Ensemble clustering for result diversification

This paper describes the participation of the University of Twente in the Web track of TREC 2012. Our baseline approach uses the Mirex toolkit, an open source tool that sequantially scans all the documents. For result diversification, we experimented with improving the quality of clusters through ensemble clustering. We combined clusters obtained by different clustering methods (such as LDA and K-means) and clusters obtained by using different types of data (such as document text and anchor text). Our two-layer ensemble run performed better than the LDA based diversification and also better than a non-diversification run

Combining Multiple Clusterings via Crowd Agreement Estimation and Multi-Granularity Link Analysis

The clustering ensemble technique aims to combine multiple clusterings into a probably better and more robust clustering and has been receiving an increasing attention in recent years. There are mainly two aspects of limitations in the existing clustering ensemble approaches. Firstly, many approaches lack the ability to weight the base clusterings without access to the original data and can be affected significantly by the low-quality, or even ill clusterings. Secondly, they generally focus on the instance level or cluster level in the ensemble system and fail to integrate multi-granularity cues into a unified model. To address these two limitations, this paper proposes to solve the clustering ensemble problem via crowd agreement estimation and multi-granularity link analysis. We present the normalized crowd agreement index (NCAI) to evaluate the quality of base clusterings in an unsupervised manner and thus weight the base clusterings in accordance with their clustering validity. To explore the relationship between clusters, the source aware connected triple (SACT) similarity is introduced with regard to their common neighbors and the source reliability. Based on NCAI and multi-granularity information collected among base clusterings, clusters, and data instances, we further propose two novel consensus functions, termed weighted evidence accumulation clustering (WEAC) and graph partitioning with multi-granularity link analysis (GP-MGLA) respectively. The experiments are conducted on eight real-world datasets. The experimental results demonstrate the effectiveness and robustness of the proposed methods.Comment: The MATLAB source code of this work is available at: https://www.researchgate.net/publication/28197031

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

EC3: Combining Clustering and Classification for Ensemble Learning

Classification and clustering algorithms have been proved to be successful individually in different contexts. Both of them have their own advantages and limitations. For instance, although classification algorithms are more powerful than clustering methods in predicting class labels of objects, they do not perform well when there is a lack of sufficient manually labeled reliable data. On the other hand, although clustering algorithms do not produce label information for objects, they provide supplementary constraints (e.g., if two objects are clustered together, it is more likely that the same label is assigned to both of them) that one can leverage for label prediction of a set of unknown objects. Therefore, systematic utilization of both these types of algorithms together can lead to better prediction performance. In this paper, We propose a novel algorithm, called EC3 that merges classification and clustering together in order to support both binary and multi-class classification. EC3 is based on a principled combination of multiple classification and multiple clustering methods using an optimization function. We theoretically show the convexity and optimality of the problem and solve it by block coordinate descent method. We additionally propose iEC3, a variant of EC3 that handles imbalanced training data. We perform an extensive experimental analysis by comparing EC3 and iEC3 with 14 baseline methods (7 well-known standalone classifiers, 5 ensemble classifiers, and 2 existing methods that merge classification and clustering) on 13 standard benchmark datasets. We show that our methods outperform other baselines for every single dataset, achieving at most 10% higher AUC. Moreover our methods are faster (1.21 times faster than the best baseline), more resilient to noise and class imbalance than the best baseline method.Comment: 14 pages, 7 figures, 11 table

The multiplex structure of interbank networks

The interbank market has a natural multiplex network representation. We employ a unique database of supervisory reports of Italian banks to the Banca d'Italia that includes all bilateral exposures broken down by maturity and by the secured and unsecured nature of the contract. We find that layers have different topological properties and persistence over time. The presence of a link in a layer is not a good predictor of the presence of the same link in other layers. Maximum entropy models reveal different unexpected substructures, such as network motifs, in different layers. Using the total interbank network or focusing on a specific layer as representative of the other layers provides a poor representation of interlinkages in the interbank market and could lead to biased estimation of systemic risk.Comment: 41 pages, 8 figures, 10 table

Ranked List Loss for Deep Metric Learning

The objective of deep metric learning (DML) is to learn embeddings that can capture semantic similarity and dissimilarity information among data points. Existing pairwise or tripletwise loss functions used in DML are known to suffer from slow convergence due to a large proportion of trivial pairs or triplets as the model improves. To improve this, ranking-motivated structured losses are proposed recently to incorporate multiple examples and exploit the structured information among them. They converge faster and achieve state-of-the-art performance. In this work, we unveil two limitations of existing ranking-motivated structured losses and propose a novel ranked list loss to solve both of them. First, given a query, only a fraction of data points is incorporated to build the similarity structure. Consequently, some useful examples are ignored and the structure is less informative. To address this, we propose to build a set-based similarity structure by exploiting all instances in the gallery. The learning setting can be interpreted as few-shot retrieval: given a mini-batch, every example is iteratively used as a query, and the rest ones compose the gallery to search, i.e., the support set in few-shot setting. The rest examples are split into a positive set and a negative set. For every mini-batch, the learning objective of ranked list loss is to make the query closer to the positive set than to the negative set by a margin. Second, previous methods aim to pull positive pairs as close as possible in the embedding space. As a result, the intraclass data distribution tends to be extremely compressed. In contrast, we propose to learn a hypersphere for each class in order to preserve useful similarity structure inside it, which functions as regularisation. Extensive experiments demonstrate the superiority of our proposal by comparing with the state-of-the-art methods.Comment: Accepted to T-PAMI. Therefore, to read the offical version, please go to IEEE Xplore. Fine-grained image retrieval task. Our source code is available online: https://github.com/XinshaoAmosWang/Ranked-List-Loss-for-DM