The availability of large microarray data has led to a growing interest in biclustering methods in the past decade. Several algorithms have been proposed to identify subsets of genes and conditions according to different similarity measures and under varying constraints. In this paper we focus on the exclusive row biclustering problem for gene expression data sets, in which each row can only be a member of a single bicluster while columns can participate in multiple ones. This type of biclustering may be adequate, for example, for clustering groups of cancer patients where each patient (row) is expected to be carrying only a single type of cancer, while each cancer type is associated with multiple (and possibly overlapping) genes (columns). We present a novel method to identify these exclusive row biclusters through a combination of existing biclustering algorithms and combinatorial auction techniques. We devise an approach for tuning the threshold for our algorithm based on comparison to a null model in the spirit of the Gap statistic approach. We demonstrate our approach on both synthetic and real-world gene expression data and show its power in identifying large span non-overlapping rows sub matrices, while considering their unique nature. The Gap statistic approach succeeds in identifying appropriate thresholds in all our examples.
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Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.
Most existing approaches to disfluency detection heavily rely on human-annotated data, which is expensive to obtain in practice. To tackle the training data bottleneck, we investigate methods for combining multiple self-supervised tasks-i.e., supervised tasks where data can be collected without manual labeling. First, we construct large-scale pseudo training data by randomly adding or deleting words from unlabeled news data, and propose two self-supervised pre-training tasks: (i) tagging task to detect the added noisy words. (ii) sentence classification to distinguish original sentences from grammatically-incorrect sentences. We then combine these two tasks to jointly train a network. The pre-trained network is then fine-tuned using human-annotated disfluency detection training data. Experimental results on the commonly used English Switchboard test set show that our approach can achieve competitive performance compared to the previous systems (trained using the full dataset) by using less than 1% (1000 sentences) of the training data. Our method trained on the full dataset significantly outperforms previous methods, reducing the error by 21% on English Switchboard.
Intersection over Union (IoU) is the most popular evaluation metric used in the object detection benchmarks. However, there is a gap between optimizing the commonly used distance losses for regressing the parameters of a bounding box and maximizing this metric value. The optimal objective for a metric is the metric itself. In the case of axis-aligned 2D bounding boxes, it can be shown that $IoU$ can be directly used as a regression loss. However, $IoU$ has a plateau making it infeasible to optimize in the case of non-overlapping bounding boxes. In this paper, we address the weaknesses of $IoU$ by introducing a generalized version as both a new loss and a new metric. By incorporating this generalized $IoU$ ($GIoU$) as a loss into the state-of-the art object detection frameworks, we show a consistent improvement on their performance using both the standard, $IoU$ based, and new, $GIoU$ based, performance measures on popular object detection benchmarks such as PASCAL VOC and MS COCO.
We discuss problems with the standard approaches to evaluation for tasks like visual question answering, and argue that artificial data can be used to address these as a complement to current practice. We demonstrate that with the help of existing 'deep' linguistic processing technology we are able to create challenging abstract datasets, which enable us to investigate the language understanding abilities of multimodal deep learning models in detail, as compared to a single performance value on a static and monolithic dataset.
Clustering and classification critically rely on distance metrics that provide meaningful comparisons between data points. We present mixed-integer optimization approaches to find optimal distance metrics that generalize the Mahalanobis metric extensively studied in the literature. Additionally, we generalize and improve upon leading methods by removing reliance on pre-designated "target neighbors," "triplets," and "similarity pairs." Another salient feature of our method is its ability to enable active learning by recommending precise regions to sample after an optimal metric is computed to improve classification performance. This targeted acquisition can significantly reduce computational burden by ensuring training data completeness, representativeness, and economy. We demonstrate classification and computational performance of the algorithms through several simple and intuitive examples, followed by results on real image and medical datasets.
