arXiv subjects

John Shawe-Taylor

Publications and source records attributed to John Shawe-Taylor.

At least 55 records · Page 3Linked to original sources

arXiv2019

Adaptive Mechanism Design: Learning to Promote Cooperation

In the future, artificial learning agents are likely to become increasingly widespread in our society. They will interact with both other learning agents and humans in a variety of complex settings including social dilemmas. We consider the problem of how an external agent can promote cooperation between artificial learners by distributing additional rewards and punishments based on observing the learners' actions. We propose a rule for automatically learning how to create right incentives by considering the players' anticipated parameter updates. Using this learning rule leads to cooperation with high social welfare in matrix games in which the agents would otherwise learn to defect with high probability. We show that the resulting cooperative outcome is stable in certain games even if the planning agent is turned off after a given number of episodes, while other games require ongoing intervention to maintain mutual cooperation. However, even in the latter case, the amount of necessary additional incentives decreases over time.

cs.GT↗

arXiv2019

Deep Learning Enhanced Extended Depth-of-Field for Thick Blood-Film Malaria High-Throughput Microscopy

Fast accurate diagnosis of malaria is still a global health challenge for which automated digital-pathology approaches could provide scalable solutions amenable to be deployed in low-to-middle income countries. Here we address the problem of Extended Depth-of-Field (EDoF) in thick blood film microscopy for rapid automated malaria diagnosis. High magnification oil-objectives (100x) with large numerical aperture are usually preferred to resolve the fine structural details that help separate true parasites from distractors. However, such objectives have a very limited depth-of-field requiring the acquisition of a series of images at different focal planes per field of view (FOV). Current EDoF techniques based on multi-scale decompositions are time consuming and therefore not suited for high-throughput analysis of specimens. To overcome this challenge, we developed a new deep learning method based on Convolutional Neural Networks (EDoF-CNN) that is able to rapidly perform the extended depth-of-field while also enhancing the spatial resolution of the resulting fused image. We evaluated our approach using simulated low-resolution z-stacks from Giemsa-stained thick blood smears from patients presenting with Plasmodium falciparum malaria. The EDoF-CNN allows speed-up of our digital-pathology acquisition platform and significantly improves the quality of the EDoF compared to the traditional multi-scaled approaches when applied to lower resolution stacks corresponding to acquisitions with fewer focal planes, large camera pixel binning or lower magnification objectives (larger FOV). We use the parasite detection accuracy of a deep learning model on the EDoFs as a concrete, task-specific measure of performance of this approach.

eess.IV↗

arXiv2019

Data-Driven Malaria Prevalence Prediction in Large Densely-Populated Urban Holoendemic sub-Saharan West Africa: Harnessing Machine Learning Approaches and 22-years of Prospectively Collected Data

Plasmodium falciparum malaria still poses one of the greatest threats to human life with over 200 million cases globally leading to half-million deaths annually. Of these, 90% of cases and of the mortality occurs in sub-Saharan Africa, mostly among children. Although malaria prediction systems are central to the 2016-2030 malaria Global Technical Strategy, currently these are inadequate at capturing and estimating the burden of disease in highly endemic countries. We developed and validated a computational system that exploits the predictive power of current Machine Learning approaches on 22-years of prospective data from the high-transmission holoendemic malaria urban-densely-populated sub-Saharan West-Africa metropolis of Ibadan. Our dataset of >9x104 screened study participants attending our clinical and community services from 1996 to 2017 contains monthly prevalence, temporal, environmental and host features. Our Locality-specific Elastic-Net based Malaria Prediction System (LEMPS) achieves good generalization performance, both in magnitude and direction of the prediction, when tasked to predict monthly prevalence on previously unseen validation data (MAE<=6x10-2, MSE<=7x10-3) within a range of (+0.1 to -0.05) error-tolerance which is relevant and usable for aiding decision-support in a holoendemic setting. LEMPS is well-suited for malaria prediction, where there are multiple features which are correlated with one another, and trading-off between regularization-strength L1-norm and L2-norm allows the system to retain stability. Data-driven systems are critical for regionally-adaptable surveillance, management of control strategies and resource allocation across stretched healthcare systems.

cs.LG↗

arXiv2018

Interlacing Personal and Reference Genomes for Machine Learning Disease-Variant Detection

DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown great promise in improving on these variant calls, but the input for these is still a standardized "pile-up" image, which is not always best suited. In this paper, we present a novel method for generating images from DNA sequencing data, which interlaces the human reference genome with personalized sequencing output, to maximize usage of sequencing reads and improve machine learning algorithm performance. We demonstrate the success of this in improving standard germline variant calling. We also furthered this approach to include somatic variant calling across tumor/normal data with Siamese networks. These approaches can be used in machine learning applications on sequencing data with the hope of improving clinical outcomes, and are freely available for noncommercial use at www.ccg.ai.

