Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics. Recently, a few deep learning models have surpassed the traditional window based multilayer perceptron. Taking inspiration from the image classification domain we propose a deep convolutional neural network architecture, MUST-CNN, to predict protein properties. This architecture uses a novel multilayer shift-and-stitch (MUST) technique to generate fully dense per-position predictions on protein sequences. Our model is significantly simpler than the state-of-the-art, yet achieves better results. By combining MUST and the efficient convolution operation, we can consider far more parameters while retaining very fast prediction speeds. We beat the state-of-the-art performance on two large protein property prediction datasets.
In the image domain, @cite_15 has beaten the state-of-the-art on image classification by a large percentage through using a deep multilayer convolutional network in the ImageNet Large-Scale Visual Recognition Challenge. Scene labeling is the task of labeling each pixel of an image with one of several classes, a 2D analogue of protein property prediction. @cite_19 uses a recurrent neural network to obtain state-of-the-art results on scene labeling without any feature engineering. @cite_24 designs fully convolutional networks for dense pixel prediction by running several convolutional networks on different scales. @cite_20 increases the resolution of a bounding box based image classifier by introducing the shift-and-stitch technique, which we use on sequences instead of images and on the entire model instead of only on the last layer.
@cite_24 @cite_19 @cite_15 @cite_20
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Deep convolution neural networks (CNN) have demonstrated advanced performance on single-label image classification, and various progress also have been made to apply CNN methods on multi-label image classification, which requires to annotate objects, attributes, scene categories etc. in a single shot. Recent state-of-the-art approaches to multi-label image classification exploit the label dependencies in an image, at global level, largely improving the labeling capacity. However, predicting small objects and visual concepts is still challenging due to the limited discrimination of the global visual features. In this paper, we propose a Regional Latent Semantic Dependencies model (RLSD) to address this problem. The utilized model includes a fully convolutional localization architecture to localize the regions that may contain multiple highly-dependent labels. The localized regions are further sent to the recurrent neural networks (RNN) to characterize the latent semantic dependencies at the regional level. Experimental results on several benchmark datasets show that our proposed model achieves the best performance compared to the state-of-the-art models, especially for predicting small objects occurred in the images. In addition, we set up an upper bound model (RLSD+ft-RPN) using bounding box coordinates during training, the experimental results also show that our RLSD can approach the upper bound without using the bounding-box annotations, which is more realistic in the real world. Deep convolution neural networks (CNNs) have demonstrated advanced performance on single-label image classification, and various progress also has been made to apply CNN methods on multilabel image classification, which requires annotating objects, attributes, scene categories, etc., in a single shot. Recent state-of-the-art approaches to the multilabel image classification exploit the label dependencies in an image, at the global level, largely improving the labeling capacity. However, predicting small objects and visual concepts is still challenging due to the limited discrimination of the global visual features. In this paper, we propose a regional latent semantic dependencies model (RLSD) to address this problem. The utilized model includes a fully convolutional localization architecture to localize the regions that may contain multiple highly dependent labels. The localized regions are further sent to the recurrent neural networks to characterize the latent semantic dependencies at the regional level. Experimental results on several benchmark datasets show that our proposed model achieves the best performance compared to the state-of-the-art models, especially for predicting small objects occurring in the images. Also, we set up an upper bound model (RLSD+ft-RPN) using bounding-box coordinates during training, and the experimental results also show that our RLSD can approach the upper bound without using the bounding-box annotations, which is more realistic in the real world. Learning efficient image representations is at the core of the scene classification task of remote sensing imagery. The existing methods for solving the scene classification task, based on either feature coding approaches with low-level hand-engineered features or unsupervised feature learning, can only generate mid-level image features with limited representative ability, which essentially prevents them from achieving better performance. Recently, the deep convolutional neural networks (CNNs), which are hierarchical architectures trained on large-scale datasets, have shown astounding performance in object recognition and detection. However, it is still not clear how to use these deep convolutional neural networks for high-resolution remote sensing (HRRS) scene classification. In this paper, we investigate how to transfer features from these successfully pre-trained CNNs for HRRS scene classification. We propose two scenarios for generating image features via extracting CNN features from different layers. In the first scenario, the activation vectors extracted from fully-connected layers are regarded as the final image features; in the second scenario, we extract dense features from the last convolutional layer at multiple scales and then encode the dense features into global image features through commonly used feature coding approaches. Extensive experiments on two public scene classification datasets demonstrate that the image features obtained by the two proposed scenarios, even with a simple linear classifier, can result in remarkable performance and improve the state-of-the-art by a significant margin. The results reveal that the features from pre-trained CNNs generalize well to HRRS datasets and are more expressive than the low- and mid-level features. Moreover, we tentatively combine features extracted from different CNN models for better performance. This paper introduces WILDCAT, a deep learning method which jointly aims at aligning image regions for gaining spatial invariance and learning strongly localized features. Our model is trained using only global image labels and is devoted to three main visual recognition tasks: image classification, weakly supervised object localization and semantic segmentation. WILDCAT extends state-of-the-art Convolutional Neural Networks at three main levels: the use of Fully Convolutional Networks for maintaining spatial resolution, the explicit design in the network of local features related to different class modalities, and a new way to pool these features to provide a global image prediction required for weakly supervised training. Extensive experiments show that our model significantly outperforms state-of-the-art methods.