Cardiac indices estimation is of great importance during identification and diagnosis of cardiac disease in clinical routine. However, estimation of multitype cardiac indices with consistently reliable and high accuracy is still a great challenge due to the high variability of cardiac structures and complexity of temporal dynamics in cardiac MR sequences. While efforts have been devoted into cardiac volumes estimation through feature engineering followed by a independent regression model, these methods suffer from the vulnerable feature representation and incompatible regression model. In this paper, we propose a semi-automated method for multitype cardiac indices estimation. After manual labelling of two landmarks for ROI cropping, an integrated deep neural network Indices-Net is designed to jointly learn the representation and regression models. It comprises two tightly-coupled networks: a deep convolution autoencoder (DCAE) for cardiac image representation, and a multiple output convolution neural network (CNN) for indices regression. Joint learning of the two networks effectively enhances the expressiveness of image representation with respect to cardiac indices, and the compatibility between image representation and indices regression, thus leading to accurate and reliable estimations for all the cardiac indices. When applied with five-fold cross validation on MR images of 145 subjects, Indices-Net achieves consistently low estimation error for LV wall thicknesses (1.44$\pm$0.71mm) and areas of cavity and myocardium (204$\pm$133mm$^2$). It outperforms, with significant error reductions, segmentation method (55.1% and 17.4%) and two-phase direct volume-only methods (12.7% and 14.6%) for wall thicknesses and areas, respectively. These advantages endow the proposed method a great potential in clinical cardiac function assessment.
Cities have been a thriving place for citizens over the centuries due to their complex infrastructure. The emergence of the Cyber-Physical-Social Systems (CPSS) and context-aware technologies boost a growing interest in analysing, extracting and eventually understanding city events which subsequently can be utilised to leverage the citizen observations of their cities. In this paper, we investigate the feasibility of using Twitter textual streams for extracting city events. We propose a hierarchical multi-view deep learning approach to contextualise citizen observations of various city systems and services. Our goal has been to build a flexible architecture that can learn representations useful for tasks, thus avoiding excessive task-specific feature engineering. We apply our approach on a real-world dataset consisting of event reports and tweets of over four months from San Francisco Bay Area dataset and additional datasets collected from London. The results of our evaluations show that our proposed solution outperforms the existing models and can be used for extracting city related events with an averaged accuracy of 81% over all classes. To further evaluate the impact of our Twitter event extraction model, we have used two sources of authorised reports through collecting road traffic disruptions data from Transport for London API, and parsing the Time Out London website for sociocultural events. The analysis showed that 49.5% of the Twitter traffic comments are reported approximately five hours prior to the authorities official records. Moreover, we discovered that amongst the scheduled sociocultural event topics; tweets reporting transportation, cultural and social events are 31.75% more likely to influence the distribution of the Twitter comments than sport, weather and crime topics.
Deep neural network (DNN) based approaches hold significant potential for reinforcement learning (RL) and have already shown remarkable gains over state-of-art methods in a number of applications. The effectiveness of DNN methods can be attributed to leveraging the abundance of supervised data to learn value functions, Q-functions, and policy function approximations without the need for feature engineering. Nevertheless, the deployment of DNN-based predictors with very deep architectures can pose an issue due to computational and other resource constraints at test-time in a number of applications. We propose a novel approach for reducing the average latency by learning a computationally efficient gating function that is capable of recognizing states in a sequential decision process for which policy prescriptions of a shallow network suffices and deeper layers of the DNN have little marginal utility. The overall system is adaptive in that it dynamically switches control actions based on state-estimates in order to reduce average latency without sacrificing terminal performance. We experiment with a number of alternative loss-functions to train gating functions and shallow policies and show that in a number of applications a speed-up of up to almost 5X can be obtained with little loss in performance.
Recent advances in visual tracking showed that deep Convolutional Neural Networks (CNN) trained for image classification can be strong feature extractors for discriminative trackers. However, due to the drastic difference between image classification and tracking, extra treatments such as model ensemble and feature engineering must be carried out to bridge the two domains. Such procedures are either time consuming or hard to generalize well across datasets. In this paper we discovered that the internal structure of Region Proposal Network (RPN)'s top layer feature can be utilized for robust visual tracking. We showed that such property has to be unleashed by a novel loss function which simultaneously considers classification accuracy and bounding box quality. Without ensemble and any extra treatment on feature maps, our proposed method achieved state-of-the-art results on several large scale benchmarks including OTB50, OTB100 and VOT2016. We will make our code publicly available.
