Predictive Uncertainty through Quantization

High-risk domains require reliable confidence estimates from predictive models. Deep latent variable models provide these, but suffer from the rigid variational distributions used for tractable inference, which err on the side of overconfidence. We propose Stochastic Quantized Activation Distributions (SQUAD), which imposes a flexible yet tractable distribution over discretized latent variables. The proposed method is scalable, self-normalizing and sample efficient. We demonstrate that the model fully utilizes the flexible distribution, learns interesting non-linearities, and provides predictive uncertainty of competitive quality

Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers

The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case, developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers

Towards Better Accuracy-efficiency Trade-offs: Divide and Co-training

The width of a neural network matters since increasing the width will necessarily increase the model capacity. However, the performance of a network does not improve linearly with the width and soon gets saturated. In this case, we argue that increasing the number of networks (ensemble) can achieve better accuracy-efficiency trade-offs than purely increasing the width. To prove it, one large network is divided into several small ones regarding its parameters and regularization components. Each of these small networks has a fraction of the original one's parameters. We then train these small networks together and make them see various views of the same data to increase their diversity. During this co-training process, networks can also learn from each other. As a result, small networks can achieve better ensemble performance than the large one with few or no extra parameters or FLOPs. Small networks can also achieve faster inference speed than the large one by concurrent running on different devices. We validate our argument with 8 different neural architectures on common benchmarks through extensive experiments. The code is available at \url{https://github.com/mzhaoshuai/Divide-and-Co-training}

FedDCT: Federated Learning of Large Convolutional Neural Networks on Resource Constrained Devices using Divide and Co-Training

We introduce FedDCT, a novel distributed learning paradigm that enables the usage of large, high-performance CNNs on resource-limited edge devices. As opposed to traditional FL approaches, which require each client to train the full-size neural network independently during each training round, the proposed FedDCT allows a cluster of several clients to collaboratively train a large deep learning model by dividing it into an ensemble of several small sub-models and train them on multiple devices in parallel while maintaining privacy. In this co-training process, clients from the same cluster can also learn from each other, further improving their ensemble performance. In the aggregation stage, the server takes a weighted average of all the ensemble models trained by all the clusters. FedDCT reduces the memory requirements and allows low-end devices to participate in FL. We empirically conduct extensive experiments on standardized datasets, including CIFAR-10, CIFAR-100, and two real-world medical datasets HAM10000 and VAIPE. Experimental results show that FedDCT outperforms a set of current SOTA FL methods with interesting convergence behaviors. Furthermore, compared to other existing approaches, FedDCT achieves higher accuracy and substantially reduces the number of communication rounds (with $4-8$ times fewer memory requirements) to achieve the desired accuracy on the testing dataset without incurring any extra training cost on the server side.Comment: Under review by the IEEE Transactions on Network and Service Managemen

IIFL: Implicit Interactive Fleet Learning from Heterogeneous Human Supervisors

Imitation learning has been applied to a range of robotic tasks, but can struggle when (1) robots encounter edge cases that are not represented in the training data (distribution shift) or (2) the human demonstrations are heterogeneous: taking different paths around an obstacle, for instance (multimodality). Interactive fleet learning (IFL) mitigates distribution shift by allowing robots to access remote human teleoperators during task execution and learn from them over time, but is not equipped to handle multimodality. Recent work proposes Implicit Behavior Cloning (IBC), which is able to represent multimodal demonstrations using energy-based models (EBMs). In this work, we propose addressing both multimodality and distribution shift with Implicit Interactive Fleet Learning (IIFL), the first extension of implicit policies to interactive imitation learning (including the single-robot, single-human setting). IIFL quantifies uncertainty using a novel application of Jeffreys divergence to EBMs. While IIFL is more computationally expensive than explicit methods, results suggest that IIFL achieves 4.5x higher return on human effort in simulation experiments and an 80% higher success rate in a physical block pushing task over (Explicit) IFL, IBC, and other baselines when human supervision is heterogeneous