We demonstrate that many detection methods are designed to identify only a sufficently accurate bounding box, rather than the best available one. To address this issue we propose a simple and fast modification to the existing methods called Fitness NMS. This method is tested with the DeNet model and obtains a significantly improved MAP at greater localization accuracies without a loss in evaluation rate, and can be used in conjunction with Soft NMS for additional improvements. Next we derive a novel bounding box regression loss based on a set of IoU upper bounds that better matches the goal of IoU maximization while still providing good convergence properties. Following these novelties we investigate RoI clustering schemes for improving evaluation rates for the DeNet wide model variants and provide an analysis of localization performance at various input image dimensions. We obtain a MAP of 33.6%@79Hz and 41.8%@5Hz for MSCOCO and a Titan X (Maxwell). Source code available from: //github.com/lachlants/denet
Many resource allocation problems in the cloud can be described as a basic Virtual Network Embedding Problem (VNEP): finding mappings of request graphs (describing the workloads) onto a substrate graph (describing the physical infrastructure). In the offline setting, the two natural objectives are profit maximization, i.e., embedding a maximal number of request graphs subject to the resource constraints, and cost minimization, i.e., embedding all requests at minimal overall cost. The VNEP can be seen as a generalization of classic routing and call admission problems, in which requests are arbitrary graphs whose communication endpoints are not fixed. Due to its applications, the problem has been studied intensively in the networking community. However, the underlying algorithmic problem is hardly understood. This paper presents the first fixed-parameter tractable approximation algorithms for the VNEP. Our algorithms are based on randomized rounding. Due to the flexible mapping options and the arbitrary request graph topologies, we show that a novel linear program formulation is required. Only using this novel formulation the computation of convex combinations of valid mappings is enabled, as the formulation needs to account for the structure of the request graphs. Accordingly, to capture the structure of request graphs, we introduce the graph-theoretic notion of extraction orders and extraction width and show that our algorithms have exponential runtime in the request graphs' maximal width. Hence, for request graphs of fixed extraction width, we obtain the first polynomial-time approximations. Studying the new notion of extraction orders we show that (i) computing extraction orders of minimal width is NP-hard and (ii) that computing decomposable LP solutions is in general NP-hard, even when restricting request graphs to planar ones.
We consider the task of learning the parameters of a {\em single} component of a mixture model, for the case when we are given {\em side information} about that component, we call this the "search problem" in mixture models. We would like to solve this with computational and sample complexity lower than solving the overall original problem, where one learns parameters of all components. Our main contributions are the development of a simple but general model for the notion of side information, and a corresponding simple matrix-based algorithm for solving the search problem in this general setting. We then specialize this model and algorithm to four common scenarios: Gaussian mixture models, LDA topic models, subspace clustering, and mixed linear regression. For each one of these we show that if (and only if) the side information is informative, we obtain parameter estimates with greater accuracy, and also improved computation complexity than existing moment based mixture model algorithms (e.g. tensor methods). We also illustrate several natural ways one can obtain such side information, for specific problem instances. Our experiments on real data sets (NY Times, Yelp, BSDS500) further demonstrate the practicality of our algorithms showing significant improvement in runtime and accuracy.
A recommender system aims to recommend items that a user is interested in among many items. The need for the recommender system has been expanded by the information explosion. Various approaches have been suggested for providing meaningful recommendations to users. One of the proposed approaches is to consider a recommender system as a Markov decision process (MDP) problem and try to solve it using reinforcement learning (RL). However, existing RL-based methods have an obvious drawback. To solve an MDP in a recommender system, they encountered a problem with the large number of discrete actions that bring RL to a larger class of problems. In this paper, we propose a novel RL-based recommender system. We formulate a recommender system as a gridworld game by using a biclustering technique that can reduce the state and action space significantly. Using biclustering not only reduces space but also improves the recommendation quality effectively handling the cold-start problem. In addition, our approach can provide users with some explanation why the system recommends certain items. Lastly, we examine the proposed algorithm on a real-world dataset and achieve a better performance than the widely used recommendation algorithm.
Labeled Latent Dirichlet Allocation (LLDA) is an extension of the standard unsupervised Latent Dirichlet Allocation (LDA) algorithm, to address multi-label learning tasks. Previous work has shown it to perform in par with other state-of-the-art multi-label methods. Nonetheless, with increasing label sets sizes LLDA encounters scalability issues. In this work, we introduce Subset LLDA, a simple variant of the standard LLDA algorithm, that not only can effectively scale up to problems with hundreds of thousands of labels but also improves over the LLDA state-of-the-art. We conduct extensive experiments on eight data sets, with label sets sizes ranging from hundreds to hundreds of thousands, comparing our proposed algorithm with the previously proposed LLDA algorithms (Prior--LDA, Dep--LDA), as well as the state of the art in extreme multi-label classification. The results show a steady advantage of our method over the other LLDA algorithms and competitive results compared to the extreme multi-label classification algorithms.
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