Recent advances in combining deep learning and Reinforcement Learning have shown a promising path for designing new control agents that can learn optimal policies for challenging control tasks. These new methods address the main limitations of conventional Reinforcement Learning methods such as customized feature engineering and small action/state space dimension requirements. In this paper, we leverage one of the state-of-the-art Reinforcement Learning methods, known as Trust Region Policy Optimization, to tackle intersection management for autonomous vehicles. We show that using this method, we can perform fine-grained acceleration control of autonomous vehicles in a grid street plan to achieve a global design objective.
Feature engineering is one of the most important and time consuming tasks in predictive analytics projects. It involves understanding domain knowledge and data exploration to discover relevant hand-crafted features from raw data. In this paper, we introduce a system called One Button Machine, or OneBM for short, which automates feature discovery in relational databases. OneBM automatically performs a key activity of data scientists, namely, joining of database tables and applying advanced data transformations to extract useful features from data. We validated OneBM in Kaggle competitions in which OneBM achieved performance as good as top 16% to 24% data scientists in three Kaggle competitions. More importantly, OneBM outperformed the state-of-the-art system in a Kaggle competition in terms of prediction accuracy and ranking on Kaggle leaderboard. The results show that OneBM can be useful for both data scientists and non-experts. It helps data scientists reduce data exploration time allowing them to try and error many ideas in short time. On the other hand, it enables non-experts, who are not familiar with data science, to quickly extract value from their data with a little effort, time and cost.
We present a novel neural network model that learns POS tagging and graph-based dependency parsing jointly. Our model uses bidirectional LSTMs to learn feature representations shared for both POS tagging and dependency parsing tasks, thus handling the feature-engineering problem. Our extensive experiments, on 19 languages from the Universal Dependencies project, show that our model outperforms the state-of-the-art neural network-based Stack-propagation model for joint POS tagging and transition-based dependency parsing, resulting in a new state of the art. Our code is open-source and available together with pre-trained models at: https://github.com/datquocnguyen/jPTDP
One advantage of decision tree based methods like random forests is their ability to natively handle categorical predictors without having to first transform them (e.g., by using feature engineering techniques). However, in this paper, we show how this capability can lead to an inherent "absent levels" problem for decision tree based methods that has never been thoroughly discussed, and whose consequences have never been carefully explored. This problem occurs whenever there is an indeterminacy over how to handle an observation that has reached a categorical split which was determined when the observation in question's level was absent during training. Although these incidents may appear to be innocuous, by using Leo Breiman and Adele Cutler's random forests FORTRAN code and the randomForest R package (Liaw and Wiener, 2002) as motivating case studies, we examine how overlooking the absent levels problem can systematically bias a model. Furthermore, by using three real data examples, we illustrate how absent levels can dramatically alter a model's performance in practice, and we empirically demonstrate how some simple heuristics can be used to help mitigate the effects of the absent levels problem until a more robust theoretical solution is found.
Clinical notes are a rich source of information about patient state. However, using them to predict clinical events with machine learning models is challenging. They are very high dimensional, sparse and have complex structure. Furthermore, training data is often scarce because it is expensive to obtain reliable labels for many clinical events. These difficulties have traditionally been addressed by manual feature engineering encoding task specific domain knowledge. We explored the use of neural networks and transfer learning to learn representations of clinical notes that are useful for predicting future clinical events of interest, such as all causes mortality, inpatient admissions, and emergency room visits. Our data comprised 2.7 million notes and 115 thousand patients at Stanford Hospital. We used the learned representations, along with commonly used bag of words and topic model representations, as features for predictive models of clinical events. We evaluated the effectiveness of these representations with respect to the performance of the models trained on small datasets. Models using the neural network derived representations performed significantly better than models using the baseline representations with small ($N < 1000$) training datasets. The learned representations offer significant performance gains over commonly used baseline representations for a range of predictive modeling tasks and cohort sizes, offering an effective alternative to task specific feature engineering when plentiful labeled training data is not available.
Machine-learned models are often described as "black boxes". In many real-world applications however, models may have to sacrifice predictive power in favour of human-interpretability. When this is the case, feature engineering becomes a crucial task, which requires significant and time-consuming human effort. Whilst some features are inherently static, representing properties that cannot be influenced (e.g., the age of an individual), others capture characteristics that could be adjusted (e.g., the daily amount of carbohydrates taken). Nonetheless, once a model is learned from the data, each prediction it makes on new instances is irreversible - assuming every instance to be a static point located in the chosen feature space. There are many circumstances however where it is important to understand (i) why a model outputs a certain prediction on a given instance, (ii) which adjustable features of that instance should be modified, and finally (iii) how to alter such a prediction when the mutated instance is input back to the model. In this paper, we present a technique that exploits the internals of a tree-based ensemble classifier to offer recommendations for transforming true negative instances into positively predicted ones. We demonstrate the validity of our approach using an online advertising application. First, we design a Random Forest classifier that effectively separates between two types of ads: low (negative) and high (positive) quality ads (instances). Then, we introduce an algorithm that provides recommendations that aim to transform a low quality ad (negative instance) into a high quality one (positive instance). Finally, we evaluate our approach on a subset of the active inventory of a large ad network, Yahoo Gemini.