Representation Learning for Visual Data

Cette thèse par article contribue au domaine de l’apprentissage de représentations profondes, et plus précisément celui des modèles génératifs profonds, par l’entremise de travaux sur les machines de Boltzmann restreintes, les modèles génératifs adversariels ainsi que le pastiche automatique. Le premier article s’intéresse au problème de l’estimation du gradient de la phase négative des machines de Boltzmann par l’échantillonnage d’une réalisation physique du modèle. Nous présentons une évaluation empirique de l’impact sur la performance, mesurée par log-vraisemblance négative, de diverses contraintes associées à l’implémentation physique de machines de Boltzmann restreintes (RBMs), soit le bruit sur les paramètres, l’amplitude limitée des paramètres et une connectivité limitée. Le second article s’attaque au problème de l’inférence dans les modèles génératifs adversariels (GANs). Nous proposons une extension du modèle appelée inférence adversativement apprise (ALI) qui a la particularité d’apprendre jointement l’inférence et la génération à partir d’un principe adversariel. Nous montrons que la représentation apprise par le modèle est utile à la résolution de tâches auxiliaires comme l’apprentissage semi-supervisé en obtenant une performance comparable à l’état de l’art pour les ensembles de données SVHN et CIFAR10. Finalement, le troisième article propose une approche simple et peu coûteuse pour entraîner un réseau unique de pastiche automatique à imiter plusieurs styles artistiques. Nous présentons un mécanisme de conditionnement, appelé normalisation conditionnelle par instance, qui permet au réseau d’imiter plusieurs styles en parallèle via l’apprentissage d’un ensemble de paramètres de normalisation unique à chaque style. Ce mécanisme s’avère très efficace en pratique et a inspiré plusieurs travaux subséquents qui ont appliqué l’idée à des problèmes au-delà du domaine du pastiche automatique.This thesis by articles contributes to the field of deep learning, and more specifically the subfield of deep generative modeling, through work on restricted Boltzmann machines, generative adversarial networks and style transfer networks. The first article examines the idea of tackling the problem of estimating the negative phase gradients in Boltzmann machines by sampling from a physical implementation of the model. We provide an empirical evaluation of the impact of various constraints associated with physical implementations of restricted Boltzmann machines (RBMs), namely noisy parameters, finite parameter amplitude and restricted connectivity patterns, on their performance as measured by negative log-likelihood through software simulation. The second article tackles the inference problem in generative adversarial networks (GANs). It proposes a simple and straightforward extension to the GAN framework, named adversarially learned inference (ALI), which allows inference to be learned jointly with generation in a fully-adversarial framework. We show that the learned representation is useful for auxiliary tasks such as semi-supervised learning by obtaining a performance competitive with the then-state-of-the-art on the SVHN and CIFAR10 semi-supervised learning tasks. Finally, the third article proposes a simple and scalable technique to train a single feedforward style transfer network to model multiple styles. It introduces a conditioning mechanism named conditional instance normalization which allows the network to capture multiple styles in parallel by learning a different set of instance normalization parameters for each style. This mechanism is shown to be very efficient and effective in practice, and has inspired multiple efforts to adapt the idea to problems outside of the artistic style transfer domain

Physically inspired methods and development of data-driven predictive systems.

