We address an ensemble clustering problem, where reliable clusters are locally embedded in given multiple partitions. We propose a new nonnegative matrix factorization (NMF)-based method, in which locally reliable clusters are explicitly considered by using instance-wise weights over clusters. Our method factorizes the input cluster assignment matrix into two matrices H and W, which are optimized by iteratively 1) updating H and W while keeping the weight matrix constant and 2) updating the weight matrix while keeping H and W constant, alternatively. The weights in the second step were updated by solving a convex problem, which makes our algorithm significantly faster than existing NMF-based ensemble clustering methods. We empirically proved that our method outperformed a lot of cutting-edge ensemble clustering methods by using a variety of datasets.

In knowledge bases or information extraction results, differently expressed relations can be semantically similar (e.g., (X, wrote, Y) and (X,'s written work, Y)). Therefore, grouping semantically similar relations into clusters would facilitate and improve many applications, including knowledge base completion, information extraction, information retrieval, and more. This paper formulates relation clustering as a constrained tripartite graph clustering problem, presents an efficient clustering algorithm and exhibits the advantage of the constrained framework. We introduce several ways that provide side information via must-link and cannot link constraints to improve the clustering results. Different from traditional semi-supervised learning approaches, we propose to use the similarity of relation expressions and the knowledge of entity types to automatically construct the constraints for the algorithm. We show improved relation clustering results on two datasets extracted from human annotated knowledge base (i.e., Freebase) and open information extraction results (i.e., ReVerb data).

In this paper, we propose a stratified topic model (STM). Instead of directly modeling and inferring flat topics or hierarchically structured topics, we use the stratified relationships in topic hierarchies to regularize the flat topics. The topic structures are captured by a hierarchical clustering method and play as constraints during the learning process. We propose two theoretically sound and practical inference methods to solve the model. Experimental results with two real world data sets and various evaluation metrics demonstrate the effectiveness of the proposed model.

The Nystrom method provides an efficient sampling approach for large scale clustering problems, by generating a low-rank matrix approximation. However, existing sampling methods are limited by accuracy and computing time. This paper proposes an improved Nystrom-based clustering algorithm with a new sampling procedure, Minimum Sum of Squared Similarities (MSSS). Experiments on synthetic and real data sets show that the proposed sampling performs with higher accuracy than existing algorithms, applied to Nystrom-based spectral clustering problems. Furthermore, we provide a theoretical analysis that allows us to define the upper bound of the Frobenius norm error of the MSSS.

In this work, we first attempt to replicate an earlier study on gene selection and clustering, and then we extend this work by applying a different type of hierarchical clustering to dis- cover interesting subsets of genes from breast cancer data. Replication of such studies is a known challenge and an ac- tive area of research in bioinformatics. The work presented in this paper is three-fold. First, we replicate a study conducted at the University of North Carolina to generate an initial set of genes. Second, we apply an approach called Distance Weighted Discrimination to fuse multiple, disparate breast cancer datasets into a single validation set. Third, we per- form hierarchical clustering and k-means clustering on this validation set to discover natural groupings and compare the clusters generated by both methods. While applying the hi- erarchical clustering is part of the reproduction step, we ex- tend the research by trying two different forms of hierarchi- cal clustering. We also apply k-means clustering for the same purpose and compare all three methods using Kaplan-Meier estimation and Cox proportional hazards regression. We dis- cover that among the three methods, k-means clustering gives us the best results.

In many applications, training machine learning models involves using large amounts of human-annotated data. Obtaining precise labels for the data is expensive. Instead, training with weak supervision provides a low-cost alternative. We propose a novel weak supervision algorithm that processes noisy labels, i.e., weak signals, while also considering features of the training data to produce accurate labels for training. Our method searches over classifiers of the data representation to find plausible labelings. We call this paradigm data consistent weak supervision. A key facet of our framework is that we are able to estimate labels for data examples low or no coverage from the weak supervision. In addition, we make no assumptions about the joint distribution of the weak signals and true labels of the data. Instead, we use weak signals and the data features to solve a constrained optimization that enforces data consistency among the labels we generate. Empirical evaluation of our method on different datasets shows that it significantly outperforms state-of-the-art weak supervision methods on both text and image classification tasks.

We present a meta-method for initializing (seeding) the $k$-means clustering algorithm called PNN-smoothing. It consists in splitting a given dataset into $J$ random subsets, clustering each of them individually, and merging the resulting clusterings with the pairwise-nearest-neighbor (PNN) method. It is a meta-method in the sense that when clustering the individual subsets any seeding algorithm can be used. If the computational complexity of that seeding algorithm is linear in the size of the data $N$ and the number of clusters $k$, PNN-smoothing is also almost linear with an appropriate choice of $J$, and in fact only at most a few percent slower in most cases in practice. We show empirically, using several existing seeding methods and testing on several synthetic and real datasets, that this procedure results in systematically better costs. It can even be applied recursively, and easily parallelized. Our implementation is publicly available at https://github.com/carlobaldassi/KMeansPNNSmoothing.jl

Semidefinite programming (SDP) is a powerful tool for tackling a wide range of computationally hard problems such as clustering. Despite the high accuracy, semidefinite programs are often too slow in practice with poor scalability on large (or even moderate) datasets. In this paper, we introduce a linear time complexity algorithm for approximating an SDP relaxed $K$-means clustering. The proposed sketch-and-lift (SL) approach solves an SDP on a subsampled dataset and then propagates the solution to all data points by a nearest-centroid rounding procedure. It is shown that the SL approach enjoys a similar exact recovery threshold as the $K$-means SDP on the full dataset, which is known to be information-theoretically tight under the Gaussian mixture model. The SL method can be made adaptive with enhanced theoretic properties when the cluster sizes are unbalanced. Our simulation experiments demonstrate that the statistical accuracy of the proposed method outperforms state-of-the-art fast clustering algorithms without sacrificing too much computational efficiency, and is comparable to the original $K$-means SDP with substantially reduced runtime.

BioBERT and BioMegatron are Transformers models adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We investigate the encoding and representation of biological knowledge in these models, and its potential utility to support inference in cancer precision medicine - namely, the interpretation of the clinical significance of genomic alterations. We compare the performance of different transformer baselines; we use probing to determine the consistency of encodings for distinct entities; and we use clustering methods to compare and contrast the internal properties of the embeddings for genes, variants, drugs and diseases. We show that these models do indeed encode biological knowledge, although some of this is lost in fine-tuning for specific tasks. Finally, we analyse how the models behave with regard to biases and imbalances in the dataset.

Algorithm configuration (AC) is concerned with the automated search of the most suitable parameter configuration of a parametrized algorithm. There is currently a wide variety of AC problem variants and methods proposed in the literature. Existing reviews do not take into account all derivatives of the AC problem, nor do they offer a complete classification scheme. To this end, we introduce taxonomies to describe the AC problem and features of configuration methods, respectively. We review existing AC literature within the lens of our taxonomies, outline relevant design choices of configuration approaches, contrast methods and problem variants against each other, and describe the state of AC in industry. Finally, our review provides researchers and practitioners with a look at future research directions in the field of AC.