Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks

Protein secondary structure prediction is an important problem in bioinformatics. Inspired by the recent successes of deep neural networks, in this paper, we propose an end-to-end deep network that predicts protein secondary structures from integrated local and global contextual features. Our deep architecture leverages convolutional neural networks with different kernel sizes to extract multiscale local contextual features. In addition, considering long-range dependencies existing in amino acid sequences, we set up a bidirectional neural network consisting of gated recurrent unit to capture global contextual features. Furthermore, multi-task learning is utilized to predict secondary structure labels and amino-acid solvent accessibility simultaneously. Our proposed deep network demonstrates its effectiveness by achieving state-of-the-art performance, i.e., 69.7% Q8 accuracy on the public benchmark CB513, 76.9% Q8 accuracy on CASP10 and 73.1% Q8 accuracy on CASP11. Our model and results are publicly available.Comment: 8 pages, 3 figures, Accepted by International Joint Conferences on Artificial Intelligence (IJCAI

Revisiting the Hierarchical Multiscale LSTM

Hierarchical Multiscale LSTM (Chung et al., 2016a) is a state-of-the-art language model that learns interpretable structure from character-level input. Such models can provide fertile ground for (cognitive) computational linguistics studies. However, the high complexity of the architecture, training procedure and implementations might hinder its applicability. We provide a detailed reproduction and ablation study of the architecture, shedding light on some of the potential caveats of re-purposing complex deep-learning architectures. We further show that simplifying certain aspects of the architecture can in fact improve its performance. We also investigate the linguistic units (segments) learned by various levels of the model, and argue that their quality does not correlate with the overall performance of the model on language modeling.Comment: To appear in COLING 2018 (reproduction track

Recurrent Convolutional Neural Networks for Scene Parsing

Scene parsing is a technique that consist on giving a label to all pixels in an image according to the class they belong to. To ensure a good visual coherence and a high class accuracy, it is essential for a scene parser to capture image long range dependencies. In a feed-forward architecture, this can be simply achieved by considering a sufficiently large input context patch, around each pixel to be labeled. We propose an approach consisting of a recurrent convolutional neural network which allows us to consider a large input context, while limiting the capacity of the model. Contrary to most standard approaches, our method does not rely on any segmentation methods, nor any task-specific features. The system is trained in an end-to-end manner over raw pixels, and models complex spatial dependencies with low inference cost. As the context size increases with the built-in recurrence, the system identifies and corrects its own errors. Our approach yields state-of-the-art performance on both the Stanford Background Dataset and the SIFT Flow Dataset, while remaining very fast at test time

DeepCare: A Deep Dynamic Memory Model for Predictive Medicine

Personalized predictive medicine necessitates the modeling of patient illness and care processes, which inherently have long-term temporal dependencies. Healthcare observations, recorded in electronic medical records, are episodic and irregular in time. We introduce DeepCare, an end-to-end deep dynamic neural network that reads medical records, stores previous illness history, infers current illness states and predicts future medical outcomes. At the data level, DeepCare represents care episodes as vectors in space, models patient health state trajectories through explicit memory of historical records. Built on Long Short-Term Memory (LSTM), DeepCare introduces time parameterizations to handle irregular timed events by moderating the forgetting and consolidation of memory cells. DeepCare also incorporates medical interventions that change the course of illness and shape future medical risk. Moving up to the health state level, historical and present health states are then aggregated through multiscale temporal pooling, before passing through a neural network that estimates future outcomes. We demonstrate the efficacy of DeepCare for disease progression modeling, intervention recommendation, and future risk prediction. On two important cohorts with heavy social and economic burden -- diabetes and mental health -- the results show improved modeling and risk prediction accuracy.Comment: Accepted at JBI under the new name: "Predicting healthcare trajectories from medical records: A deep learning approach

Continuous Learning in a Hierarchical Multiscale Neural Network

We reformulate the problem of encoding a multi-scale representation of a sequence in a language model by casting it in a continuous learning framework. We propose a hierarchical multi-scale language model in which short time-scale dependencies are encoded in the hidden state of a lower-level recurrent neural network while longer time-scale dependencies are encoded in the dynamic of the lower-level network by having a meta-learner update the weights of the lower-level neural network in an online meta-learning fashion. We use elastic weights consolidation as a higher-level to prevent catastrophic forgetting in our continuous learning framework.Comment: 5 pages, 2 figures, accepted as short paper at ACL 201