Biclustering is the task of simultaneously clustering the rows and columns of the data matrix into different subgroups such that the rows and columns within a subgroup exhibit similar patterns. In this paper, we consider the case of producing block-diagonal biclusters. We provide a new formulation of the biclustering problem based on the idea of minimizing the empirical clustering risk. We develop and prove a consistency result with respect to the empirical clustering risk. Since the optimization problem is combinatorial in nature, finding the global minimum is computationally intractable. In light of this fact, we propose a simple and novel algorithm that finds a local minimum by alternating the use of an adapted version of the k-means clustering algorithm between columns and rows. We evaluate and compare the performance of our algorithm to other related biclustering methods on both simulated data and real-world gene expression data sets. The results demonstrate that our algorithm is able to detect meaningful structures in the data and outperform other competing biclustering methods in various settings and situations.
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Given its status as a classic problem and its importance to both theoreticians and practitioners, edit distance provides an excellent lens through which to understand how the theoretical analysis of algorithms impacts practical implementations. From an applied perspective, the goals of theoretical analysis are to predict the empirical performance of an algorithm and to serve as a yardstick to design novel algorithms that perform well in practice. In this paper, we systematically survey the types of theoretical analysis techniques that have been applied to edit distance and evaluate the extent to which each one has achieved these two goals. These techniques include traditional worst-case analysis, worst-case analysis parametrized by edit distance or entropy or compressibility, average-case analysis, semi-random models, and advice-based models. We find that the track record is mixed. On one hand, two algorithms widely used in practice have been born out of theoretical analysis and their empirical performance is captured well by theoretical predictions. On the other hand, all the algorithms developed using theoretical analysis as a yardstick since then have not had any practical relevance. We conclude by discussing the remaining open problems and how they can be tackled.
The Bayesian information criterion (BIC), defined as the observed data log likelihood minus a penalty term based on the sample size $N$, is a popular model selection criterion for factor analysis with complete data. This definition has also been suggested for incomplete data. However, the penalty term based on the `complete' sample size $N$ is the same no matter whether in a complete or incomplete data case. For incomplete data, there are often only $N_i<N$ observations for variable $i$, which means that using the `complete' sample size $N$ implausibly ignores the amounts of missing information inherent in incomplete data. Given this observation, a novel criterion called hierarchical BIC (HBIC) for factor analysis with incomplete data is proposed. The novelty is that it only uses the actual amounts of observed information, namely $N_i$'s, in the penalty term. Theoretically, it is shown that HBIC is a large sample approximation of variational Bayesian (VB) lower bound, and BIC is a further approximation of HBIC, which means that HBIC shares the theoretical consistency of BIC. Experiments on synthetic and real data sets are conducted to access the finite sample performance of HBIC, BIC, and related criteria with various missing rates. The results show that HBIC and BIC perform similarly when the missing rate is small, but HBIC is more accurate when the missing rate is not small.
Linear mixed models (LMMs) are instrumental for regression analysis with structured dependence, such as grouped, clustered, or multilevel data. However, selection among the covariates--while accounting for this structured dependence--remains a challenge. We introduce a Bayesian decision analysis for subset selection with LMMs. Using a Mahalanobis loss function that incorporates the structured dependence, we derive optimal linear coefficients for (i) any given subset of variables and (ii) all subsets of variables that satisfy a cardinality constraint. Crucially, these estimates inherit shrinkage or regularization and uncertainty quantification from the underlying Bayesian model, and apply for any well-specified Bayesian LMM. More broadly, our decision analysis strategy deemphasizes the role of a single "best" subset, which is often unstable and limited in its information content, and instead favors a collection of near-optimal subsets. This collection is summarized by key member subsets and variable-specific importance metrics. Customized subset search and out-of-sample approximation algorithms are provided for more scalable computing. These tools are applied to simulated data and a longitudinal physical activity dataset, and demonstrate excellent prediction, estimation, and selection ability.
This paper considers the problem of inference in cluster randomized experiments when cluster sizes are non-ignorable. Here, by a cluster randomized experiment, we mean one in which treatment is assigned at the level of the cluster; by non-ignorable cluster sizes we mean that "large" clusters and "small" clusters may be heterogeneous, and, in particular, the effects of the treatment may vary across clusters of differing sizes. In order to permit this sort of flexibility, we consider a sampling framework in which cluster sizes themselves are random. In this way, our analysis departs from earlier analyses of cluster randomized experiments in which cluster sizes are treated as non-random. We distinguish between two different parameters of interest: the equally-weighted cluster-level average treatment effect, and the size-weighted cluster-level average treatment effect. For each parameter, we provide methods for inference in an asymptotic framework where the number of clusters tends to infinity and treatment is assigned using simple random sampling. We additionally permit the experimenter to sample only a subset of the units within each cluster rather than the entire cluster and demonstrate the implications of such sampling for some commonly used estimators. A small simulation study shows the practical relevance of our theoretical results.
