Biclustering Bioinformatics Data Sets. A Possibilistic Approach

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1 Possibilistic algorithm Bioinformatics Data Sets: A Possibilistic Approach Dept Computer and Information Sciences, University of Genova ITALY EMFCSC Erice 20/4/2007 Bioinformatics Data Sets

2 Outline Introduction Possibilistic algorithm 1 Introduction 2 3 Possibilistic algorithm 4 Bioinformatics Data Sets

3 Possibilistic algorithm BIOINFORMATICS DATA SETS Data representation Nowadays, in the Post-Genomic era, we have many Bioinformatics data sets available (most of them released in public domain on the Internet) The information embedded in most of them has no yet completely exploited, due to the lack of accurate machine learning tools and/or of their diffusion in the Bioinformatics community. Bioinformatics Data Sets

4 Possibilistic algorithm Most of Bioinformatics data sets come from DNA microarray experiments and are normally given as a rectangular m n matrix X, where each column represents a feature (e.g., gene) and each row represents a data sample or condition (e.g., patient) X = (x ij ) m n, (1) where the value x ij is the expression of i-th gene in j-th condition. The analysis of microarray data sets can give a valuable information on the biological relevance of genes and correlations between them [Madei, 2004]. Bioinformatics Data Sets

5 Possibilistic algorithm BIOINFORMATICS DATA SETS Major Machine Learning tasks Clustering (Unsupervised): Given a set of samples, partition them into groups containg similar samples according to some similarity criteria (CLASS DISCOVERING). Classification (Supervised): Find classes of the test data set using known classification of training data set (CLASS PREDICTION). Feature Selection (Dimensionality reduction): Select a subset of features responsible for creating the condition corresponding to the class (GENE SELECTION, BIOMARKER SELECTION). Outlier Detection: Detect data samples that are not good representative of any of the classes, and disregard them while performing data analysis. Bioinformatics Data Sets

6 Possibilistic algorithm BIOINFORMATICS DATA SETS Major Machine Learning tasks Clustering (Unsupervised): Given a set of samples, partition them into groups containg similar samples according to some similarity criteria (CLASS DISCOVERING). Classification (Supervised): Find classes of the test data set using known classification of training data set (CLASS PREDICTION). Feature Selection (Dimensionality reduction): Select a subset of features responsible for creating the condition corresponding to the class (GENE SELECTION, BIOMARKER SELECTION). Outlier Detection: Detect data samples that are not good representative of any of the classes, and disregard them while performing data analysis. Bioinformatics Data Sets

7 Possibilistic algorithm BIOINFORMATICS DATA SETS Major Machine Learning tasks Clustering (Unsupervised): Given a set of samples, partition them into groups containg similar samples according to some similarity criteria (CLASS DISCOVERING). Classification (Supervised): Find classes of the test data set using known classification of training data set (CLASS PREDICTION). Feature Selection (Dimensionality reduction): Select a subset of features responsible for creating the condition corresponding to the class (GENE SELECTION, BIOMARKER SELECTION). Outlier Detection: Detect data samples that are not good representative of any of the classes, and disregard them while performing data analysis. Bioinformatics Data Sets

8 Possibilistic algorithm BIOINFORMATICS DATA SETS Major Machine Learning tasks Clustering (Unsupervised): Given a set of samples, partition them into groups containg similar samples according to some similarity criteria (CLASS DISCOVERING). Classification (Supervised): Find classes of the test data set using known classification of training data set (CLASS PREDICTION). Feature Selection (Dimensionality reduction): Select a subset of features responsible for creating the condition corresponding to the class (GENE SELECTION, BIOMARKER SELECTION). Outlier Detection: Detect data samples that are not good representative of any of the classes, and disregard them while performing data analysis. Bioinformatics Data Sets

9 Possibilistic algorithm BIOINFORMATICS DATA SETS Major challenges in Machine Learning Noisiness of data complicates solution of Machine Learning Tasks (robustness to noise). High-dimensionality of data makes complete search in most of data mining problems computationally infeasible (curse of dimensionality). Some data values may be inaccurate or missing. = The available data may be not sufficient to obtain statistically significant conclusions. Bioinformatics Data Sets

10 Possibilistic algorithm BIOINFORMATICS DATA SETS Major challenges in Machine Learning Noisiness of data complicates solution of Machine Learning Tasks (robustness to noise). High-dimensionality of data makes complete search in most of data mining problems computationally infeasible (curse of dimensionality). Some data values may be inaccurate or missing. = The available data may be not sufficient to obtain statistically significant conclusions. Bioinformatics Data Sets

