Transfer Learning for Clinical Time Series Analysis using Deep Neural Networks

Deep neural networks have shown promising results for various clinical prediction tasks. However, training deep networks such as those based on Recurrent Neural Networks (RNNs) requires large labeled data, significant hyper-parameter tuning effort and expertise, and high computational resources. In this work, we investigate as to what extent can transfer learning address these issues when using deep RNNs to model multivariate clinical time series. We consider two scenarios for transfer learning using RNNs: i) domain-adaptation, i.e., leveraging a deep RNN - namely, TimeNet - pre-trained for feature extraction on time series from diverse domains, and adapting it for feature extraction and subsequent target tasks in healthcare domain, ii) task-adaptation, i.e., pre-training a deep RNN - namely, HealthNet - on diverse tasks in healthcare domain, and adapting it to new target tasks in the same domain. We evaluate the above approaches on publicly available MIMIC-III benchmark dataset, and demonstrate that (a) computationally-efficient linear models trained using features extracted via pre-trained RNNs outperform or, in the worst case, perform as well as deep RNNs and statistical hand-crafted features based models trained specifically for target task; (b) models obtained by adapting pre-trained models for target tasks are significantly more robust to the size of labeled data compared to task-specific RNNs, while also being computationally efficient. We, therefore, conclude that pre-trained deep models like TimeNet and HealthNet allow leveraging the advantages of deep learning for clinical time series analysis tasks, while also minimize dependence on hand-crafted features, deal robustly with scarce labeled training data scenarios without overfitting, as well as reduce dependence on expertise and resources required to train deep networks from scratch.

Learning to Clean: A GAN Perspective

In the big data era, the impetus to digitize the vast reservoirs of data trapped in unstructured scanned documents such as invoices, bank documents and courier receipts has gained fresh momentum. The scanning process often results in the introduction of artifacts such as background noise, blur due to camera motion, watermarkings, coffee stains, or faded text. These artifacts pose many readability challenges to current text recognition algorithms and significantly degrade their performance. Existing learning based denoising techniques require a dataset comprising of noisy documents paired with cleaned versions. In such scenarios, a model can be trained to generate clean documents from noisy versions. However, very often in the real world such a paired dataset is not available, and all we have for training our denoising model are unpaired sets of noisy and clean images. This paper explores the use of GANs to generate denoised versions of the noisy documents. In particular, where paired information is available, we formulate the problem as an image-to-image translation task i.e, translating a document from noisy domain ( i.e., background noise, blurred, faded, watermarked ) to a target clean document using Generative Adversarial Networks (GAN). However, in the absence of paired images for training, we employed CycleGAN which is known to learn a mapping between the distributions of the noisy images to the denoised images using unpaired data to achieve image-to-image translation for cleaning the noisy documents. We compare the performance of CycleGAN for document cleaning tasks using unpaired images with a Conditional GAN trained on paired data from the same dataset. Experiments were performed on a public document dataset on which different types of noise were artificially induced, results demonstrate that CycleGAN learns a more robust mapping from the space of noisy to clean documents.

Automatic Information Extraction from Piping and Instrumentation Diagrams

One of the most common modes of representing engineering schematics are Piping and Instrumentation diagrams (P&IDs) that describe the layout of an engineering process flow along with the interconnected process equipment. Over the years, P&ID diagrams have been manually generated, scanned and stored as image files. These files need to be digitized for purposes of inventory management and updation, and easy reference to different components of the schematics. There are several challenging vision problems associated with digitizing real world P&ID diagrams. Real world P&IDs come in several different resolutions, and often contain noisy textual information. Extraction of instrumentation information from these diagrams involves accurate detection of symbols that frequently have minute visual differences between them. Identification of pipelines that may converge and diverge at different points in the image is a further cause for concern. Due to these reasons, to the best of our knowledge, no system has been proposed for end-to-end data extraction from P&ID diagrams. However, with the advent of deep learning and the spectacular successes it has achieved in vision, we hypothesized that it is now possible to re-examine this problem armed with the latest deep learning models. To that end, we present a novel pipeline for information extraction from P&ID sheets via a combination of traditional vision techniques and state-of-the-art deep learning models to identify and isolate pipeline codes, pipelines, inlets and outlets, and for detecting symbols. This is followed by association of the detected components with the appropriate pipeline. The extracted pipeline information is used to populate a tree-like data-structure for capturing the structure of the piping schematics. We evaluated proposed method on a real world dataset of P&ID sheets obtained from an oil firm and have obtained promising results.

MEETING BOT: Reinforcement Learning for Dialogue Based Meeting Scheduling

In this paper we present Meeting Bot, a reinforcement learning based conversational system that interacts with multiple users to schedule meetings. The system is able to interpret user utterences and map them to preferred time slots, which are then fed to a reinforcement learning (RL) system with the goal of converging on an agreeable time slot. The RL system is able to adapt to user preferences and environmental changes in meeting arrival rate while still scheduling effectively. Learning is performed via policy gradient with exploration, by utilizing an MLP as an approximator of the policy function. Results demonstrate that the system outperforms standard scheduling algorithms in terms of overall scheduling efficiency. Additionally, the system is able to adapt its strategy to situations when users consistently reject or accept meetings in certain slots (such as Friday afternoon versus Thursday morning), or when the meeting is called by members who are at a more senior designation.