In this study, we examine a clustering problem in which the covariates of each individual element in a dataset are associated with an uncertainty specific to that element. More specifically, we consider a clustering approach in which a pre-processing applying a non-linear transformation to the covariates is used to capture the hidden data structure. To this end, we approximate the sets representing the propagated uncertainty for the pre-processed features empirically. To exploit the empirical uncertainty sets, we propose a greedy and optimistic clustering (GOC) algorithm that finds better feature candidates over such sets, yielding more condensed clusters. As an important application, we apply the GOC algorithm to synthetic datasets of the orbital properties of stars generated through our numerical simulation mimicking the formation process of the Milky Way. The GOC algorithm demonstrates an improved performance in finding sibling stars originating from the same dwarf galaxy. These realistic datasets have also been made publicly available.
This paper presents a density-based topology optimization approach considering additive manufacturing limitations. The presented method considers the minimum size of parts, the minimum size of cavities, the inability of printing overhanging parts without the use of sacrificial supporting structures, and the printing directions. These constraints are geometrically addressed and implemented. The minimum size on solid and void zones is imposed through a well-known filtering technique. The sacrificial support material is reduced using a constraint that limits the maximum overhang angle of parts by comparing the structural gradient with a critical reference slope. Due to the local nature of the gradient, the chosen restriction is prone to introduce parts that meet the structural slope but that may not be self-supporting. The restriction limits the maximum overhang angle for a user-defined printing direction, which could reduce structural performance if the orientation is not properly selected. To ease these challenges, a new approach to reduce the introduction of such non-self-supporting parts and a novel method that includes different printing directions in the maximum overhang angle constraint are presented. The proposed strategy for considering the minimum size of solid and void phases, maximum overhang angle, and printing direction, is illustrated by solving a set of 2D benchmark design problems including stiff structures and compliant mechanisms. We also provide MATLAB codes in the appendix for educational purposes and for replication of the results.
In this paper, we propose a one-stage online clustering method called Contrastive Clustering (CC) which explicitly performs the instance- and cluster-level contrastive learning. To be specific, for a given dataset, the positive and negative instance pairs are constructed through data augmentations and then projected into a feature space. Therein, the instance- and cluster-level contrastive learning are respectively conducted in the row and column space by maximizing the similarities of positive pairs while minimizing those of negative ones. Our key observation is that the rows of the feature matrix could be regarded as soft labels of instances, and accordingly the columns could be further regarded as cluster representations. By simultaneously optimizing the instance- and cluster-level contrastive loss, the model jointly learns representations and cluster assignments in an end-to-end manner. Extensive experimental results show that CC remarkably outperforms 17 competitive clustering methods on six challenging image benchmarks. In particular, CC achieves an NMI of 0.705 (0.431) on the CIFAR-10 (CIFAR-100) dataset, which is an up to 19\% (39\%) performance improvement compared with the best baseline.
Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster. However, the eigendecomposition of the Laplacian is expensive and, since clustering results are graph-specific, pooling methods based on SC must perform a new optimization for each new sample. In this paper, we propose a graph clustering approach that addresses these limitations of SC. We formulate a continuous relaxation of the normalized minCUT problem and train a GNN to compute cluster assignments that minimize this objective. Our GNN-based implementation is differentiable, does not require to compute the spectral decomposition, and learns a clustering function that can be quickly evaluated on out-of-sample graphs. From the proposed clustering method, we design a graph pooling operator that overcomes some important limitations of state-of-the-art graph pooling techniques and achieves the best performance in several supervised and unsupervised tasks.
Clustering is one of the most fundamental and wide-spread techniques in exploratory data analysis. Yet, the basic approach to clustering has not really changed: a practitioner hand-picks a task-specific clustering loss to optimize and fit the given data to reveal the underlying cluster structure. Some types of losses---such as k-means, or its non-linear version: kernelized k-means (centroid based), and DBSCAN (density based)---are popular choices due to their good empirical performance on a range of applications. Although every so often the clustering output using these standard losses fails to reveal the underlying structure, and the practitioner has to custom-design their own variation. In this work we take an intrinsically different approach to clustering: rather than fitting a dataset to a specific clustering loss, we train a recurrent model that learns how to cluster. The model uses as training pairs examples of datasets (as input) and its corresponding cluster identities (as output). By providing multiple types of training datasets as inputs, our model has the ability to generalize well on unseen datasets (new clustering tasks). Our experiments reveal that by training on simple synthetically generated datasets or on existing real datasets, we can achieve better clustering performance on unseen real-world datasets when compared with standard benchmark clustering techniques. Our meta clustering model works well even for small datasets where the usual deep learning models tend to perform worse.
In this paper, we present an accurate and scalable approach to the face clustering task. We aim at grouping a set of faces by their potential identities. We formulate this task as a link prediction problem: a link exists between two faces if they are of the same identity. The key idea is that we find the local context in the feature space around an instance (face) contains rich information about the linkage relationship between this instance and its neighbors. By constructing sub-graphs around each instance as input data, which depict the local context, we utilize the graph convolution network (GCN) to perform reasoning and infer the likelihood of linkage between pairs in the sub-graphs. Experiments show that our method is more robust to the complex distribution of faces than conventional methods, yielding favorably comparable results to state-of-the-art methods on standard face clustering benchmarks, and is scalable to large datasets. Furthermore, we show that the proposed method does not need the number of clusters as prior, is aware of noises and outliers, and can be extended to a multi-view version for more accurate clustering accuracy.
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