Recently several deep learning models have been used for DNA sequence based classification tasks. Often such tasks require long and variable length DNA sequences in the input. In this work, we use a sequence-to-sequence autoencoder model to learn a latent representation of a fixed dimension for long and variable length DNA sequences in an unsupervised manner. We evaluate both quantitatively and qualitatively the learned latent representation for a supervised task of splice site classification. The quantitative evaluation is done under two different settings. Our experiments show that these representations can be used as features or priors in closely related tasks such as splice site classification. Further, in our qualitative analysis, we use a model attribution technique Integrated Gradients to infer significant sequence signatures influencing the classification accuracy. We show the identified splice signatures resemble well with the existing knowledge.
Most of the previous work for feature learning and motif identification has been in the context of supervised learning. @cite_10 proposed a method for learning distributed feature representation of splice junctions using k-mers. Spline transformation was introduced by @cite_0 to improve upon traditional neural networks to learn better representations and improve prediction accuracy. @cite_11 used a memory matching network to dynamically learn a memory bank of motifs using sequence classification task. @cite_5 proposed a Restricted Boltzmann Machine based model with a new training method called boosted Contrastive Divergence to predict non-canonical splice sites and learn non-canonical feature vectors that couldn't be identified by traditional methods. Some works have also used Convolutional Neural Networks(CNN) in order to learn representations implicitly @cite_9 @cite_3 @cite_7 @cite_8 @cite_12 .
@cite_7 @cite_8 @cite_9 @cite_3 @cite_0 @cite_5 @cite_10 @cite_12 @cite_11
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Recently, neuron activations extracted from a pre-trained convolutional neural network (CNN) show promising performance in various visual tasks. However, due to the domain and task bias, using the features generated from the model pre-trained for image classification as image representations for instance retrieval is problematic. In this paper, we propose quartet-net learning to improve the discriminative power of CNN features for instance retrieval. The general idea is to map the features into a space where the image similarity can be better evaluated. Our network differs from the traditional Siamese-net in two ways. First, we adopt a double-margin contrastive loss with a dynamic margin tuning strategy to train the network which leads to more robust performance. Second, we introduce in the mimic learning regularization to improve the generalization ability of the network by preventing it from overfitting to the training data. Catering for the network learning, we collect a large-scale dataset, namely GeoPair, which consists of 68k matching image pairs and 63k non-matching pairs. Experiments on several standard instance retrieval datasets demonstrate the effectiveness of our method. Over the last years, deep convolutional neural networks (ConvNets) have transformed the field of computer vision thanks to their unparalleled capacity to learn high level semantic image features. However, in order to successfully learn those features, they usually require massive amounts of manually labeled data, which is both expensive and impractical to scale. Therefore, unsupervised semantic feature learning, i.e., learning without requiring manual annotation effort, is of crucial importance in order to successfully harvest the vast amount of visual data that are available today. In our work we propose to learn image features by training ConvNets to recognize the 2d rotation that is applied to the image that it gets as input. We demonstrate both qualitatively and quantitatively that this apparently simple task actually provides a very powerful supervisory signal for semantic feature learning. We exhaustively evaluate our method in various unsupervised feature learning benchmarks and we exhibit in all of them state-of-the-art performance. Specifically, our results on those benchmarks demonstrate dramatic improvements w.r.t. prior state-of-the-art approaches in unsupervised representation learning and thus significantly close the gap with supervised feature learning. For instance, in PASCAL VOC 2007 detection task our unsupervised pre-trained AlexNet model achieves the state-of-the-art (among unsupervised methods) mAP of 54.4 that is only 2.4 points lower from the supervised case. We get similarly striking results when we transfer our unsupervised learned features on various other tasks, such as ImageNet classification, PASCAL classification, PASCAL segmentation, and CIFAR-10 classification. The code and models of our paper will be published on: this https URL . Over the last years, deep convolutional neural networks (ConvNets) have transformed the field of computer vision thanks to their unparalleled capacity to learn high level semantic image features. However, in order to successfully learn those features, they usually require massive amounts of manually labeled data, which is both expensive and impractical to scale. Therefore, unsupervised semantic feature learning, i.e., learning without requiring manual annotation effort, is of crucial importance in order to successfully harvest the vast amount of visual data that are available today. In our work we propose to learn image features by training ConvNets to recognize the 2d rotation that is applied to the image that it gets as input. We demonstrate both qualitatively and quantitatively that this apparently simple task actually provides a very powerful supervisory signal for semantic feature learning. We exhaustively evaluate our method in various unsupervised feature learning benchmarks and we exhibit in all of them state-of-the-art performance. Specifically, our results on those benchmarks demonstrate dramatic improvements w.r.t. prior state-of-the-art approaches in unsupervised representation learning and thus significantly close the gap with supervised feature learning. For instance, in PASCAL VOC 2007 detection task our unsupervised pre-trained AlexNet model achieves the state-of-the-art (among unsupervised methods) mAP of 54.4 that is only 2.4 points lower from the supervised case. We get similar striking results when we transfer our unsupervised learned features on various other tasks, such as ImageNet classification, PASCAL classification, PASCAL segmentation, and CIFAR-10 classification. The main contribution of this paper is a simple semi-supervised pipeline that only uses the original training set without collecting extra data. It is challenging in 1) how to obtain more training data only from the training set and 2) how to use the newly generated data. In this work, the generative adversarial network (GAN) is used to generate unlabeled samples. We propose the label smoothing regularization for outliers (LSRO). This method assigns a uniform label distribution to the unlabeled images, which regularizes the supervised model and improves the baseline. We verify the proposed method on a practical problem: person re-identification (re-ID). This task aims to retrieve a query person from other cameras. We adopt the deep convolutional generative adversarial network (DCGAN) for sample generation, and a baseline convolutional neural network (CNN) for representation learning. Experiments show that adding the GAN-generated data effectively improves the discriminative ability of learned CNN embeddings. On three large-scale datasets, Market-1501, CUHK03 and DukeMTMC-reID, we obtain +4.37 , +1.6 and +2.46 improvement in rank-1 precision over the baseline CNN, respectively. We additionally apply the proposed method to fine-grained bird recognition and achieve a +0.6 improvement over a strong baseline. The code is available at this https URL