11 Possibilistic algorithm BIOINFORMATICS DATA SETS Major challenges in Machine Learning Noisiness of data complicates solution of Machine Learning Tasks (robustness to noise). High-dimensionality of data makes complete search in most of data mining problems computationally infeasible (curse of dimensionality). Some data values may be inaccurate or missing. = The available data may be not sufficient to obtain statistically significant conclusions. Bioinformatics Data Sets

12 Possibilistic algorithm BIOINFORMATICS DATA SETS Major challenges in Machine Learning Noisiness of data complicates solution of Machine Learning Tasks (robustness to noise). High-dimensionality of data makes complete search in most of data mining problems computationally infeasible (curse of dimensionality). Some data values may be inaccurate or missing. = The available data may be not sufficient to obtain statistically significant conclusions. Bioinformatics Data Sets

13 Possibilistic algorithm Problem we shall focus today: How to identify genes with similar behavior with respect to different conditions? Instance of the problem of biclustering (also known as co-clustering, two-way clustering,...) [Cheng & Church, 2000; Hartigan, 1972; Kung et al, 2005; Turner et al, 2005] Bioinformatics Data Sets

14 Possibilistic algorithm Problem we shall focus today: How to identify genes with similar behavior with respect to different conditions? Instance of the problem of biclustering (also known as co-clustering, two-way clustering,...) [Cheng & Church, 2000; Hartigan, 1972; Kung et al, 2005; Turner et al, 2005] Bioinformatics Data Sets

15 Possibilistic algorithm BICLUSTERING is a methodology allowing for feature set and data points clustering simultaneously. It finds clusters of samples possessing similar characteristics together with features creating these similarities. It replies to the question: What characteristics make similar objects similar among them? Bioinformatics Data Sets

16 Possibilistic algorithm BICLUSTERING is a methodology allowing for feature set and data points clustering simultaneously. It finds clusters of samples possessing similar characteristics together with features creating these similarities. It replies to the question: What characteristics make similar objects similar among them? Bioinformatics Data Sets

17 Possibilistic algorithm BICLUSTERING is a methodology allowing for feature set and data points clustering simultaneously. It finds clusters of samples possessing similar characteristics together with features creating these similarities. It replies to the question: What characteristics make similar objects similar among them? Bioinformatics Data Sets

18 Possibilistic algorithm BICLUSTERING Surveys S. Madeira, A.L. Oliveira, Algorithms for Biological Data Analysis: A Survey, A. Tanay, R. Sharan, R. Shamir, Algorithms: A Survey, D. Jiang, C. Tang, A. Zhang, Cluster Analysis for Gene Expression Data: A Survey, Bioinformatics Data Sets

19 Possibilistic algorithm BICLUSTERING Applications Biological and Medical: Microarray data analysis Analysis of drug activity [Liu & Wang, 2003] Analysis of nutritional data [Lazzeroni et al., 2000] Bioinformatics Data Sets

20 Possibilistic algorithm BICLUSTERING Applications Text Mining [Dhillon, 2001, 2003] Marketing [Gaul & Schader, 1996] Others: electoral data [Hartigan, 1972] currency exchange [Lazzeroni et al., 2000] Dimensionality Reduction in Databases [Agrawal et al., 1998] Bioinformatics Data Sets

21 Possibilistic algorithm BICLUSTERING State of the art Cheng & Church algorithm [2000] The algorithm constructs one bicluster at a time using a statistical criterion - a low mean squared residue (the variance of the set of all elements in the bicluster, plus the mean row variance and the mean column variance). Once a bicluster is created, its entries are replaced by random numbers, and the procedure is repeated iteratively. Drawback: The masking procedure results in a phenomenon of random interference, affecting the subsequent discovery of large-sized biclusters [Yang et al., 2003]. Bioinformatics Data Sets

22 Possibilistic algorithm BICLUSTERING State of the art Cheng & Church algorithm [2000] The algorithm constructs one bicluster at a time using a statistical criterion - a low mean squared residue (the variance of the set of all elements in the bicluster, plus the mean row variance and the mean column variance). Once a bicluster is created, its entries are replaced by random numbers, and the procedure is repeated iteratively. Drawback: The masking procedure results in a phenomenon of random interference, affecting the subsequent discovery of large-sized biclusters [Yang et al., 2003]. Bioinformatics Data Sets

