Integrating Multiple Data Views
Derek Greene, Padraig Cunningham
ECML/PKDD (1)2
2009 Gaining insight through case-based explanation
Conor Nugent, Dónal Doyle, Padraig Cunningham
J. Intell. Inf. Syst.3
2009 A Taxonomy of Similarity Mechanisms for Case-Based Reasoning
abstract
Assessing the similarity between cases is a key aspect of the retrieval phase in case-based reasoning (CBR). In most CBR work, similarity is assessed based on feature value descriptions of cases using similarity metrics, which use these feature values. In fact, it might be said that this notion of a feature value representation is a defining part of the CBR worldview-it underpins the idea of a problem space with cases located relative to each other in this space. Recently, a variety of similarity mechanisms have emerged that are not founded on this feature space idea. Some of these new similarity mechanisms have emerged in CBR research and some have arisen in other areas of data analysis. In fact, research on kernel-based learning is a rich source of novel similarity representations because of the emphasis on encoding domain knowledge in the kernel function. In this paper, we present a taxonomy that organizes these new similarity mechanisms and more established similarity mechanisms in a coherent framework.
Padraig Cunningham
IEEE Trans. Knowl. Data Eng.1
2008 Parallel integration of heterogeneous genome-wide data sources
abstract
Heterogeneous genome-wide data sources capture information on various aspects of complex biological systems. For instance, transcriptome, interactome and phenome-level information may be derived from mRNA expression data, protein-protein interaction networks, and biomedical literature corpora. Each source provides a distinct ldquoviewrdquo of the same domain, but potentially encodes different biologically-relevant patterns. Effective integration of such views can provide a richer, more informative model of an organismpsilas functional modules than that produced on a single view alone. Existing machine learning strategies for information fusion largely focus on the production of a consensus model that reflects patterns shared between views. However, the information provided by different views may not always be easily reconciled, due to the incomplete nature of the data, or the fact that some patterns will be present in one view but not in another. To address this problem, we present the Parallel Integration Clustering Algorithm (PICA), a novel cluster analysis approach which supports the simultaneous integration of information from two or more sources. The resulting model preserves patterns that are unique to individual views, as well as those common to all views. We demonstrate the effectiveness of PICA in identifying significant patterns corresponding to functional groupings, when applied to three genome-wide datasets.
Derek Greene, Kenneth Bryan, Padraig Cunningham
BIBE3
2008 Unsupervised retrieval of attack profiles in collaborative recommender systems
abstract
Trust, reputation and recommendation are key components of successful e-commerce systems. However, e-commerce systems are also vulnerable in this respect because there are opportunities for sellers to gain advantage through manipulation of reputation and recommendation. One such vulnerability is the use of fraudulent user profiles to boost (or damage) the ratings of items in an online recommender system. In this paper we cast this problem as a problem of detecting anomalous structure in network analysis and propose a novel mechanism for detecting this anomalous structure. We present an evaluation that shows that this approach is effective at uncovering the types of recommender systems attack described in the literature.
Kenneth Bryan, Michael P. O'Mahony, Padraig Cunningham
RecSys3
2008 Ensemble non-negative matrix factorization methods for clustering protein-protein interactions
abstract
MOTIVATION: When working with large-scale protein interaction data, an important analysis task is the assignment of pairs of proteins to groups that correspond to higher order assemblies. Previously a common approach to this problem has been to apply standard hierarchical clustering methods to identify such a groups. Here we propose a new algorithm for aggregating a diverse collection of matrix factorizations to produce a more informative clustering, which takes the form of a 'soft' hierarchy of clusters. RESULTS: We apply the proposed Ensemble non-negative matrix factorization (NMF) algorithm to a high-quality assembly of binary protein interactions derived from two proteome-wide studies in yeast. Our experimental evaluation demonstrates that the algorithm lends itself to discovering small localized structures in this data, which correspond to known functional groupings of complexes. In addition, we show that the algorithm also supports the assignment of putative functions for previously uncharacterized proteins, for instance the protein YNR024W, which may be an uncharacterized component of the exosome.
