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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Scene labeling can be seen as a sequence-sequence prediction task (pixels-labels), and it is quite important to leverage relevant context to enhance the performance of pixel classification. In this paper, we introduce an episodic attention-based memory network to achieve the goal. We present a unified framework that mainly consists of a Convolutional Neural Network (CNN), specifically, Fully Convolutional Network (FCN) and an attention-based memory module with feedback connections to perform context selection and refinement. The full model produces context-aware representation for each target patch by aggregating the activated context and its original local representation produced by the convolution layers. We evaluate our model on PASCAL Context, SIFT Flow and PASCAL VOC 2011 datasets and achieve competitive results to other state-of-the-art methods in scene labeling. Recent approaches for instance-aware semantic labeling have augmented convolutional neural networks (CNNs) with complex multi-task architectures or computationally expensive graphical models. We present a method that leverages a fully convolutional network (FCN) to predict semantic labels, depth and an instance-based encoding using each pixel’s direction towards its corresponding instance center. Subsequently, we apply low-level computer vision techniques to generate state-of-the-art instance segmentation on the street scene datasets KITTI and Cityscapes. Our approach outperforms existing works by a large margin and can additionally predict absolute distances of individual instances from a monocular image as well as a pixel-level semantic labeling. Scene labeling is a challenging computer vision task. It requires the use of both local discriminative features and global context information. We adopt a deep recurrent convolutional neural network (RCNN) for this task, which is originally proposed for object recognition. Different from traditional convolutional neural networks (CNN), this model has intra-layer recurrent connections in the convolutional layers. Therefore each convolutional layer becomes a two-dimensional recurrent neural network. The units receive constant feed-forward inputs from the previous layer and recurrent inputs from their neighborhoods. While recurrent iterations proceed, the region of context captured by each unit expands. In this way, feature extraction and context modulation are seamlessly integrated, which is different from typical methods that entail separate modules for the two steps. To further utilize the context, a multi-scale RCNN is proposed. Over two benchmark datasets, Standford Background and Sift Flow, the model outperforms many state-of-the-art models in accuracy and efficiency. Pixel wise image labeling is an interesting and challenging problem with great significance in the computer vision community. In order for a dense labeling algorithm to be able to achieve accurate and precise results, it has to consider the dependencies that exist in the joint space of both the input and the output variables. An implicit approach for modeling those dependencies is by training a deep neural network that, given as input an initial estimate of the output labels and the input image, it will be able to predict a new refined estimate for the labels. In this context, our work is concerned with what is the optimal architecture for performing the label improvement task. We argue that the prior approaches of either directly predicting new label estimates or predicting residual corrections w.r.t. the initial labels with feed-forward deep network architectures are sub-optimal. Instead, we propose a generic architecture that decomposes the label improvement task to three steps: 1) detecting the initial label estimates that are incorrect, 2) replacing the incorrect labels with new ones, and finally 3) refining the renewed labels by predicting residual corrections w.r.t. them. Furthermore, we explore and compare various other alternative architectures that consist of the aforementioned Detection, Replace, and Refine components. We extensively evaluate the examined architectures in the challenging task of dense disparity estimation (stereo matching) and we report both quantitative and qualitative results on three different datasets. Finally, our dense disparity estimation network that implements the proposed generic architecture, achieves state-of-the-art results in the KITTI 2015 test surpassing prior approaches by a significant margin. We plan to release the Torch code that implements the paper in: https: github.com gidariss DRR_struct_pred .