23 Possibilistic algorithm BICLUSTERING State of the art Direct Clustering [Hartigan, 1972] Flexible Overlapped Clusters (FLOC) [Yang et al., 2003] (probabilistic algorithm) Bipartite graphs [Tanay et al 2002] Genetic algorithms [Mitra et al, 2006] Simulated Annealing [Bryan et al, 2005] Bioinformatics Data Sets

24 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Joint work: Maurizio Filippone,, Stefano Rovetta DISI Dept Computer and Information Science, University of Genova ITALY Sushmita Mitra, Haider Banka Indian Statistical Institute, Kolkata INDIA Bioinformatics Data Sets

25 Possibilistic algorithm POSSIBILISTIC BICLUSTERING We propose a new approach to the biclustering problem using the possibilistic clustering paradigm [Krishnapuram & Keller, 1993]. PBC algorithm finds one bicluster at a time, assigning to each data matrix element a membership to the bicluster The membership model is of the fuzzy possibilistic type. Bioinformatics Data Sets

26 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Definitions Let x ij be the expression level of the i-th gene in the j-th condition. A bicluster is defined as a subset of the m n data matrix X, i.e., a bicluster is a pair (g, c), where g {1,...,m} is a subset of genes and c {1,...,n} is a subset of conditions [Cheng & Church, 2000; Hartigan, 1972; Kung et al, 2005; Turner et al, 2005]. We are interested in largest biclusters from DNA microarray data that do not exceed an assigned homogeneity constraint [Cheng & Church, 2000] as they can supply relevant biological information. Bioinformatics Data Sets

27 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Definitions The size (or volume) n of a bicluster is usually defined as the number of cells in the gene expression matrix X belonging to it, that is the product of the cardinalities n g = g and n c = c : n = n g n c (2) Normalized square residual ( ) 2 dij 2 xij + x IJ x ij x Ij = n where the elements x IJ, x ij and x Ij are respectively the bicluster mean, the row mean and the column mean of X for the selected genes and conditions: (3) Bioinformatics Data Sets

28 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Definitions bicluster mean: x IJ = 1 x ij (4) n i g bicluster row mean: x ij = 1 x ij (5) n c bicluster column mean: x Ij = 1 x ij (6) n g j c i g j c Bioinformatics Data Sets

29 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Definitions Mean Square Residual [Cheng & Church, 2000]: G = dij 2 (7) i g j c G measures the bicluster homogeneity, i.e., the difference between the actual value of an element x ij and its expected value as predicted from the corresponding row mean, column mean, and bicluster mean. OUR AIM: maximizing the bicluster cardinality n and at the same time minimizing the residual G (NP-complete task [Peete, 2003]) using the Possibilistic Clustering Paradigm. Bioinformatics Data Sets

30 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Approaches to clustering Bioinformatics data sets Data clustering is a routine step in biological data analysis, and a basic tool in Bioinformatics [Golub, et al., 1999; P. Tamayo, et al., 1999; Azuaje, 2003] Main approaches: Hierarchical Clustering [Eisen et al., 1998; Orengo et al., 2003] Partitional (or Central) Clustering: including C-Means [Duda & Hart, 1973], Self Organizing Map [Kohonen, 2001], Fuzzy C-Means [Bezdek, 1981], Deterministic Annealing [Rose et al, 1990], Alternating Cluster Estimation [Runkler, 1999], etc. Bioinformatics Data Sets

31 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Probabilistic constraint in central clustering Let X = {x 1,...,x r } be a set of unlabeled data points, Y = {y 1,...,y s } a set of cluster centers (or prototypes) and U = [u pq ] the fuzzy membership matrix. Often, central clustering algorithms impose a probabilistic constraint on memberships, according to which the sum of the membership values of a point in all the clusters must be equal to one: r u pq = 1 (8) q=1 Bioinformatics Data Sets

32 Possibilistic algorithm POSSIBILISTIC BICLUSTERING From Probabilistic to Possibilistic Clustering Probabilistic constraint r u pq = 1: q=1 PROS - competitive constraint allowing the unsupervised learning algorithms to find the barycenter of clusters CONS - membership to clusters (a) not interpretable as a degree of typicality - (b) can give sensibility to outliers (a) (b) Bioinformatics Data Sets

33 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Possibilistic Clustering In the Possibilistic C-Means (PCM) Algorithm [Krishnapuram & Keller, 1993] the constraints on the elements of U are relaxed to: u pq [0, 1] p, q; (9) 0 < r u pq < r p; (10) q=1 u pq > 0 q. (11) p i.e., clusters cannot be empty and each pattern must be assigned to at least one cluster mode seeking algorithm [Krishnapuram & Keller, 1993] Bioinformatics Data Sets