Derek Greene, Gerard Cagney, Nevan J. Krogan, Padraig Cunningham
Bioinform.4
2008 MetaFIND: A feature analysis tool for metabolomics data
abstract
BACKGROUND: Metabolomics, or metabonomics, refers to the quantitative analysis of all metabolites present within a biological sample and is generally carried out using NMR spectroscopy or Mass Spectrometry. Such analysis produces a set of peaks, or features, indicative of the metabolic composition of the sample and may be used as a basis for sample classification. Feature selection may be employed to improve classification accuracy or aid model explanation by establishing a subset of class discriminating features. Factors such as experimental noise, choice of technique and threshold selection may adversely affect the set of selected features retrieved. Furthermore, the high dimensionality and multi-collinearity inherent within metabolomics data may exacerbate discrepancies between the set of features retrieved and those required to provide a complete explanation of metabolite signatures. Given these issues, the latter in particular, we present the MetaFIND application for 'post-feature selection' correlation analysis of metabolomics data. RESULTS: In our evaluation we show how MetaFIND may be used to elucidate metabolite signatures from the set of features selected by diverse techniques over two metabolomics datasets. Importantly, we also show how MetaFIND may augment standard feature selection and aid the discovery of additional significant features, including those which represent novel class discriminating metabolites. MetaFIND also supports the discovery of higher level metabolite correlations. CONCLUSION: Standard feature selection techniques may fail to capture the full set of relevant features in the case of high dimensional, multi-collinear metabolomics data. We show that the MetaFIND 'post-feature selection' analysis tool may aid metabolite signature elucidation, feature discovery and inference of metabolic correlations.
Kenneth Bryan, Lorraine Brennan, Padraig Cunningham
BMC Bioinform.3
2007 BALBOA: Extending Bicluster Analysis to Classify ORFs using Expression Data
abstract
Microarrays have the capacity to measure the expressions of thousands of genes in parallel over many experimental samples. The unsupervised technique of bicluster analysis has been employed previously to uncover gene expression correlations over subsets of samples with the aim of modelling the natural gene functional classes. However the bicluster model also has the potential to shed light on the functions of unannotated open reading frames (ORFs). This aspect of biclustering has been under-explored. In this work we illustrate how the bicluster representation of expression data may be extended to enable putative functional classification of unannotated ORFs. We develop an ORF annotation approach, referred to as BALBOA, in which classifiers are constructed from the class specific expression patterns discovered by bicluster analysis. We demonstrate the efficacy of this approach via cross validation and carry out a comparative evaluation with kNN classification across three yeast expression datasets. Finally, we assign putative functions to unannotated ORFs and attempt to corroborate the best supported annotations with external experimental and protein sequence information.
Kenneth Bryan, Padraig Cunningham
BIBE2
2007 Constraint Selection by Committee: An Ensemble Approach to Identifying Informative Constraints for Semi-supervised Clustering
Derek Greene, Padraig Cunningham
ECML2
2006 Comparison of the Data-based and Gene Ontology-Based Approaches to Cluster Validation Methods for Gene Microarrays
abstract
The paper presents a comparison of the data-based and gene ontology (GO)-based approaches to cluster validation methods for gene microarray analysis. We apply a homogeneous approach to obtaining metrics from different GO-based similarity measures and a normalization of validation index values, that allows us to compare them to each other as well as to data-based validation indices. The results show strong correlation between both GO-based and data-based validation indices. The results suggest that this may represent an effective tool to support biomedical knowledge discovery tasks based on gene expression data
Nadia Bolshakova, Anton Zamolotskikh, Padraig Cunningham
CBMS3
2006 Handling Local Concept Drift with Dynamic Integration of Classifiers: Domain of Antibiotic Resistance in Nosocomial Infections
abstract
In the real world concepts and data distributions are often not stable but change with time. This problem, known as concept drift, complicates the task of learning a model from data and requires special approaches, different from commonly used techniques, which treat arriving instances as equally important contributors to the target concept. Among the most popular and effective approaches to handle concept drift is ensemble learning, where a set of models built over different time periods is maintained and the best model is selected or the predictions of models are combined. In this paper we consider the use of an ensemble integration technique that helps to better handle concept drift at the instance level. Our experiments with real-world antibiotic resistance data demonstrate that dynamic integration of classifiers built over small time intervals can be more effective than globally weighted voting which is currently the most commonly used integration approach for handling concept drift with ensembles
