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

Combining clusterings in the belief function framework

International audienceIn this paper, we propose a clustering ensemble method based on Dempster-Shafer Theory. In the first step, base partitions are generated by evidential clustering algorithms such as the evidential c-means or EVCLUS. Base credal partitions are then converted to their relational representations, which are combined by averaging. The combined relational representation is then made transitive using the theory of intuitionistic fuzzy relations. Finally, the consensus solution is obtained by minimizing an error function. Experiments with simulated and real datasets show the good performances of this method

Feedback-Driven Data Clustering

The acquisition of data and its analysis has become a common yet critical task in many areas of modern economy and research. Unfortunately, the ever-increasing scale of datasets has long outgrown the capacities and abilities humans can muster to extract information from them and gain new knowledge. For this reason, research areas like data mining and knowledge discovery steadily gain importance. The algorithms they provide for the extraction of knowledge are mandatory prerequisites that enable people to analyze large amounts of information. Among the approaches offered by these areas, clustering is one of the most fundamental. By finding groups of similar objects inside the data, it aims to identify meaningful structures that constitute new knowledge. Clustering results are also often used as input for other analysis techniques like classification or forecasting. As clustering extracts new and unknown knowledge, it obviously has no access to any form of ground truth. For this reason, clustering results have a hypothetical character and must be interpreted with respect to the application domain. This makes clustering very challenging and leads to an extensive and diverse landscape of available algorithms. Most of these are expert tools that are tailored to a single narrowly defined application scenario. Over the years, this specialization has become a major trend that arose to counter the inherent uncertainty of clustering by including as much domain specifics as possible into algorithms. While customized methods often improve result quality, they become more and more complicated to handle and lose versatility. This creates a dilemma especially for amateur users whose numbers are increasing as clustering is applied in more and more domains. While an abundance of tools is offered, guidance is severely lacking and users are left alone with critical tasks like algorithm selection, parameter configuration and the interpretation and adjustment of results. This thesis aims to solve this dilemma by structuring and integrating the necessary steps of clustering into a guided and feedback-driven process. In doing so, users are provided with a default modus operandi for the application of clustering. Two main components constitute the core of said process: the algorithm management and the visual-interactive interface. Algorithm management handles all aspects of actual clustering creation and the involved methods. It employs a modular approach for algorithm description that allows users to understand, design, and compare clustering techniques with the help of building blocks. In addition, algorithm management offers facilities for the integration of multiple clusterings of the same dataset into an improved solution. New approaches based on ensemble clustering not only allow the utilization of different clustering techniques, but also ease their application by acting as an abstraction layer that unifies individual parameters. Finally, this component provides a multi-level interface that structures all available control options and provides the docking points for user interaction. The visual-interactive interface supports users during result interpretation and adjustment. For this, the defining characteristics of a clustering are communicated via a hybrid visualization. In contrast to traditional data-driven visualizations that tend to become overloaded and unusable with increasing volume/dimensionality of data, this novel approach communicates the abstract aspects of cluster composition and relations between clusters. This aspect orientation allows the use of easy-to-understand visual components and makes the visualization immune to scale related effects of the underlying data. This visual communication is attuned to a compact and universally valid set of high-level feedback that allows the modification of clustering results. Instead of technical parameters that indirectly cause changes in the whole clustering by influencing its creation process, users can employ simple commands like merge or split to directly adjust clusters. The orchestrated cooperation of these two main components creates a modus operandi, in which clusterings are no longer created and disposed as a whole until a satisfying result is obtained. Instead, users apply the feedback-driven process to iteratively refine an initial solution. Performance and usability of the proposed approach were evaluated with a user study. Its results show that the feedback-driven process enabled amateur users to easily create satisfying clustering results even from different and not optimal starting situations

Discovering New Intents via Constrained Deep Adaptive Clustering with Cluster Refinement

Identifying new user intents is an essential task in the dialogue system. However, it is hard to get satisfying clustering results since the definition of intents is strongly guided by prior knowledge. Existing methods incorporate prior knowledge by intensive feature engineering, which not only leads to overfitting but also makes it sensitive to the number of clusters. In this paper, we propose constrained deep adaptive clustering with cluster refinement (CDAC+), an end-to-end clustering method that can naturally incorporate pairwise constraints as prior knowledge to guide the clustering process. Moreover, we refine the clusters by forcing the model to learn from the high confidence assignments. After eliminating low confidence assignments, our approach is surprisingly insensitive to the number of clusters. Experimental results on the three benchmark datasets show that our method can yield significant improvements over strong baselines.Comment: Accepted by AAAI202