34 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Possibilistic Clustering PCM objective function [Krishnapuram & Keller, 1996]: s r s 1 r J m (U, Y) = u pq E pq + (u pq log u pq u pq ), p=1 q=1 β p p=1 q=1 (12) where: E pq = x q y p 2 (squared Euclidean distance) β p (scale) depending on the average size of the p-th cluster. Thanks to the penality term, points with a high degree of typicality have high u pq values, and points not very representative have low u pq values in all the clusters. Note that if β p p = trivial solution u pq = 0 is assumed. p, q, as no probabilistic constraint Bioinformatics Data Sets

35 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Possibilistic Clustering The pair (U, Y) minimizes J m, under the possibilistic constraints 9-11 only if: and u pq = e Epq/βp p, q, (13) y p = r q=1 x qu pq r q=1 u pq p. (14) Picard iteration Membership refinement algorithm, membership to clusters as cluster typicality degree (initialization of centroids using, e.g., Fuzzy C-Means). High outliers rejection capability as PCM makes their membership very low. Bioinformatics Data Sets

36 Possibilistic algorithm POSSIBILISTIC BICLUSTERING Possibilistic Clustering PCM approach = equivalent to a set of s independent estimation problems [Nasraoui, 1995]: (u pq, y) = arg r u pq E pq + 1 r (u pq log u pq u pq ) p, β p u pq,y q=1 q=1 (15) that can be solved independently one at a time through a Picard iteration. Bioinformatics Data Sets

37 Possibilistic algorithm POSSIBILISTIC BICLUSTERING ALGORITHM (PBC) PBC Formulation For each bicluster we assign two vectors of membership, one for the rows and one other for the columns, denoting them respectively a and b. In a crisp sets framework row i and column j can either belong to the bicluster (a i = 1 and b j = 1) or not (a i = 0 or b j = 0). An element x ij of X belongs to the bicluster if both a i = 1 and b j = 1, i.e., its membership u ij to the bicluster is: u ij = and(a i, b j ) (16) The cardinality of the bicluster is then defined as: n = u ij (17) i j Bioinformatics Data Sets

38 Possibilistic algorithm POSSIBILISTIC BICLUSTERING ALGORITHM (PBC) PBC Formulation Fuzzy set theory framework: We allow membership u ij, a i and b j to belong in the interval [0, 1]. The membership u ij of an element x ij of X to the bicluster can be obtained by the aggregation of row and column memberships, using, e.g., a fuzzy t-norm like: or u ij = a i b j (product) (18) u ij = a i + b j (average) (19) 2 The fuzzy cardinality of the bicluster is defined as the sum of the memberships u ij for all i and j as in eq. 17. Bioinformatics Data Sets

39 Possibilistic algorithm POSSIBILISTIC BICLUSTERING ALGORITHM (PBC) PBC Formulation Homogeneity measures (eqs. 4 to 7) generalization: Fuzzy normalized square residual ( ) 2 dij 2 xij + x IJ x ij x Ij = (20) n where fuzzy bicluster mean, fuzzy bicluster row mean, fuzzy bicluster column mean are defined as : i j x IJ = u ijx ij j i j u, x ij = u ijx ij ij j u, x Ij = i u ijx ij ij i u (21) ij and fuzzy mean square residual: G = u ij dij 2 (22) i j Bioinformatics Data Sets

40 Possibilistic algorithm POSSIBILISTIC BICLUSTERING ALGORITHM (PBC) PBC Formulation Possibilistic Problem: maximizing the bicluster cardinality n and minimizing the fuzzy residual G under the fuzzy possibilistic paradigm. To this aim we make the following assumptions: we treat one bicluster at a time; the fuzzy memberships a i and b j are interpreted as typicality degrees of gene i and condition j with respect to the bicluster; we compute the membership u ij using the average aggregator (eq. 19). Bioinformatics Data Sets

41 Possibilistic algorithm POSSIBILISTIC BICLUSTERING ALGORITHM (PBC) PBC Formulation All those requirements are fulfilled by minimizing the following functional J B with respect to a and b: J B = ( ) ai + b j dij 2 2 +λ (a i ln a i a i )+µ (b j ln b j b j ) ij i j (23) The first term is the fuzzy mean square residual G, while the other two are penalization terms. The parameters λ and µ control the size of the bicluster. Their values can be estimated by simple statistics over the training set, and then hand-tuned to incorporate possible a-priori knowledge and to obtain the expected results. Bioinformatics Data Sets

