Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used handcrafted features on human-annotated data sets. In this paper, we propose a novel tree recurrent neural network with structured attention architecture for doing PPI. Our architecture achieves state of the art results (precision, recall, and F1-score) on the AIMed and BioInfer benchmark data sets. Moreover, our models achieve a significant improvement over previous best models without any explicit feature extraction. Our experimental results show that traditional recurrent networks have inferior performance compared to tree recurrent networks for the supervised PPI problem.
@cite_41 adopt a convolutional neural network (CNN) based approach in which they utilize two channels of CNN for high level feature extraction. In one channel, they use raw words along with some syntactic features such as parts-of speech, chunk parsing information, named entities, syntactic dependencies and two distance vectors for each word representing the distance from the word to the two proteins being considered as interacting. In another channel they use parent word information for each word and pass this to an embedding layer to get a distributed representation of the sentence in terms of parent words. Following this, they apply convolution on these two channels separately and map them via a fully connected layer to the required number of classes.
@cite_41
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Convolutional neural network (CNN) has achieved the state-of-the-art performance in many different visual tasks. Learned from a large-scale training data set, CNN features are much more discriminative and accurate than the handcrafted features. Moreover, CNN features are also transferable among different domains. On the other hand, traditional dictionary-based features (such as BoW and spatial pyramid matching) contain much more local discriminative and structural information, which is implicitly embedded in the images. To further improve the performance, in this paper, we propose to combine CNN with dictionary-based models for scene recognition and visual domain adaptation (DA). Specifically, based on the well-tuned CNN models (e.g., AlexNet and VGG Net), two dictionary-based representations are further constructed, namely, mid-level local representation (MLR) and convolutional Fisher vector (CFV) representation. In MLR, an efficient two-stage clustering method, i.e., weighted spatial and feature space spectral clustering on the parts of a single image followed by clustering all representative parts of all images, is used to generate a class-mixture or a class-specific part dictionary. After that, the part dictionary is used to operate with the multiscale image inputs for generating mid-level representation. In CFV, a multiscale and scale-proportional Gaussian mixture model training strategy is utilized to generate Fisher vectors based on the last convolutional layer of CNN. By integrating the complementary information of MLR, CFV, and the CNN features of the fully connected layer, the state-of-the-art performance can be achieved on scene recognition and DA problems. An interested finding is that our proposed hybrid representation (from VGG net trained on ImageNet) is also complementary to GoogLeNet and or VGG-11 (trained on Place205) greatly. We introduce a novel, simple convolution neural network (CNN) architecture ‐ multi-group norm constraint CNN (MGNC-CNN) ‐ that capitalizes on multiple sets of word embeddings for sentence classification. MGNCCNN extracts features from input embedding sets independently and then joins these at the penultimate layer in the network to form a final feature vector. We then adopt a group regularization strategy that differentially penalizes weights associated with the subcomponents generated from the respective embedding sets. This model is much simpler than comparable alternative architectures and requires substantially less training time. Furthermore, it is flexible in that it does not require input word embeddings to be of the same dimensionality. We show that MGNC-CNN consistently outperforms baseline models. Convolutional neural networks (CNNs) have recently achieved remarkable successes in various image classification and understanding tasks. The deep features obtained at the top fully connected layer of the CNN (FC-features) exhibit rich global semantic information and are extremely effective in image classification. On the other hand, the convolutional features in the middle layers of the CNN also contain meaningful local information, but are not fully explored for image representation. In this paper, we propose a novel locally supervised deep hybrid model (LS-DHM) that effectively enhances and explores the convolutional features for scene recognition. First, we notice that the convolutional features capture local objects and fine structures of scene images, which yield important cues for discriminating ambiguous scenes, whereas these features are significantly eliminated in the highly compressed FC representation. Second, we propose a new local convolutional supervision layer to enhance the local structure of the image by directly propagating the label information to the convolutional layers. Third, we propose an efficient Fisher convolutional vector (FCV) that successfully rescues the orderless mid-level semantic information (e.g., objects and textures) of scene image. The FCV encodes the large-sized convolutional maps into a fixed-length mid-level representation, and is demonstrated to be strongly complementary to the high-level FC-features. Finally, both the FCV and FC-features are collaboratively employed in the LS-DHM representation, which achieves outstanding performance in our experiments. It obtains 83.75 and 67.56 accuracies, respectively, on the heavily benchmarked MIT Indoor67 and SUN397 data sets, advancing the state-of-the-art substantially. This paper proposes a learning strategy that extracts object-part concepts from a pre-trained convolutional neural network (CNN), in an attempt to 1) explore explicit semantics hidden in CNN units and 2) gradually grow a semantically interpretable graphical model on the pre-trained CNN for hierarchical object understanding. Given part annotations on very few (e.g., 3-12) objects, our method mines certain latent patterns from the pre-trained CNN and associates them with different semantic parts. We use a four-layer And-Or graph to organize the mined latent patterns, so as to clarify their internal semantic hierarchy. Our method is guided by a small number of part annotations, and it achieves superior performance (about 13 -107 improvement) in part center prediction on the PASCAL VOC and ImageNet datasets.