Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

PaccMannRL^{RL}: Designing anticancer drugs from transcriptomic data via reinforcement learning

With the advent of deep generative models in computational chemistry, in silico anticancer drug design has undergone an unprecedented transformation. While state-of-the-art deep learning approaches have shown potential in generating compounds with desired chemical properties, they disregard the genetic profile and properties of the target disease. Here, we introduce the first generative model capable of tailoring anticancer compounds for a specific biomolecular profile. Using a RL framework, the transcriptomic profiles of cancer cells are used as a context for the generation of candidate molecules. Our molecule generator combines two separately pretrained variational autoencoders (VAEs) - the first VAE encodes transcriptomic profiles into a smooth, latent space which in turn is used to condition a second VAE to generate novel molecular structures on the given transcriptomic profile. The generative process is optimized through PaccMann, a previously developed drug sensitivity prediction model to obtain effective anticancer compounds for the given context (i.e., transcriptomic profile). We demonstrate how the molecule generation can be biased towards compounds with high predicted inhibitory effect against individual cell lines or specific cancer sites. We verify our approach by investigating candidate drugs generated against specific cancer types and find the highest structural similarity to existing compounds with known efficacy against these cancer types. We envision our approach to transform in silico anticancer drug design by leveraging the biomolecular characteristics of the disease in order to increase success rates in lead compound discovery.Comment: 18 pages total (12 pages main text, 4 pages references, 11 pages appendix) 8 figure

Time-delay neural network for continuous emotional dimension prediction from facial expression sequences

"(c) 2015 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works."Automatic continuous affective state prediction from naturalistic facial expression is a very challenging research topic but very important in human-computer interaction. One of the main challenges is modeling the dynamics that characterize naturalistic expressions. In this paper, a novel two-stage automatic system is proposed to continuously predict affective dimension values from facial expression videos. In the first stage, traditional regression methods are used to classify each individual video frame, while in the second stage, a Time-Delay Neural Network (TDNN) is proposed to model the temporal relationships between consecutive predictions. The two-stage approach separates the emotional state dynamics modeling from an individual emotional state prediction step based on input features. In doing so, the temporal information used by the TDNN is not biased by the high variability between features of consecutive frames and allows the network to more easily exploit the slow changing dynamics between emotional states. The system was fully tested and evaluated on three different facial expression video datasets. Our experimental results demonstrate that the use of a two-stage approach combined with the TDNN to take into account previously classified frames significantly improves the overall performance of continuous emotional state estimation in naturalistic facial expressions. The proposed approach has won the affect recognition sub-challenge of the third international Audio/Visual Emotion Recognition Challenge (AVEC2013)1

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

A survey of deep learning models in medical therapeutic areas.

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Automatic Prediction of Impressions in Time and across Varying Context: Personality, Attractiveness and Likeability

© 2010-2012 IEEE. In this paper, we propose a novel multimodal framework for automatically predicting the impressions of extroversion, agreeableness, conscientiousness, neuroticism , openness, attractiveness and likeability continuously in time and across varying situational contexts. Differently from the existing works, we obtain visual-only and audio-only annotations continuously in time for the same set of subjects, for the first time in the literature, and compare them to their audio-visual annotations. We propose a time-continuous prediction approach that learns the temporal relationships rather than treating each time instant separately. Our experiments show that the best prediction results are obtained when regression models are learned from audio-visual annotations and visual cues, and from audio-visual annotations and visual cues combined with audio cues at the decision level. Continuously generated annotations have the potential to provide insight into better understanding which impressions can be formed and predicted more dynamically, varying with situational context, and which ones appear to be more static and stable over time.This research work was supported by the EPSRC MAPTRAITS Project (Grant Ref: EP/K017500/1) and the EPSRC HARPS Project under its IDEAS Factory Sandpits call on Digital Personhood (Grant Ref: EP/L00416X/1)