Real-valued (Medical) Time Series Generation with Recurrent Conditional GANs

Generative Adversarial Networks (GANs) have shown remarkable success as a framework for training models to produce realistic-looking data. In this work, we propose a Recurrent GAN (RGAN) and Recurrent Conditional GAN (RCGAN) to produce realistic real-valued multi-dimensional time series, with an emphasis on their application to medical data. RGANs make use of recurrent neural networks in the generator and the discriminator. In the case of RCGANs, both of these RNNs are conditioned on auxiliary information. We demonstrate our models in a set of toy datasets, where we show visually and quantitatively (using sample likelihood and maximum mean discrepancy) that they can successfully generate realistic time-series. We also describe novel evaluation methods for GANs, where we generate a synthetic labelled training dataset, and evaluate on a real test set the performance of a model trained on the synthetic data, and vice-versa. We illustrate with these metrics that RCGANs can generate time-series data useful for supervised training, with only minor degradation in performance on real test data. This is demonstrated on digit classification from 'serialised' MNIST and by training an early warning system on a medical dataset of 17,000 patients from an intensive care unit. We further discuss and analyse the privacy concerns that may arise when using RCGANs to generate realistic synthetic medical time series data.Comment: 13 pages, 4 figures, 3 tables (update with differential privacy

Generative Adversarial Networks for Electronic Health Records: A Framework for Exploring and Evaluating Methods for Predicting Drug-Induced Laboratory Test Trajectories

Generative Adversarial Networks (GANs) represent a promising class of generative networks that combine neural networks with game theory. From generating realistic images and videos to assisting musical creation, GANs are transforming many fields of arts and sciences. However, their application to healthcare has not been fully realized, more specifically in generating electronic health records (EHR) data. In this paper, we propose a framework for exploring the value of GANs in the context of continuous laboratory time series data. We devise an unsupervised evaluation method that measures the predictive power of synthetic laboratory test time series. Further, we show that when it comes to predicting the impact of drug exposure on laboratory test data, incorporating representation learning of the training cohorts prior to training GAN models is beneficial.Comment: NIPS ML4H 201

Generating Synthetic but Plausible Healthcare Record Datasets

Generating datasets that "look like" given real ones is an interesting tasks for healthcare applications of ML and many other fields of science and engineering. In this paper we propose a new method of general application to binary datasets based on a method for learning the parameters of a latent variable moment that we have previously used for clustering patient datasets. We compare our method with a recent proposal (MedGan) based on generative adversarial methods and find that the synthetic datasets we generate are globally more realistic in at least two senses: real and synthetic instances are harder to tell apart by Random Forests, and the MMD statistic. The most likely explanation is that our method does not suffer from the "mode collapse" which is an admitted problem of GANs. Additionally, the generative models we generate are easy to interpret, unlike the rather obscure GANs. Our experiments are performed on two patient datasets containing ICD-9 diagnostic codes: the publicly available MIMIC-III dataset and a dataset containing admissions for congestive heart failure during 7 years at Hospital de Sant Pau in Barcelona.Comment: MLMH 2018 : 2018 KDD workshop on Machine Learning for Medicine and Healthcar

tsBNgen: A Python Library to Generate Time Series Data from an Arbitrary Dynamic Bayesian Network Structure

Synthetic data is widely used in various domains. This is because many modern algorithms require lots of data for efficient training, and data collection and labeling usually are a time-consuming process and are prone to errors. Furthermore, some real-world data, due to its nature, is confidential and cannot be shared. Bayesian networks are a type of probabilistic graphical model widely used to model the uncertainties in real-world processes. Dynamic Bayesian networks are a special class of Bayesian networks that model temporal and time series data. In this paper, we introduce the tsBNgen, a Python library to generate time series and sequential data based on an arbitrary dynamic Bayesian network. The package, documentation, and examples can be downloaded from https://github.com/manitadayon/tsBNgen

Interaction-aware Multi-agent Tracking and Probabilistic Behavior Prediction via Adversarial Learning