Alexey Tsymbal, Mykola Pechenizkiy, Padraig Cunningham, Seppo Puuronen
CBMS3
2006 Bottom-Up Biclustering of Expression Data
abstract
In a gene expression data matrix a bicluster is a sub-matrix of genes and conditions that exhibits a high correlation of expression activity across both rows and columns. The premise behind biclustering is that even related genes may only be expressed in a synchronized fashion over certain conditions. Conventional clustering groups over all features and may not capture these local relationships. Biclustering has the potential to retrieve these local signals and also to model overlapping groups of genes. These factors allow better representation of the natural state of functional modules in the cell. The mean squared residue is a popular measure of bicluster quality. One drawback however is that it is biased toward flat biclusters with low row variance. In this paper we introduce an improved bicluster score that removes this bias and promotes the discovery the most significant biclusters in the dataset. We employ this score within a new biclustering approach based on the bottom-up search strategy. We believe that the bottom-up search approach better models the underlying functional modules of the gene expression dataset. We evaluate our new score against the mean squared residue score using a yeast cell cycle expression dataset. We then carry out a comparative analysis of our biclustering technique against previously published clustering and biclustering approaches. Lastly, we use the biclusters discovered by our method to attempt to putatively annotate unclassified genes
Kenneth Bryan, Padraig Cunningham
CIBCB2
2006 Calibrating Probability Density Forecasts with Multi-Objective Search
Michael Carney, Padraig Cunningham
ECAI2
2006 ECUE: A Spam Filter that Uses Machine Leaming to Track Concept Drift
Sarah Jane Delany, Padraig Cunningham, Barry Smyth
ECAI2
2006 Making Good Probability Estimates for Regression
Michael Carney, Padraig Cunningham
ECML2
2006 Efficient Prediction-Based Validation for Document Clustering
Derek Greene, Padraig Cunningham
ECML2
2006 Dynamic Integration with Random Forests
Alexey Tsymbal, Mykola Pechenizkiy, Padraig Cunningham
ECML3
2006 Practical solutions to the problem of diagonal dominance in kernel document clustering
abstract
In supervised kernel methods, it has been observed that the performance of the SVM classifier is poor in cases where the diagonal entries of the Gram matrix are large relative to the off-diagonal entries. This problem, referred to as diagonal dominance, often occurs when certain kernel functions are applied to sparse high-dimensional data, such as text corpora. In this paper we investigate the implications of diagonal dominance for unsupervised kernel methods, specifically in the task of document clustering. We propose a selection of strategies for addressing this issue, and evaluate their effectiveness in producing more accurate and stable clusterings.
Derek Greene, Padraig Cunningham
ICML2
2006 An Evaluation of the Usefulness of Explanation in a Case-Based Reasoning System for Decision Support in Bronchiolitis Treatment
abstract
The research presented here explores the hypothesis that the deployment and acceptance of decision support systems in medicine will be enhanced if the basis for the recommendation produced by the system is apparent. We describe a decision support system for advising on patients suffering from bronchiolitis. This system supports its recommendations with precedent cases selected to support the recommendation along with justification text that highlights aspects of these cases relevant to the query case. It also presents an estimate of its confidence in the recommendation. The main contribution of this paper is an evaluation of this system in a clinical context. The evaluation shows that this type of explanation does enhance the usefulness of the system for practitioners.
Dónal Doyle, Padraig Cunningham, Paul Walsh
Comput. Intell.2
2006 Discrete wavelet packet transform and ensembles of lazy and eager learners for music genre classification
Marco Grimaldi, Padraig Cunningham, Anil C. Kokaram
Multim. Syst.2
2006 Application of Simulated Annealing to the Biclustering of Gene Expression Data
abstract
In a gene expression data matrix, a bicluster is a submatrix of genes and conditions that exhibits a high correlation of expression activity across both rows and columns. The problem of locating the most significant bicluster has been shown to be NP-complete. Heuristic approaches such as Cheng and Church's greedy node deletion algorithm have been previously employed. It is to be expected that stochastic search techniques such as evolutionary algorithms or simulated annealing might improve upon such greedy techniques. In this paper we show that an approach based on simulated annealing is well suited to this problem, and we present a comparative evaluation of simulated annealing and node deletion on a variety of datasets. We show that simulated annealing discovers more significant biclusters in many cases. Furthermore, we also test the ability of our technique to locate biologically verifiable biclusters within an annotated set of genes.