Traditionally building of predictive models is perceived as a combination of both science and art. Although the designer of a predictive system effectively follows a prescribed procedure, his domain knowledge as well as expertise and intuition in the field of machine learning are often irreplaceable. However, in many practical situations it is possible to build well–performing predictive systems by following a rigorous methodology and offsetting not only the lack of domain knowledge but also partial lack of expertise and intuition, by computational power. The generalised predictive model development cycle discussed in this thesis is an example of such methodology, which despite being computationally expensive, has been successfully applied to real–world problems. The proposed predictive system design cycle is a purely data–driven approach. The quality of data used to build the system is thus of crucial importance. In practice however, the data is rarely perfect. Common problems include missing values, high dimensionality or very limited amount of labelled exemplars. In order to address these issues, this work investigated and exploited inspirations coming from physics. The novel use of well–established physical models in the form of potential fields, has resulted in derivation of a comprehensive Electrostatic Field Classification Framework for supervised and semi–supervised learning from incomplete data. Although the computational power constantly becomes cheaper and more accessible, it is not infinite. Therefore efficient techniques able to exploit finite amount of predictive information content of the data and limit the computational requirements of the resource–hungry predictive system design procedure are very desirable. In designing such techniques this work once again investigated and exploited inspirations coming from physics. By using an analogy with a set of interacting particles and the resulting Information Theoretic Learning framework, the Density Preserving Sampling technique has been derived. This technique acts as a computationally efficient alternative for cross–validation, which fits well within the proposed methodology. All methods derived in this thesis have been thoroughly tested on a number of benchmark datasets. The proposed generalised predictive model design cycle has been successfully applied to two real–world environmental problems, in which a comparative study of Density Preserving Sampling and cross–validation has also been performed confirming great potential of the proposed methods

Physically inspired methods and development of data-driven predictive systems

Traditionally building of predictive models is perceived as a combination of both science and art. Although the designer of a predictive system effectively follows a prescribed procedure, his domain knowledge as well as expertise and intuition in the field of machine learning are often irreplaceable. However, in many practical situations it is possible to build well–performing predictive systems by following a rigorous methodology and offsetting not only the lack of domain knowledge but also partial lack of expertise and intuition, by computational power. The generalised predictive model development cycle discussed in this thesis is an example of such methodology, which despite being computationally expensive, has been successfully applied to real–world problems. The proposed predictive system design cycle is a purely data–driven approach. The quality of data used to build the system is thus of crucial importance. In practice however, the data is rarely perfect. Common problems include missing values, high dimensionality or very limited amount of labelled exemplars. In order to address these issues, this work investigated and exploited inspirations coming from physics. The novel use of well–established physical models in the form of potential fields, has resulted in derivation of a comprehensive Electrostatic Field Classification Framework for supervised and semi–supervised learning from incomplete data. Although the computational power constantly becomes cheaper and more accessible, it is not infinite. Therefore efficient techniques able to exploit finite amount of predictive information content of the data and limit the computational requirements of the resource–hungry predictive system design procedure are very desirable. In designing such techniques this work once again investigated and exploited inspirations coming from physics. By using an analogy with a set of interacting particles and the resulting Information Theoretic Learning framework, the Density Preserving Sampling technique has been derived. This technique acts as a computationally efficient alternative for cross–validation, which fits well within the proposed methodology. All methods derived in this thesis have been thoroughly tested on a number of benchmark datasets. The proposed generalised predictive model design cycle has been successfully applied to two real–world environmental problems, in which a comparative study of Density Preserving Sampling and cross–validation has also been performed confirming great potential of the proposed methods.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Methods for generating and evaluating synthetic longitudinal patient data: a systematic review

The proliferation of data in recent years has led to the advancement and utilization of various statistical and deep learning techniques, thus expediting research and development activities. However, not all industries have benefited equally from the surge in data availability, partly due to legal restrictions on data usage and privacy regulations, such as in medicine. To address this issue, various statistical disclosure and privacy-preserving methods have been proposed, including the use of synthetic data generation. Synthetic data are generated based on some existing data, with the aim of replicating them as closely as possible and acting as a proxy for real sensitive data. This paper presents a systematic review of methods for generating and evaluating synthetic longitudinal patient data, a prevalent data type in medicine. The review adheres to the PRISMA guidelines and covers literature from five databases until the end of 2022. The paper describes 17 methods, ranging from traditional simulation techniques to modern deep learning methods. The collected information includes, but is not limited to, method type, source code availability, and approaches used to assess resemblance, utility, and privacy. Furthermore, the paper discusses practical guidelines and key considerations for developing synthetic longitudinal data generation methods