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Gene Selection for Cancer Classification using Support Vector Machines   总被引:71,自引:0,他引:71  
DNA micro-arrays now permit scientists to screen thousands of genes simultaneously and determine whether those genes are active, hyperactive or silent in normal or cancerous tissue. Because these new micro-array devices generate bewildering amounts of raw data, new analytical methods must be developed to sort out whether cancer tissues have distinctive signatures of gene expression over normal tissues or other types of cancer tissues.In this paper, we address the problem of selection of a small subset of genes from broad patterns of gene expression data, recorded on DNA micro-arrays. Using available training examples from cancer and normal patients, we build a classifier suitable for genetic diagnosis, as well as drug discovery. Previous attempts to address this problem select genes with correlation techniques. We propose a new method of gene selection utilizing Support Vector Machine methods based on Recursive Feature Elimination (RFE). We demonstrate experimentally that the genes selected by our techniques yield better classification performance and are biologically relevant to cancer.In contrast with the baseline method, our method eliminates gene redundancy automatically and yields better and more compact gene subsets. In patients with leukemia our method discovered 2 genes that yield zero leave-one-out error, while 64 genes are necessary for the baseline method to get the best result (one leave-one-out error). In the colon cancer database, using only 4 genes our method is 98% accurate, while the baseline method is only 86% accurate.  相似文献
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Recently, large scale image annotation datasets have been collected with millions of images and thousands of possible annotations. Latent variable models, or embedding methods, that simultaneously learn semantic representations of object labels and image representations can provide tractable solutions on such tasks. In this work, we are interested in jointly learning representations both for the objects in an image, and the parts of those objects, because such deeper semantic representations could bring a leap forward in image retrieval or browsing. Despite the size of these datasets, the amount of annotated data for objects and parts can be costly and may not be available. In this paper, we propose to bypass this cost with a method able to learn to jointly label objects and parts without requiring exhaustively labeled data. We design a model architecture that can be trained under a proxy supervision obtained by combining standard image annotation (from ImageNet) with semantic part-based within-label relations (from WordNet). The model itself is designed to model both object image to object label similarities, and object label to object part label similarities in a single joint system. Experiments conducted on our combined data and a precisely annotated evaluation set demonstrate the usefulness of our approach.  相似文献
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Large-scale relational learning becomes crucial for handling the huge amounts of structured data generated daily in many application domains ranging from computational biology or information retrieval, to natural language processing. In this paper, we present a new neural network architecture designed to embed multi-relational graphs into a flexible continuous vector space in which the original data is kept and enhanced. The network is trained to encode the semantics of these graphs in order to assign high probabilities to plausible components. We empirically show that it reaches competitive performance in link prediction on standard datasets from the literature as well as on data from a real-world knowledge base (WordNet). In addition, we present how our method can be applied to perform word-sense disambiguation in a context of open-text semantic parsing, where the goal is to learn to assign a structured meaning representation to almost any sentence of free text, demonstrating that it can scale up to tens of thousands of nodes and thousands of types of relation.  相似文献
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Image annotation datasets are becoming larger and larger, with tens of millions of images and tens of thousands of possible annotations. We propose a strongly performing method that scales to such datasets by simultaneously learning to optimize precision at k of the ranked list of annotations for a given image and learning a low-dimensional joint embedding space for both images and annotations. Our method both outperforms several baseline methods and, in comparison to them, is faster and consumes less memory. We also demonstrate how our method learns an interpretable model, where annotations with alternate spellings or even languages are close in the embedding space. Hence, even when our model does not predict the exact annotation given by a human labeler, it often predicts similar annotations, a fact that we try to quantify by measuring the newly introduced “sibling” precision metric, where our method also obtains excellent results.  相似文献
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