42 Possibilistic algorithm POSSIBILISTIC BICLUSTERING ALGORITHM (PBC) PBC Formulation Setting the derivatives of J B with respect to the memberships a i and b j to zero we obtain: a i = exp b j = exp ( ( j d ) ij 2 2λ i d ) ij 2 2µ (24) (25) Those necessary conditions for the minimization of J B together with the definition of the fuzzy normalized square residual dij 2 (eq. 20) can be used to find a numerical solution for the optimization problem (Picard iteration). Bioinformatics Data Sets

43 Possibilistic algorithm POSSIBILISTIC BICLUSTERING ALGORITHM (PBC) PBC Formulation Table: Possibilistic (PBC) algorithm. 1 Initialize memberships a and b and threshold ε 2 Compute d 2 ij i, j (eq. 20) 3 Update a i i (eq. 24) 4 Update b j j (eq. 25) 5 if a a < ε and b b < ε then stop 6 else jump to step 2 Bioinformatics Data Sets

44 Possibilistic algorithm POSSIBILISTIC BICLUSTERING ALGORITHM (PBC) PBC Formulation The memberships initialization can be made: randomly using some a priori information about relevant genes and conditions. using the results already obtained from another biclustering algorithm (in this case PBC will work as a refinement algorithm) ε controls the convergence of the algorithm. After convergence of the algorithm the memberships a and b can be defuzzified by applying an α-cut, i.e., by comparing with a threshold. Bioinformatics Data Sets

45 n Introduction Possibilistic algorithm RESULTS Yeast data set [Tavazoie et al.; 1999][Ball et al, 2000] [Aach et al 2000] 2879 genes and 17 conditions α-cut=.5 for a and b defuzzification. ε = (results averaged on 20 runs) Size of biclusters vs λ and µ mu lambda Bioinformatics Data Sets

46 RESULTS Yeast data set Introduction Possibilistic algorithm PBC is slightly sensitive to initialization of memberships while strongly sensitive to parameters λ and µ. PBC can find biclusters of a desired size just tuning the parameters λ and µ (results averaged on 20 runs). λ µ n g n c n G Bioinformatics Data Sets

47 RESULTS Yeast data set Introduction Possibilistic algorithm Method avg. G avg. n avg. n g avg. n c Largest n DBF [Zhang et al 2004] FLOC [Yang et al 2003] Cheng-Church [2000] Single-objective GA [Mitra & Banka 2006] Multi-objective GA [Mitra & Banka 2006] Possibilistic Comparative study on Yeast data Bioinformatics Data Sets

48 RESULTS Yeast data set Introduction Possibilistic algorithm λ µ n g n c n G Method avg. G avg. n avg. n g avg. n c Largest n DBF [Zhang et al 2004] FLOC [Yang et al 2003] Cheng-Church [2000] Single-objective GA [Mitra & Banka 2006] Multi-objective GA [Mitra & Banka 2006] Possibilistic Bioinformatics Data Sets

49 RESULTS Yeast data set Introduction Possibilistic algorithm λ µ n g n c n G Method avg. G avg. n avg. n g avg. n c Largest n DBF [Zhang et al 2004] FLOC [Yang et al 2003] Cheng-Church [2000] Single-objective GA [Mitra & Banka 2006] Multi-objective GA [Mitra & Banka 2006] Possibilistic Bioinformatics Data Sets

50 RESULTS Yeast data set Introduction Possibilistic algorithm Expression Values Expression Values Conditions Conditions Plot of a small and a large bicluster Bioinformatics Data Sets

51 Possibilistic algorithm CONCLUSIONS The Possibilistic (PBC) algorithm extends the possibilistic clustering paradigm for the solution of the biclustering problem. The membership u ij of an element x ij of X to the bicluster is obtained by aggregation of memberships (typicality) of his row (gene) and column (condition) with respect to bicluster. The quality (residual G) of the large biclusters obtained is better than other biclustering methods. Further studies: biological validation of the obtained results automatically selection of parameters λ and µ other aggregators for obtaining u ij Bioinformatics Data Sets

52 Possibilistic algorithm CONCLUSIONS The Possibilistic (PBC) algorithm extends the possibilistic clustering paradigm for the solution of the biclustering problem. The membership u ij of an element x ij of X to the bicluster is obtained by aggregation of memberships (typicality) of his row (gene) and column (condition) with respect to bicluster. The quality (residual G) of the large biclusters obtained is better than other biclustering methods. Further studies: biological validation of the obtained results automatically selection of parameters λ and µ other aggregators for obtaining u ij Bioinformatics Data Sets