Kenneth Bryan, Padraig Cunningham, Nadia Bolshakova
IEEE Trans. Inf. Technol. Biomed.2
2005 Biclustering of Expression Data Using Simulated Annealing
abstract
In a gene expression data matrix a bicluster is a grouping of a subset of genes and a subset of conditions which show correlating levels of expression activity. The difficulty of finding significant biclusters in gene expression data grows exponentially with the size of the dataset and heuristic approaches such as Cheng and Church's greedy node deletion algorithm are required. It is to be expected that stochastic search techniques such as genetic algorithms or simulated annealing might produce better solutions than greedy search. In this paper we show that a simulated annealing approach is well suited to this problem and we present a comparative evaluation of simulated annealing and node deletion on a variety of datasets. We show that simulated annealing discovers more significant biclusters in many cases.
Kenneth Bryan, Padraig Cunningham, Nadia Bolshakova
CBMS2
2005 Generating Estimates of Classification Confidence for a Case-Based Spam Filter
Sarah Jane Delany, Padraig Cunningham, Dónal Doyle, Anton Zamolotskikh
ICCBR2
2005 Re-using Implicit Knowledge in Short-Term Information Profiles for Context-Sensitive Tasks
Conor Hayes, Paolo Avesani, Emiliano Baldo, Padraig Cunningham
ICCBR4
2005 The Best Way to Instil Confidence Is by Being Right
Conor Nugent, Padraig Cunningham, Dónal Doyle
ICCBR2
2005 Predicting probability distributions for surf height using an ensemble of mixture density networks
abstract
Abstract. There is a range of potential applications of Machine Learning where it would be more useful to predict the probability distribution for a variable rather than simply the most likely value for that variable. In meteorology and in finance it is often important to know the probability of a variable falling within (or outside) different ranges. In this paper we consider the prediction of surf height with the objective of predicting if it will fall within a given ‘surfable ’ range. Prediction problems such as this are considerably more difficult if the distribution of the phenomenon is significantly different from a normal distribution. This is the case with the surf data we have studied. To address this we use an ensemble of mixture density networks to predict the probability density function. Our evaluation shows that this is an effective solution. We also describe a web-based application that presents these predictions in a usable manner. 1
Michael Carney, Padraig Cunningham, Jim Dowling, Ciaran Lee
ICML2
2005 Sequential Genetic Search for Ensemble Feature Selection
Alexey Tsymbal, Mykola Pechenizkiy, Padraig Cunningham
IJCAI3
2005 Producing Accurate Interpretable Clusters from High-Dimensional Data
Derek Greene, Padraig Cunningham
PKDD2
2005 An integrated tool for microarray data clustering and cluster validity assessment
abstract
UNLABELLED: In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality of the data analysis results, and may support the prediction of the number of relevant clusters in the microarray datasets. This systematic evaluation approach may significantly aid genome expression analyses for knowledge discovery applications. The developed software system may be effectively used for clustering and validating not only DNA microarray expression analysis applications but also other biomedical and physical data with no limitations. AVAILABILITY: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html CONTACT: [email protected].
Nadia Bolshakova, Francisco Azuaje, Padraig Cunningham
Bioinform.3
2005 A knowledge-driven approach to cluster validity assessment
abstract
Summary: This paper presents an approach to assessing cluster validity based on similarity knowledge extracted from the Gene Ontology. Availability: The program is freely available for non-profit use on request from the authors. Contact: [email protected] Supplementary information: http://www.cs.tcd.ie/Nadia.Bolshakova/GOtool.html
Nadia Bolshakova, Francisco Azuaje, Padraig Cunningham
Bioinform.3
2005 A case-based technique for tracking concept drift in spam filtering
Sarah Jane Delany, Padraig Cunningham, Alexey Tsymbal, Lorcan Coyle
Knowl. Based Syst.2
2004 Ensemble Clustering in Medical Diagnostics
abstract
Ensemble techniques have been successfully applied in the context of supervised learning to increase the accuracy and stability of classification. Recently, analogous techniques for cluster analysis have been suggested. Research has demonstrated that, by combining a collection of dissimilar clusterings, an improved solution can be obtained. In this paper, we examine the potential of applying ensemble clustering techniques with a focus on the area of medical diagnostics. We present several ensemble generation and integration strategies, and evaluate each approach on a number of synthetic and real-world datasets. In addition, we show that diversity among ensemble members is necessary, but not sufficient to yield an improved solution without the selection of an appropriate integration method.