Deep Reader: Information extraction from Document images via relation extraction and Natural Language

Recent advancements in the area of Computer Vision with state-of-art Neural Networks has given a boost to Optical Character Recognition (OCR) accuracies. However, extracting characters/text alone is often insufficient for relevant information extraction as documents also have a visual structure that is not captured by OCR. Extracting information from tables, charts, footnotes, boxes, headings and retrieving the corresponding structured representation for the document remains a challenge and finds application in a large number of real-world use cases. In this paper, we propose a novel enterprise based end-to-end framework called DeepReader which facilitates information extraction from document images via identification of visual entities and populating a meta relational model across different entities in the document image. The model schema allows for an easy to understand abstraction of the entities detected by the deep vision models and the relationships between them. DeepReader has a suite of state-of-the-art vision algorithms which are applied to recognize handwritten and printed text, eliminate noisy effects, identify the type of documents and detect visual entities like tables, lines and boxes. Deep Reader maps the extracted entities into a rich relational schema so as to capture all the relevant relationships between entities (words, textboxes, lines etc) detected in the document. Relevant information and fields can then be extracted from the document by writing SQL queries on top of the relationship tables. A natural language based interface is added on top of the relationship schema so that a non-technical user, specifying the queries in natural language, can fetch the information with minimal effort. In this paper, we also demonstrate many different capabilities of Deep Reader and report results on a real-world use case.

Reading Industrial Inspection Sheets by Inferring Visual Relations

The traditional mode of recording faults in heavy factory equipment has been via hand marked inspection sheets, wherein a machine engineer manually marks the faulty machine regions on a paper outline of the machine. Over the years, millions of such inspection sheets have been recorded and the data within these sheets has remained inaccessible. However, with industries going digital and waking up to the potential value of fault data for machine health monitoring, there is an increased impetus towards digitization of these hand marked inspection records. To target this digitization, we propose a novel visual pipeline combining state of the art deep learning models, with domain knowledge and low level vision techniques, followed by inference of visual relationships. Our framework is robust to the presence of both static and non-static background in the document, variability in the machine template diagrams, unstructured shape of graphical objects to be identified and variability in the strokes of handwritten text. The proposed pipeline incorporates a capsule and spatial transformer network based classifier for accurate text reading, and a customized CTPN network for text detection in addition to hybrid techniques for arrow detection and dialogue cloud removal. We have tested our approach on a real world dataset of 50 inspection sheets for large containers and boilers. The results are visually appealing and the pipeline achieved an accuracy of 87.1% for text detection and 94.6% for text reading.

Prosocial or Selfish? Agents with different behaviors for Contract Negotiation using Reinforcement Learning

We present an effective technique for training deep learning agents capable of negotiating on a set of clauses in a contract agreement using a simple communication protocol. We use Multi Agent Reinforcement Learning to train both agents simultaneously as they negotiate with each other in the training environment. We also model selfish and prosocial behavior to varying degrees in these agents. Empirical evidence is provided showing consistency in agent behaviors. We further train a meta agent with a mixture of behaviors by learning an ensemble of different models using reinforcement learning. Finally, to ascertain the deployability of the negotiating agents, we conducted experiments pitting the trained agents against human players. Results demonstrate that the agents are able to hold their own against human players, often emerging as winners in the negotiation. Our experiments demonstrate that the meta agent is able to reasonably emulate human behavior.

An Efficient End-to-End Neural Model for Handwritten Text Recognition

Offline handwritten text recognition from images is an important problem for enterprises attempting to digitize large volumes of handmarked scanned documents/reports. Deep recurrent models such as Multi-dimensional LSTMs have been shown to yield superior performance over traditional Hidden Markov Model based approaches that suffer from the Markov assumption and therefore lack the representational power of RNNs. In this paper we introduce a novel approach that combines a deep convolutional network with a recurrent Encoder-Decoder network to map an image to a sequence of characters corresponding to the text present in the image. The entire model is trained end-to-end using Focal Loss, an improvement over the standard Cross-Entropy loss that addresses the class imbalance problem, inherent to text recognition. To enhance the decoding capacity of the model, Beam Search algorithm is employed which searches for the best sequence out of a set of hypotheses based on a joint distribution of individual characters. Our model takes as input a downsampled version of the original image thereby making it both computationally and memory efficient. The experimental results were benchmarked against two publicly available datasets, IAM and RIMES. We surpass the state-of-the-art word level accuracy on the evaluation set of both datasets by 3.5% & 1.1%, respectively.

Transfer Learning for Clinical Time Series Analysis using Recurrent Neural Networks

Deep neural networks have shown promising results for various clinical prediction tasks such as diagnosis, mortality prediction, predicting duration of stay in hospital, etc. However, training deep networks -- such as those based on Recurrent Neural Networks (RNNs) -- requires large labeled data, high computational resources, and significant hyperparameter tuning effort. In this work, we investigate as to what extent can transfer learning address these issues when using deep RNNs to model multivariate clinical time series. We consider transferring the knowledge captured in an RNN trained on several source tasks simultaneously using a large labeled dataset to build the model for a target task with limited labeled data. An RNN pre-trained on several tasks provides generic features, which are then used to build simpler linear models for new target tasks without training task-specific RNNs. For evaluation, we train a deep RNN to identify several patient phenotypes on time series from MIMIC-III database, and then use the features extracted using that RNN to build classifiers for identifying previously unseen phenotypes, and also for a seemingly unrelated task of in-hospital mortality. We demonstrate that (i) models trained on features extracted using pre-trained RNN outperform or, in the worst case, perform as well as task-specific RNNs; (ii) the models using features from pre-trained models are more robust to the size of labeled data than task-specific RNNs; and (iii) features extracted using pre-trained RNN are generic enough and perform better than typical statistical hand-crafted features.