In order to enable high-quality decision making and motion planning of intelligent systems such as robotics and autonomous vehicles, accurate probabilistic predictions for surrounding interactive objects is a crucial prerequisite. Although many research studies have been devoted to making predictions on a single entity, it remains an open challenge to forecast future behaviors for multiple interactive agents simultaneously. In this work, we take advantage of the Generative Adversarial Network (GAN) due to its capability of distribution learning and propose a generic multi-agent probabilistic prediction and tracking framework which takes the interactions among multiple entities into account, in which all the entities are treated as a whole. However, since GAN is very hard to train, we make an empirical research and present the relationship between training performance and hyperparameter values with a numerical case study. The results imply that the proposed model can capture both the mean, variance and multi-modalities of the groundtruth distribution. Moreover, we apply the proposed approach to a real-world task of vehicle behavior prediction to demonstrate its effectiveness and accuracy. The results illustrate that the proposed model trained by adversarial learning can achieve a better prediction performance than other state-of-the-art models trained by traditional supervised learning which maximizes the data likelihood. The well-trained model can also be utilized as an implicit proposal distribution for particle filtered based Bayesian state estimation.Comment: Accepted by 2019 International Conference on Robotics and Automation (ICRA

Synthetic Event Time Series Health Data Generation

Synthetic medical data which preserves privacy while maintaining utility can be used as an alternative to real medical data, which has privacy costs and resource constraints associated with it. At present, most models focus on generating cross-sectional health data which is not necessarily representative of real data. In reality, medical data is longitudinal in nature, with a single patient having multiple health events, non-uniformly distributed throughout their lifetime. These events are influenced by patient covariates such as comorbidities, age group, gender etc. as well as external temporal effects (e.g. flu season). While there exist seminal methods to model time series data, it becomes increasingly challenging to extend these methods to medical event time series data. Due to the complexity of the real data, in which each patient visit is an event, we transform the data by using summary statistics to characterize the events for a fixed set of time intervals, to facilitate analysis and interpretability. We then train a generative adversarial network to generate synthetic data. We demonstrate this approach by generating human sleep patterns, from a publicly available dataset. We empirically evaluate the generated data and show close univariate resemblance between synthetic and real data. However, we also demonstrate how stratification by covariates is required to gain a deeper understanding of synthetic data quality.Comment: Machine Learning for Health (ML4H) at NeurIPS 2019 - Extended Abstrac

Measuring the quality of Synthetic data for use in competitions

Machine learning has the potential to assist many communities in using the large datasets that are becoming more and more available. Unfortunately, much of that potential is not being realized because it would require sharing data in a way that compromises privacy. In order to overcome this hurdle, several methods have been proposed that generate synthetic data while preserving the privacy of the real data. In this paper we consider a key characteristic that synthetic data should have in order to be useful for machine learning researchers - the relative performance of two algorithms (trained and tested) on the synthetic dataset should be the same as their relative performance (when trained and tested) on the original dataset.Comment: 3 pages, 1 figure, 2018 KDD Workshop on Machine Learning for Medicine and Healthcar

Synthesizing Tabular Data using Generative Adversarial Networks

Generative adversarial networks (GANs) implicitly learn the probability distribution of a dataset and can draw samples from the distribution. This paper presents, Tabular GAN (TGAN), a generative adversarial network which can generate tabular data like medical or educational records. Using the power of deep neural networks, TGAN generates high-quality and fully synthetic tables while simultaneously generating discrete and continuous variables. When we evaluate our model on three datasets, we find that TGAN outperforms conventional statistical generative models in both capturing the correlation between columns and scaling up for large datasets

Feedback GAN (FBGAN) for DNA: a Novel Feedback-Loop Architecture for Optimizing Protein Functions

Generative Adversarial Networks (GANs) represent an attractive and novel approach to generate realistic data, such as genes, proteins, or drugs, in synthetic biology. Here, we apply GANs to generate synthetic DNA sequences encoding for proteins of variable length. We propose a novel feedback-loop architecture, called Feedback GAN (FBGAN), to optimize the synthetic gene sequences for desired properties using an external function analyzer. The proposed architecture also has the advantage that the analyzer need not be differentiable. We apply the feedback-loop mechanism to two examples: 1) generating synthetic genes coding for antimicrobial peptides, and 2) optimizing synthetic genes for the secondary structure of their resulting peptides. A suite of metrics demonstrate that the GAN generated proteins have desirable biophysical properties. The FBGAN architecture can also be used to optimize GAN-generated datapoints for useful properties in domains beyond genomics

Automated Treatment Planning in Radiation Therapy using Generative Adversarial Networks

Knowledge-based planning (KBP) is an automated approach to radiation therapy treatment planning that involves predicting desirable treatment plans before they are then corrected to deliverable ones. We propose a generative adversarial network (GAN) approach for predicting desirable 3D dose distributions that eschews the previous paradigms of site-specific feature engineering and predicting low-dimensional representations of the plan. Experiments on a dataset of oropharyngeal cancer patients show that our approach significantly outperforms previous methods on several clinical satisfaction criteria and similarity metrics.Comment: 15 pages. Accepted for publication in PMLR. Presented at Machine Learning for Health Car