Derek Greene, Alexey Tsymbal, Nadia Bolshakova, Padraig Cunningham
CBMS4
2004 Diversity in Random Subspacing Ensembles
Alexey Tsymbal, Mykola Pechenizkiy, Padraig Cunningham
DaWaK3
2004 Context boosting collaborative recommendations
Conor Hayes, Padraig Cunningham
Knowl. Based Syst.2
2003 Search Strategies for Ensemble Feature Selection in Medical Diagnostics
abstract
The goal of this paper is to propose, evaluate, and compare four search strategies for ensemble feature selection, and to consider their application to medical diagnostics, with a focus on the problem of the classification of acute abdominal pain. Ensembles of learnt models constitute one of the main current directions in machine learning and data mining. Ensembles allow us to get higher accuracy, sensitivity, and specificity, which are often not achievable with single models. One technique, which proved to be effective for ensemble construction, is feature selection. Lately, several strategies for ensemble feature selection were proposed, including random subspacing, hill-climbing-based search, and genetic search. In this paper, we propose two new sequential-search-based strategies for ensemble feature selection, and evaluate them, constructing ensembles of simple Bayesian classifiers for the problem of acute abdominal pain classification. We compare the search strategies with regard to achieved accuracy, sensitivity, specificity, and the average number of features they select.
Alexey Tsymbal, Padraig Cunningham, Mykola Pechenizkiy, Seppo Puuronen
CBMS2
2003 An Evaluation of the Usefulness of Case-Based Explanation
Padraig Cunningham, Dónal Doyle, John Loughrey
ICCBR1
2003 Case-Based Plan Recognition in Computer Games
Michael Fagan 0003, Padraig Cunningham
ICCBR2
2003 Explaining the output of ensembles in medical decision support on a case by case basis
Robert Wall, Padraig Cunningham, Paul Walsh, Stephen Byrne
Artif. Intell. Medicine2
2002 Programme driven music radio
Conor Hayes, Padraig Cunningham, Patrick Clerkin, Marco Grimaldi
ECAI2
2002 Explaining Predictions from a Neural Network Ensemble One at a Time
Robert Wall, Padraig Cunningham, Paul Walsh
PKDD2
2002 The problem of bias in training data in regression problems in medical decision support
Brian Mac Namee, Padraig Cunningham, Stephen Byrne, O. I. Corrigan
Artif. Intell. Medicine2
2001 Using Diversity in Preparing Ensembles of Classifiers Based on Different Feature Subsets to Minimize Generalization Error
Gabriele Zenobi, Padraig Cunningham
ECML2
2001 Case Representation Issues for Case-Based Reasoning from Ensemble Research
Padraig Cunningham, Gabriele Zenobi
ICCBR1
2001 A Case-Based Reasoning View of Automated Collaborative Filtering
Conor Hayes, Padraig Cunningham, Barry Smyth
ICCBR2
2001 Using Case Retrieval to Seed Genetic Algorithms
abstract
In this paper we evaluate the usefulness of seeding genetic algorithms (GAs) from a case-base. This is motivated by the expectation that the seeding will speed up the GA by starting the search in promising regions of the search space. We evaluate this case-based seeding on popular GA solutions to the Travelling Salesman Problem (TSP) and the Job-Shop Scheduling Problem (JSSP). We find that seeding the initial population gives the GA a head start and that this advantage is maintained to the end of the GA in both problem domains. In addition, we have also found that the scale of the initial advantage can be greatly improved through the introduction of problem specific information in the seeding process. Finally, the improvements of the seeded GA over the random GA can be used to reduce the number of generations required to find suitably fit solutions.
Stephen Oman, Padraig Cunningham
Int. J. Comput. Intell. Appl.2
2001 Smart radio - community based music radio
Conor Hayes, Padraig Cunningham
Knowl. Based Syst.2
2001 Hierarchical Case-Based Reasoning Integrating Case-Based and Decompositional Problem-Solving Techniques for Plant-Control Software Design
abstract
Case based reasoning (CBR) is an artificial intelligence technique that emphasises the role of past experience during future problem solving. New problems are solved by retrieving and adapting the solutions to similar problems, solutions that have been stored and indexed for future reuse as cases in a case-base. The power of CBR is severely curtailed if problem solving is limited to the retrieval and adaptation of a single case, so most CBR systems dealing with complex problem solving tasks have to use multiple cases. The paper describes and evaluates the technique of hierarchical case based reasoning, which allows complex problems to be solved by reusing multiple cases at various levels of abstraction. The technique is described in the context of Deja Vu, a CBR system aimed at automating plant-control software design.