In the last few years, we have seen the transformative impact of deep learning in many applications, particularly in speech recognition and computer vision. Inspired by Google's Inception-ResNet deep convolutional neural network (CNN) for image classification, we have developed "Chemception", a deep CNN for the prediction of chemical properties, using just the images of 2D drawings of molecules. We develop Chemception without providing any additional explicit chemistry knowledge, such as basic concepts like periodicity, or advanced features like molecular descriptors and fingerprints. We then show how Chemception can serve as a general-purpose neural network architecture for predicting toxicity, activity, and solvation properties when trained on a modest database of 600 to 40,000 compounds. When compared to multi-layer perceptron (MLP) deep neural networks trained with ECFP fingerprints, Chemception slightly outperforms in activity and solvation prediction and slightly underperforms in toxicity prediction. Having matched the performance of expert-developed QSAR/QSPR deep learning models, our work demonstrates the plausibility of using deep neural networks to assist in computational chemistry research, where the feature engineering process is performed primarily by a deep learning algorithm.
Research in analysis of microblogging platforms is experiencing a renewed surge with a large number of works applying representation learning models for applications like sentiment analysis, semantic textual similarity computation, hashtag prediction, etc. Although the performance of the representation learning models has been better than the traditional baselines for such tasks, little is known about the elementary properties of a tweet encoded within these representations, or why particular representations work better for certain tasks. Our work presented here constitutes the first step in opening the black-box of vector embeddings for tweets. Traditional feature engineering methods for high-level applications have exploited various elementary properties of tweets. We believe that a tweet representation is effective for an application because it meticulously encodes the application-specific elementary properties of tweets. To understand the elementary properties encoded in a tweet representation, we evaluate the representations on the accuracy to which they can model each of those properties such as tweet length, presence of particular words, hashtags, mentions, capitalization, etc. Our systematic extensive study of nine supervised and four unsupervised tweet representations against most popular eight textual and five social elementary properties reveal that Bi-directional LSTMs (BLSTMs) and Skip-Thought Vectors (STV) best encode the textual and social properties of tweets respectively. FastText is the best model for low resource settings, providing very little degradation with reduction in embedding size. Finally, we draw interesting insights by correlating the model performance obtained for elementary property prediction tasks with the highlevel downstream applications.
Background. Previous state-of-the-art systems on Drug Name Recognition (DNR) and Clinical Concept Extraction (CCE) have focused on a combination of text "feature engineering" and conventional machine learning algorithms such as conditional random fields and support vector machines. However, developing good features is inherently heavily time-consuming. Conversely, more modern machine learning approaches such as recurrent neural networks (RNNs) have proved capable of automatically learning effective features from either random assignments or automated word "embeddings". Objectives. (i) To create a highly accurate DNR and CCE system that avoids conventional, time-consuming feature engineering. (ii) To create richer, more specialized word embeddings by using health domain datasets such as MIMIC-III. (iii) To evaluate our systems over three contemporary datasets. Methods. Two deep learning methods, namely the Bidirectional LSTM and the Bidirectional LSTM-CRF, are evaluated. A CRF model is set as the baseline to compare the deep learning systems to a traditional machine learning approach. The same features are used for all the models. Results. We have obtained the best results with the Bidirectional LSTM-CRF model, which has outperformed all previously proposed systems. The specialized embeddings have helped to cover unusual words in DDI-DrugBank and DDI-MedLine, but not in the 2010 i2b2/VA IRB Revision dataset. Conclusion. We present a state-of-the-art system for DNR and CCE. Automated word embeddings has allowed us to avoid costly feature engineering and achieve higher accuracy. Nevertheless, the embeddings need to be retrained over datasets that are adequate for the domain, in order to adequately cover the domain-specific vocabulary.
Neural word segmentation has attracted more and more research interests for its ability to alleviate the effort of feature engineering and utilize the external resource by the pre-trained character or word embeddings. In this paper, we propose a new neural model to incorporate the word-level information for Chinese word segmentation. Unlike the previous word-based models, our model still adopts the framework of character-based sequence labeling, which has advantages on both effectiveness and efficiency at the inference stage. To utilize the word-level information, we also propose a new long short-term memory (LSTM) architecture over directed acyclic graph (DAG). Experimental results demonstrate that our model leads to better performances than the baseline models.