q-bio.GN↗

arXiv2018

Faster Convergence & Generalization in DNNs

Deep neural networks have gained tremendous popularity in last few years. They have been applied for the task of classification in almost every domain. Despite the success, deep networks can be incredibly slow to train for even moderate sized models on sufficiently large datasets. Additionally, these networks require large amounts of data to be able to generalize. The importance of speeding up convergence, and generalization in deep networks can not be overstated. In this work, we develop an optimization algorithm based on generalized-optimal updates derived from minibatches that lead to faster convergence. Towards the end, we demonstrate on two benchmark datasets that the proposed method achieves two orders of magnitude speed up over traditional back-propagation, and is more robust to noise/over-fitting.

cs.LG↗

arXiv2018

Structured Multi-Label Biomedical Text Tagging via Attentive Neural Tree Decoding

We propose a model for tagging unstructured texts with an arbitrary number of terms drawn from a tree-structured vocabulary (i.e., an ontology). We treat this as a special case of sequence-to-sequence learning in which the decoder begins at the root node of an ontological tree and recursively elects to expand child nodes as a function of the input text, the current node, and the latent decoder state. In our experiments the proposed method outperforms state-of-the-art approaches on the important task of automatically assigning MeSH terms to biomedical abstracts.

cs.IR↗

arXiv2018

PAC-Bayes bounds for stable algorithms with instance-dependent priors

PAC-Bayes bounds have been proposed to get risk estimates based on a training sample. In this paper the PAC-Bayes approach is combined with stability of the hypothesis learned by a Hilbert space valued algorithm. The PAC-Bayes setting is used with a Gaussian prior centered at the expected output. Thus a novelty of our paper is using priors defined in terms of the data-generating distribution. Our main result estimates the risk of the randomized algorithm in terms of the hypothesis stability coefficients. We also provide a new bound for the SVM classifier, which is compared to other known bounds experimentally. Ours appears to be the first stability-based bound that evaluates to non-trivial values.

stat.ML↗

arXiv2018

Spatiotemporal Prediction of Ambulance Demand using Gaussian Process Regression

Accurately predicting when and where ambulance call-outs occur can reduce response times and ensure the patient receives urgent care sooner. Here we present a novel method for ambulance demand prediction using Gaussian process regression (GPR) in time and geographic space. The method exhibits superior accuracy to MEDIC, a method which has been used in industry. The use of GPR has additional benefits such as the quantification of uncertainty with each prediction, the choice of kernel functions to encode prior knowledge and the ability to capture spatial correlation. Measures to increase the utility of GPR in the current context, with large training sets and a Poisson-distributed output, are outlined.

stat.ML↗

arXiv2018

Improving Active Learning in Systematic Reviews

Systematic reviews are essential to summarizing the results of different clinical and social science studies. The first step in a systematic review task is to identify all the studies relevant to the review. The task of identifying relevant studies for a given systematic review is usually performed manually, and as a result, involves substantial amounts of expensive human resource. Lately, there have been some attempts to reduce this manual effort using active learning. In this work, we build upon some such existing techniques, and validate by experimenting on a larger and comprehensive dataset than has been attempted until now. Our experiments provide insights on the use of different feature extraction models for different disciplines. More importantly, we identify that a naive active learning based screening process is biased in favour of selecting similar documents. We aimed to improve the performance of the screening process using a novel active learning algorithm with success. Additionally, we propose a mechanism to choose the best feature extraction method for a given review.

cs.IR↗

arXiv2017

A Tutorial on Canonical Correlation Methods

Canonical correlation analysis is a family of multivariate statistical methods for the analysis of paired sets of variables. Since its proposition, canonical correlation analysis has for instance been extended to extract relations between two sets of variables when the sample size is insufficient in relation to the data dimensionality, when the relations have been considered to be non-linear, and when the dimensionality is too large for human interpretation. This tutorial explains the theory of canonical correlation analysis including its regularised, kernel, and sparse variants. Additionally, the deep and Bayesian CCA extensions are briefly reviewed. Together with the numerical examples, this overview provides a coherent compendium on the applicability of the variants of canonical correlation analysis. By bringing together techniques for solving the optimisation problems, evaluating the statistical significance and generalisability of the canonical correlation model, and interpreting the relations, we hope that this article can serve as a hands-on tool for applying canonical correlation methods in data analysis.

cs.LG↗

arXiv2016

Probabilistic map-matching using particle filters

Increasing availability of vehicle GPS data has created potentially transformative opportunities for traffic management, route planning and other location-based services. Critical to the utility of the data is their accuracy. Map-matching is the process of improving the accuracy by aligning GPS data with the road network. In this paper, we propose a purely probabilistic approach to map-matching based on a sequential Monte Carlo algorithm known as particle filters. The approach performs map-matching by producing a range of candidate solutions, each with an associated probability score. We outline implementation details and thoroughly validate the technique on GPS data of varied quality.

stat.ML↗

arXiv2016

Improved Particle Filters for Vehicle Localisation

The ability to track a moving vehicle is of crucial importance in numerous applications. The task has often been approached by the importance sampling technique of particle filters due to its ability to model non-linear and non-Gaussian dynamics, of which a vehicle travelling on a road network is a good example. Particle filters perform poorly when observations are highly informative. In this paper, we address this problem by proposing particle filters that sample around the most recent observation. The proposal leads to an order of magnitude improvement in accuracy and efficiency over conventional particle filters, especially when observations are infrequent but low-noise.