Applications of a Graph Theoretic Based Clustering Framework in Computer Vision and Pattern Recognition

Recently, several clustering algorithms have been used to solve variety of problems from different discipline. This dissertation aims to address different challenging tasks in computer vision and pattern recognition by casting the problems as a clustering problem. We proposed novel approaches to solve multi-target tracking, visual geo-localization and outlier detection problems using a unified underlining clustering framework, i.e., dominant set clustering and its extensions, and presented a superior result over several state-of-the-art approaches.Comment: doctoral dissertatio

Constrained Distance Based Clustering for Satellite Image Time-Series

International audienceThe advent of high-resolution instruments for time-series sampling poses added complexity for the formal definition of thematic classes in the remote sensing domain-required by supervised methods-while unsupervised methods ignore expert knowledge and intuition. Constrained clustering is becoming an increasingly popular approach in data mining because it offers a solution to these problems, however, its application in remote sensing is relatively unknown. This article addresses this divide by adapting publicly available constrained clustering implementations to use the dynamic time warping (DTW) dissimilarity measure, which is sometimes used for time-series analysis. A comparative study is presented, in which their performance is evaluated (using both DTW and Euclidean distances). It is found that adding constraints to the clustering problem results in an increase in accuracy when compared to unconstrained clustering. The output of such algorithms are homogeneous in spatially defined regions. Declarative approaches and k-Means based algorithms are simple to apply, requiring little or no choice of parameter values. Spectral methods, however, require careful tuning, which is unrealistic in a semi-supervised setting, although they offer the highest accuracy. These conclusions were drawn from two applications: crop clustering using 11 multi-spectral Landsat images non-uniformly sampled over a period of eight months in 2007; and tree-cut detection using 10 NDVI Sentinel-2 images non-uniformly sampled between 2016 and 2018

Enhanced fold recognition using efficient short fragment clustering

The main structure aligner in the CCP4 Software Suite, SSM (Secondary Structure Matching) has a limited applicability on the intermediate stages of the structure solution process, when the secondary structure cannot be reliably computed due to structural incompleteness or a fragmented mainchain. In this study, we describe a new algorithm for the alignment and comparison of protein structures in CCP4, which was designed to overcome SSM's limitations but retain its quality and speed. The new algorithm, named GESAMT (General Efficient Structural Alignment of Macromolecular Targets), employs the old idea of deriving the global structure similarity from a promising set of locally similar short fragments, but uses a few technical solutions that make it considerably faster. A comparative sensitivity and selectivity analysis revealed an unexpected significant improvement in the fold recognition properties of the new algorithm, which also makes it useful for applications in the structural bioinformatics domain. The new tool is included in the CCP4 Software Suite starting from version 6.3

Associative Pattern Recognition for Biological Regulation Data

In the last decade, bioinformatics data has been accumulated at an unprecedented rate, thanks to the advancement in sequencing technologies. Such rapid development poses both challenges and promising research topics. In this dissertation, we propose a series of associative pattern recognition algorithms in biological regulation studies. In particular, we emphasize efficiently recognizing associative patterns between genes, transcription factors, histone modifications and functional labels using heterogeneous data sources (numeric, sequences, time series data and textual labels). In protein-DNA associative pattern recognition, we introduce an efficient algorithm for affinity test by searching for over-represented DNA sequences using a hash function and modulo addition calculation. This substantially improves the efficiency of \textit{next generation sequencing} data analysis. In gene regulatory network inference, we propose a framework for refining weak networks based on transcription factor binding sites, thus improved the precision of predicted edges by up to 52%. In histone modification code analysis, we propose an approach to genome-wide combinatorial pattern recognition for histone code to function associative pattern recognition, and achieved improvement by up to $38.1\%$. We also propose a novel shape based modification pattern analysis approach, using this to successfully predict sub-classes of genes in flowering-time category. We also propose a combination to combination associative pattern recognition, and achieved better performance compared against multi-label classification and bidirectional associative memory methods. Our proposed approaches recognize associative patterns from different types of data efficiently, and provides a useful toolbox for biological regulation analysis. This dissertation presents a road-map to associative patterns recognition at genome wide level