Barry Smyth, Mark T. Keane, Padraig Cunningham
IEEE Trans. Knowl. Data Eng.3
2000 Diversity versus Quality in Classification Ensembles Based on Feature Selection
Padraig Cunningham, John Carney
ECML1
2000 Stability problems with artificial neural networks and the ensemble solution
Padraig Cunningham, John Carney, Saji Jacob
Artif. Intell. Medicine1
2000 Tuning Diversity in Bagged Ensembles
abstract
In this paper, we investigate how the level of diversity amongst individual neural networks in a bagged ensemble can significantly influence overall ensemble generalization performance. We propose a new technique that tunes this diversity so that ensemble generalization performance is optimized and evaluate its performance on benchmark regression data-sets.
John Carney, Padraig Cunningham
Int. J. Neural Syst.2
1999 The NeuralBAG algorithm: optimizing generalization performance in bagged neural networks
John Carney, Padraig Cunningham
ESANN2
1999 Shaping a CBR View with XML
Conor Hayes, Padraig Cunningham
ICCBR2
1999 Confidence and prediction intervals for neural network ensembles
abstract
We propose a technique that uses the bootstrap method to estimate confidence and prediction intervals for neural network (regression) ensembles. Our proposed technique can be applied to any ensemble technique that uses the bootstrap to generate the training sets for the ensemble, such as bagging and balancing. Confidence and prediction intervals are estimated that include a significantly improved estimate of underlying model uncertainty (i.e.) the uncertainty of our estimate of the "true" regression. Unlike existing techniques, this estimate of uncertainty will vary according to which ensemble technique is used if the effect of using a specific ensemble technique is to produce less model uncertainty than using another ensemble technique, then this will be reflected in the confidence and prediction intervals. Preliminary results illustrate how our technique can provide more accurate confidence and prediction intervals (intervals that better reflect the desired level of confidence (e.g.) 90%, 95%, etc.) for neural network ensembles than previous attempts.
John Carney, Padraig Cunningham, Umesh Bhagwan
IJCNN2
1999 Knowledge engineering issues in developing a case-based reasoning application
Padraig Cunningham, Andrea Bonzano
Knowl. Based Syst.1
1998 Hierarchical CBR for Multiple Aircraft Conflict Resolution
Andrea Bonzano, Padraig Cunningham
ECAI2
1998 A case study on the use of model-based systems for electronic fault diagnosis
Padraig Cunningham
Artif. Intell. Eng.1
1998 Solution reuse for model generation in numerical simulation
Donal Finn, Padraig Cunningham
Artif. Intell. Eng.2
1998 Neural Networks for Language Identification: A Comparative Study
Shane MacNamara, Padraig Cunningham, John Byrne
Inf. Process. Manag.2
1998 An incremental retrieval mechanism for case-based electronic fault diagnosis
Padraig Cunningham, Barry Smyth, Andrea Bonzano
Knowl. Based Syst.1
1997 Using Introspective Learning to Improve Retrieval in CBR: A Case Study in Air Traffic Control
Andrea Bonzano, Padraig Cunningham, Barry Smyth
ICCBR2
1995 On the use of CBR in optimisation problems such as the TSP
Padraig Cunningham, Barry Smyth, Neil J. Hurley
ICCBR1
1995 Systems, Tasks and Adaptation Knowledge: Revealing Some Revealing Dependencies
Kathleen Hanney, Mark T. Keane, Barry Smyth, Padraig Cunningham
ICCBR4
1992 Déjà Vu: A Hierarchical Case-Based Reasoning System for Software Design
Barry Smyth, Padraig Cunningham
ECAI2
1992 Competitive Hypothesis Resolution in TWIG, a Blackboard-Driven Text Understanding System
Tony Veale, Padraig Cunningham
ECAI2
1991 Organizational Issues Arising from the Integration of the Lexicon and Concept Network in a Text Understanding System
Padraig Cunningham, Tony Veale
IJCAI1
1987 Qualitative Reasoning in Electronic Fault Diagnosis
Padraig Cunningham
IJCAI1