stat.ML↗

arXiv2016

Localized Lasso for High-Dimensional Regression

We introduce the localized Lasso, which is suited for learning models that are both interpretable and have a high predictive power in problems with high dimensionality $d$ and small sample size $n$. More specifically, we consider a function defined by local sparse models, one at each data point. We introduce sample-wise network regularization to borrow strength across the models, and sample-wise exclusive group sparsity (a.k.a., $\ell_{1,2}$ norm) to introduce diversity into the choice of feature sets in the local models. The local models are interpretable in terms of similarity of their sparsity patterns. The cost function is convex, and thus has a globally optimal solution. Moreover, we propose a simple yet efficient iterative least-squares based optimization procedure for the localized Lasso, which does not need a tuning parameter, and is guaranteed to converge to a globally optimal solution. The solution is empirically shown to outperform alternatives for both simulated and genomic personalized medicine data.

stat.ML↗

arXiv2016

PAC-Bayes Analysis of Multi-view Learning

This paper presents eight PAC-Bayes bounds to analyze the generalization performance of multi-view classifiers. These bounds adopt data dependent Gaussian priors which emphasize classifiers with high view agreements. The center of the prior for the first two bounds is the origin, while the center of the prior for the third and fourth bounds is given by a data dependent vector. An important technique to obtain these bounds is two derived logarithmic determinant inequalities whose difference lies in whether the dimensionality of data is involved. The centers of the fifth and sixth bounds are calculated on a separate subset of the training set. The last two bounds use unlabeled data to represent view agreements and are thus applicable to semi-supervised multi-view learning. We evaluate all the presented multi-view PAC-Bayes bounds on benchmark data and compare them with previous single-view PAC-Bayes bounds. The usefulness and performance of the multi-view bounds are discussed.

cs.LG↗

arXiv2016

Image Retrieval with a Bayesian Model of Relevance Feedback

A content-based image retrieval system based on multinomial relevance feedback is proposed. The system relies on an interactive search paradigm where at each round a user is presented with k images and selects the one closest to their ideal target. Two approaches, one based on the Dirichlet distribution and one based the Beta distribution, are used to model the problem motivating an algorithm that trades exploration and exploitation in presenting the images in each round. Experimental results show that the new approach compares favourably with previous work.

cs.IR↗

arXiv2016

Learning Shared Representations in Multi-task Reinforcement Learning

We investigate a paradigm in multi-task reinforcement learning (MT-RL) in which an agent is placed in an environment and needs to learn to perform a series of tasks, within this space. Since the environment does not change, there is potentially a lot of common ground amongst tasks and learning to solve them individually seems extremely wasteful. In this paper, we explicitly model and learn this shared structure as it arises in the state-action value space. We will show how one can jointly learn optimal value-functions by modifying the popular Value-Iteration and Policy-Iteration procedures to accommodate this shared representation assumption and leverage the power of multi-task supervised learning. Finally, we demonstrate that the proposed model and training procedures, are able to infer good value functions, even under low samples regimes. In addition to data efficiency, we will show in our analysis, that learning abstractions of the state space jointly across tasks leads to more robust, transferable representations with the potential for better generalization. this shared representation assumption and leverage the power of multi-task supervised learning. Finally, we demonstrate that the proposed model and training procedures, are able to infer good value functions, even under low samples regimes. In addition to data efficiency, we will show in our analysis, that learning abstractions of the state space jointly across tasks leads to more robust, transferable representations with the potential for better generalization.

cs.AI↗

arXiv2014

PinView: Implicit Feedback in Content-Based Image Retrieval

This paper describes PinView, a content-based image retrieval system that exploits implicit relevance feedback collected during a search session. PinView contains several novel methods to infer the intent of the user. From relevance feedback, such as eye movements or pointer clicks, and visual features of images, PinView learns a similarity metric between images which depends on the current interests of the user. It then retrieves images with a specialized online learning algorithm that balances the tradeoff between exploring new images and exploiting the already inferred interests of the user. We have integrated PinView to the content-based image retrieval system PicSOM, which enables applying PinView to real-world image databases. With the new algorithms PinView outperforms the original PicSOM, and in online experiments with real users the combination of implicit and explicit feedback gives the best results.

cs.IR↗

arXiv2014

A Note on Improved Loss Bounds for Multiple Kernel Learning

In this paper, we correct an upper bound, presented in~\cite{hs-11}, on the generalisation error of classifiers learned through multiple kernel learning. The bound in~\cite{hs-11} uses Rademacher complexity and has an\emph{additive} dependence on the logarithm of the number of kernels and the margin achieved by the classifier. However, there are some errors in parts of the proof which are corrected in this paper. Unfortunately, the final result turns out to be a risk bound which has a \emph{multiplicative} dependence on the logarithm of the number of kernels and the margin achieved by the classifier.

cs.LG↗