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

Full Resolution Image Compression with Recurrent Neural Networks

This paper presents a set of full-resolution lossy image compression methods based on neural networks. Each of the architectures we describe can provide variable compression rates during deployment without requiring retraining of the network: each network need only be trained once. All of our architectures consist of a recurrent neural network (RNN)-based encoder and decoder, a binarizer, and a neural network for entropy coding. We compare RNN types (LSTM, associative LSTM) and introduce a new hybrid of GRU and ResNet. We also study "one-shot" versus additive reconstruction architectures and introduce a new scaled-additive framework. We compare to previous work, showing improvements of 4.3%-8.8% AUC (area under the rate-distortion curve), depending on the perceptual metric used. As far as we know, this is the first neural network architecture that is able to outperform JPEG at image compression across most bitrates on the rate-distortion curve on the Kodak dataset images, with and without the aid of entropy coding.Comment: Updated with content for CVPR and removed supplemental material to an external link for size limitation

An end-to-end convolutional selective autoencoder approach to Soybean Cyst Nematode eggs detection

This paper proposes a novel selective autoencoder approach within the framework of deep convolutional networks. The crux of the idea is to train a deep convolutional autoencoder to suppress undesired parts of an image frame while allowing the desired parts resulting in efficient object detection. The efficacy of the framework is demonstrated on a critical plant science problem. In the United States, approximately $1 billion is lost per annum due to a nematode infection on soybean plants. Currently, plant-pathologists rely on labor-intensive and time-consuming identification of Soybean Cyst Nematode (SCN) eggs in soil samples via manual microscopy. The proposed framework attempts to significantly expedite the process by using a series of manually labeled microscopic images for training followed by automated high-throughput egg detection. The problem is particularly difficult due to the presence of a large population of non-egg particles (disturbances) in the image frames that are very similar to SCN eggs in shape, pose and illumination. Therefore, the selective autoencoder is trained to learn unique features related to the invariant shapes and sizes of the SCN eggs without handcrafting. After that, a composite non-maximum suppression and differencing is applied at the post-processing stage.Comment: A 10 pages, 8 figures International Conference on Machine Leaning(ICML) Submissio

Leaning Robust Sequence Features via Dynamic Temporal Pattern Discovery

As a major type of data, time series possess invaluable latent knowledge for describing the real world and human society. In order to improve the ability of intelligent systems for understanding the world and people, it is critical to design sophisticated machine learning algorithms for extracting robust time series features from such latent knowledge. Motivated by the successful applications of deep learning in computer vision, more and more machine learning researchers put their attentions on the topic of applying deep learning techniques to time series data. However, directly employing current deep models in most time series domains could be problematic. A major reason is that temporal pattern types that current deep models are aiming at are very limited, which cannot meet the requirement of modeling different underlying patterns of data coming from various sources. In this study we address this problem by designing different network structures explicitly based on specific domain knowledge such that we can extract features via most salient temporal patterns. More specifically, we mainly focus on two types of temporal patterns: order patterns and frequency patterns. For order patterns, which are usually related to brain and human activities, we design a hashing-based neural network layer to globally encode the ordinal pattern information into the resultant features. It is further generalized into a specially designed Recurrent Neural Networks (RNN) cell which can learn order patterns in an online fashion. On the other hand, we believe audio-related data such as music and speech can benefit from modeling frequency patterns. Thus, we do so by developing two types of RNN cells. The first type tries to directly learn the long-term dependencies on frequency domain rather than time domain. The second one aims to dynamically filter out the noise frequencies based on temporal contexts. By proposing various deep models based on different domain knowledge and evaluating them on extensive time series tasks, we hope this work can provide inspirations for others and increase the community\u27s interests on the problem of applying deep learning techniques to more time series tasks

Learned Quality Enhancement via Multi-Frame Priors for HEVC Compliant Low-Delay Applications

Networked video applications, e.g., video conferencing, often suffer from poor visual quality due to unexpected network fluctuation and limited bandwidth. In this paper, we have developed a Quality Enhancement Network (QENet) to reduce the video compression artifacts, leveraging the spatial and temporal priors generated by respective multi-scale convolutions spatially and warped temporal predictions in a recurrent fashion temporally. We have integrated this QENet as a standard-alone post-processing subsystem to the High Efficiency Video Coding (HEVC) compliant decoder. Experimental results show that our QENet demonstrates the state-of-the-art performance against default in-loop filters in HEVC and other deep learning based methods with noticeable objective gains in Peak-Signal-to-Noise Ratio (PSNR) and subjective gains visually