Recently, neural network models for natural language processing tasks have been increasingly focused on for their ability of alleviating the burden of manual feature engineering. However, the previous neural models cannot extract the complicated feature compositions as the traditional methods with discrete features. In this work, we propose a feature-enriched neural model for joint Chinese word segmentation and part-of-speech tagging task. Specifically, to simulate the feature templates of traditional discrete feature based models, we use different filters to model the complex compositional features with convolutional and pooling layer, and then utilize long distance dependency information with recurrent layer. Experimental results on five different datasets show the effectiveness of our proposed model.
This paper presents an approach for automation of interpretable feature selection for Internet Of Things Analytics (IoTA) using machine learning (ML) techniques. Authors have conducted a survey over different people involved in different IoTA based application development tasks. The survey reveals that feature selection is the most time consuming and niche skill demanding part of the entire workflow. This paper shows how feature selection is successfully automated without sacrificing the decision making accuracy and thereby reducing the project completion time and cost of hiring expensive resources. Several pattern recognition principles and state of art (SoA) ML techniques are followed to design the overall approach for the proposed automation. Three data sets are considered to establish the proof-of-concept. Experimental results show that the proposed automation is able to reduce the time for feature selection to $2$ days instead of $4-6$ months which would have been required in absence of the automation. This reduction in time is achieved without any sacrifice in the accuracy of the decision making process. Proposed method is also compared against Multi Layer Perceptron (MLP) model as most of the state of the art works on IoTA uses MLP based Deep Learning. Moreover the feature selection method is compared against SoA feature reduction technique namely Principal Component Analysis (PCA) and its variants. The results obtained show that the proposed method is effective.
Existing approaches to automatic VerbNet-style verb classification are heavily dependent on feature engineering and therefore limited to languages with mature NLP pipelines. In this work, we propose a novel cross-lingual transfer method for inducing VerbNets for multiple languages. To the best of our knowledge, this is the first study which demonstrates how the architectures for learning word embeddings can be applied to this challenging syntactic-semantic task. Our method uses cross-lingual translation pairs to tie each of the six target languages into a bilingual vector space with English, jointly specialising the representations to encode the relational information from English VerbNet. A standard clustering algorithm is then run on top of the VerbNet-specialised representations, using vector dimensions as features for learning verb classes. Our results show that the proposed cross-lingual transfer approach sets new state-of-the-art verb classification performance across all six target languages explored in this work.
The introduction of cheap RGB-D cameras, stereo cameras, and LIDAR devices has given the computer vision community 3D information that conventional RGB cameras cannot provide. This data is often stored as a point cloud. In this paper, we present a novel method to apply the concept of convolutional neural networks to this type of data. By creating a mapping of nearest neighbors in a dataset, and individually applying weights to spatial relationships between points, we achieve an architecture that works directly with point clouds, but closely resembles a convolutional neural net in both design and behavior. Such a method bypasses the need for extensive feature engineering, while proving to be computationally efficient and requiring few parameters.
Recently we proposed a general, ensemble-based feature engineering wrapper (FEW) that was paired with a number of machine learning methods to solve regression problems. Here, we adapt FEW for supervised classification and perform a thorough analysis of fitness and survival methods within this framework. Our tests demonstrate that two fitness metrics, one introduced as an adaptation of the silhouette score, outperform the more commonly used Fisher criterion. We analyze survival methods and demonstrate that $\epsilon$-lexicase survival works best across our test problems, followed by random survival which outperforms both tournament and deterministic crowding. We conduct a benchmark comparison to several classification methods using a large set of problems and show that FEW can improve the best classifier performance in several cases. We show that FEW generates consistent, meaningful features for a biomedical problem with different ML pairings.
Medical practitioners use survival models to explore and understand the relationships between patients' covariates (e.g. clinical and genetic features) and the effectiveness of various treatment options. Standard survival models like the linear Cox proportional hazards model require extensive feature engineering or prior medical knowledge to model treatment interaction at an individual level. While nonlinear survival methods, such as neural networks and survival forests, can inherently model these high-level interaction terms, they have yet to be shown as effective treatment recommender systems. We introduce DeepSurv, a Cox proportional hazards deep neural network and state-of-the-art survival method for modeling interactions between a patient's covariates and treatment effectiveness in order to provide personalized treatment recommendations. We perform a number of experiments training DeepSurv on simulated and real survival data. We demonstrate that DeepSurv performs as well as or better than other state-of-the-art survival models and validate that DeepSurv successfully models increasingly complex relationships between a patient's covariates and their risk of failure. We then show how DeepSurv models the relationship between a patient's features and effectiveness of different treatment options to show how DeepSurv can be used to provide individual treatment recommendations. Finally, we train DeepSurv on real clinical studies to demonstrate how it's personalized treatment recommendations would increase the survival time of a set of patients. The predictive and modeling capabilities of DeepSurv will enable medical researchers to use deep neural networks as a tool in their exploration, understanding, and prediction of the effects of a patient's characteristics on their risk of failure.