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Register a new userMining Functionally Related Genes with Semi-Supervised Learning
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The study of biological processes can greatly benefit from tools that automatically predict gene functions or directly cluster genes based on shared functionality. Existing data mining methods predict protein functionality by exploiting data obtained from high-throughput experiments or meta-scale information from public databases. Most existing prediction tools are targeted at predicting protein functions that are described in the gene ontology (GO). However, in many cases biologists wish to discover functionally related genes for which GO terms are inadequate. In this paper, we introduce a rich set of features and use them in conjunction with semisupervised learning approaches in order to expand an initial set of seed genes to a larger cluster of functionally related genes. Among all the semi-supervised methods that were evaluated, the framework of learning with positive and unlabeled examples (LPU) is shown to be especially appropriate for mining functionally related genes. When evaluated on experimentally validated benchmark data, the LPU approaches1 significantly outperform a standard supervised learning algorithm as well as an established state-of-the-art method. Given an initial set of seed genes, our best performing approach could be used to mine functionally related genes in a wide range of organisms.
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While semi-supervised learning (SSL) has received tremendous attentions in many machine learning tasks due to its successful use of unlabeled data, existing SSL algorithms use either all unlabeled examples or the unlabeled examples with a fixed high-confidence prediction during the training progress. However, it is possible that too many correct/wrong pseudo labeled examples are eliminated/selected. In this work we develop a simple yet powerful framework, whose key idea is to select a subset of training examples from the unlabeled data when performing existing SSL methods so that only the unlabeled examples with pseudo labels related to the labeled data will be used to train models. The selection is performed at each updating iteration by only keeping the examples whose losses are smaller than a given threshold that is dynamically adjusted through the iteration. Our proposed approach, Dash, enjoys its adaptivity in terms of unlabeled data selection and its theoretical guarantee. Specifically, we theoretically establish the convergence rate of Dash from the view of non-convex optimization. Finally, we empirically demonstrate the effectiveness of the proposed method in comparison with state-of-the-art over benchmarks.
We propose a data-efficient Gaussian process-based Bayesian approach to the semi-supervised learning problem on graphs. The proposed model shows extremely competitive performance when compared to the state-of-the-art graph neural networks on semi-supervised learning benchmark experiments, and outperforms the neural networks in active learning experiments where labels are scarce. Furthermore, the model does not require a validation data set for early stopping to control over-fitting. Our model can be viewed as an instance of empirical distribution regression weighted locally by network connectivity. We further motivate the intuitive construction of the model with a Bayesian linear model interpretation where the node features are filtered by an operator related to the graph Laplacian. The method can be easily implemented by adapting off-the-shelf scalable variational inference algorithms for Gaussian processes.
Semi-Supervised Learning (SSL) has achieved great success in overcoming the difficulties of labeling and making full use of unlabeled data. However, SSL has a limited assumption that the numbers of samples in different classes are balanced, and many SSL algorithms show lower performance for the datasets with the imbalanced class distribution. In this paper, we introduce a task of class-imbalanced semi-supervised learning (CISSL), which refers to semi-supervised learning with class-imbalanced data. In doing so, we consider class imbalance in both labeled and unlabeled sets. First, we analyze existing SSL methods in imbalanced environments and examine how the class imbalance affects SSL methods. Then we propose Suppressed Consistency Loss (SCL), a regularization method robust to class imbalance. Our method shows better performance than the conventional methods in the CISSL environment. In particular, the more severe the class imbalance and the smaller the size of the labeled data, the better our method performs.
The Mean Teacher (MT) model of Tarvainen and Valpola has shown favorable performance on several semi-supervised benchmark datasets. MT maintains a teacher models weights as the exponential moving average of a student models weights and minimizes the divergence between their probability predictions under diverse perturbations of the inputs. However, MT is known to suffer from confirmation bias, that is, reinforcing incorrect teacher model predictions. In this work, we propose a simple yet effective method called Local Clustering (LC) to mitigate the effect of confirmation bias. In MT, each data point is considered independent of other points during training; however, data points are likely to be close to each other in feature space if they share similar features. Motivated by this, we cluster data points locally by minimizing the pairwise distance between neighboring data points in feature space. Combined with a standard classification cross-entropy objective on labeled data points, the misclassified unlabeled data points are pulled towards high-density regions of their correct class with the help of their neighbors, thus improving model performance. We demonstrate on semi-supervised benchmark datasets SVHN and CIFAR-10 that adding our LC loss to MT yields significant improvements compared to MT and performance comparable to the state of the art in semi-supervised learning.
Generative Adversarial Networks (GANs) based semi-supervised learning (SSL) approaches are shown to improve classification performance by utilizing a large number of unlabeled samples in conjunction with limited labeled samples. However, their performance still lags behind the state-of-the-art non-GAN based SSL approaches. We identify that the main reason for this is the lack of consistency in class probability predictions on the same image under local perturbations. Following the general literature, we address this issue via label consistency regularization, which enforces the class probability predictions for an input image to be unchanged under various semantic-preserving perturbations. In this work, we introduce consistency regularization into the vanilla semi-GAN to address this critical limitation. In particular, we present a new composite consistency regularization method which, in spirit, leverages both local consistency and interpolation consistency. We demonstrate the efficacy of our approach on two SSL image classification benchmark datasets, SVHN and CIFAR-10. Our experiments show that this new composite consistency regularization based semi-GAN significantly improves its performance and achieves new state-of-the-art performance among GAN-based SSL approaches.
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