arXiv subjects

Nick Pawlowski

Publications and source records attributed to Nick Pawlowski.

30 records · Page 2Linked to original sources

arXiv2020

Needles in Haystacks: On Classifying Tiny Objects in Large Images

In some important computer vision domains, such as medical or hyperspectral imaging, we care about the classification of tiny objects in large images. However, most Convolutional Neural Networks (CNNs) for image classification were developed using biased datasets that contain large objects, in mostly central image positions. To assess whether classical CNN architectures work well for tiny object classification we build a comprehensive testbed containing two datasets: one derived from MNIST digits and one from histopathology images. This testbed allows controlled experiments to stress-test CNN architectures with a broad spectrum of signal-to-noise ratios. Our observations indicate that: (1) There exists a limit to signal-to-noise below which CNNs fail to generalize and that this limit is affected by dataset size - more data leading to better performances; however, the amount of training data required for the model to generalize scales rapidly with the inverse of the object-to-image ratio (2) in general, higher capacity models exhibit better generalization; (3) when knowing the approximate object sizes, adapting receptive field is beneficial; and (4) for very small signal-to-noise ratio the choice of global pooling operation affects optimization, whereas for relatively large signal-to-noise values, all tested global pooling operations exhibit similar performance.

cs.CV↗

arXiv2019

Representation Disentanglement for Multi-task Learning with application to Fetal Ultrasound

One of the biggest challenges for deep learning algorithms in medical image analysis is the indiscriminate mixing of image properties, e.g. artifacts and anatomy. These entangled image properties lead to a semantically redundant feature encoding for the relevant task and thus lead to poor generalization of deep learning algorithms. In this paper we propose a novel representation disentanglement method to extract semantically meaningful and generalizable features for different tasks within a multi-task learning framework. Deep neural networks are utilized to ensure that the encoded features are maximally informative with respect to relevant tasks, while an adversarial regularization encourages these features to be disentangled and minimally informative about irrelevant tasks. We aim to use the disentangled representations to generalize the applicability of deep neural networks. We demonstrate the advantages of the proposed method on synthetic data as well as fetal ultrasound images. Our experiments illustrate that our method is capable of learning disentangled internal representations. It outperforms baseline methods in multiple tasks, especially on images with new properties, e.g. previously unseen artifacts in fetal ultrasound.

cs.LG↗

arXiv2019

Is Texture Predictive for Age and Sex in Brain MRI?

Deep learning builds the foundation for many medical image analysis tasks where neuralnetworks are often designed to have a large receptive field to incorporate long spatialdependencies. Recent work has shown that large receptive fields are not always necessaryfor computer vision tasks on natural images. We explore whether this translates to certainmedical imaging tasks such as age and sex prediction from a T1-weighted brain MRI scans.

eess.IV↗

arXiv2018

Deep Generative Models in the Real-World: An Open Challenge from Medical Imaging

Recent advances in deep learning led to novel generative modeling techniques that achieve unprecedented quality in generated samples and performance in learning complex distributions in imaging data. These new models in medical image computing have important applications that form clinically relevant and very challenging unsupervised learning problems. In this paper, we explore the feasibility of using state-of-the-art auto-encoder-based deep generative models, such as variational and adversarial auto-encoders, for one such task: abnormality detection in medical imaging. We utilize typical, publicly available datasets with brain scans from healthy subjects and patients with stroke lesions and brain tumors. We use the data from healthy subjects to train different auto-encoder based models to learn the distribution of healthy images and detect pathologies as outliers. Models that can better learn the data distribution should be able to detect outliers more accurately. We evaluate the detection performance of deep generative models and compare them with non-deep learning based approaches to provide a benchmark of the current state of research. We conclude that abnormality detection is a challenging task for deep generative models and large room exists for improvement. In order to facilitate further research, we aim to provide carefully pre-processed imaging data available to the research community.

cs.CV↗

arXiv2018

NeuroNet: Fast and Robust Reproduction of Multiple Brain Image Segmentation Pipelines

NeuroNet is a deep convolutional neural network mimicking multiple popular and state-of-the-art brain segmentation tools including FSL, SPM, and MALPEM. The network is trained on 5,000 T1-weighted brain MRI scans from the UK Biobank Imaging Study that have been automatically segmented into brain tissue and cortical and sub-cortical structures using the standard neuroimaging pipelines. Training a single model from these complementary and partially overlapping label maps yields a new powerful "all-in-one", multi-output segmentation tool. The processing time for a single subject is reduced by an order of magnitude compared to running each individual software package. We demonstrate very good reproducibility of the original outputs while increasing robustness to variations in the input data. We believe NeuroNet could be an important tool in large-scale population imaging studies and serve as a new standard in neuroscience by reducing the risk of introducing bias when choosing a specific software package.

cs.CV↗

arXiv2018

Implicit Weight Uncertainty in Neural Networks

Modern neural networks tend to be overconfident on unseen, noisy or incorrectly labelled data and do not produce meaningful uncertainty measures. Bayesian deep learning aims to address this shortcoming with variational approximations (such as Bayes by Backprop or Multiplicative Normalising Flows). However, current approaches have limitations regarding flexibility and scalability. We introduce Bayes by Hypernet (BbH), a new method of variational approximation that interprets hypernetworks as implicit distributions. It naturally uses neural networks to model arbitrarily complex distributions and scales to modern deep learning architectures. In our experiments, we demonstrate that our method achieves competitive accuracies and predictive uncertainties on MNIST and a CIFAR5 task, while being the most robust against adversarial attacks.

stat.ML↗

arXiv2017

Rasa: Open Source Language Understanding and Dialogue Management

We introduce a pair of tools, Rasa NLU and Rasa Core, which are open source python libraries for building conversational software. Their purpose is to make machine-learning based dialogue management and language understanding accessible to non-specialist software developers. In terms of design philosophy, we aim for ease of use, and bootstrapping from minimal (or no) initial training data. Both packages are extensively documented and ship with a comprehensive suite of tests. The code is available at https://github.com/RasaHQ/

cs.CL↗

arXiv2017

Feature Control as Intrinsic Motivation for Hierarchical Reinforcement Learning

The problem of sparse rewards is one of the hardest challenges in contemporary reinforcement learning. Hierarchical reinforcement learning (HRL) tackles this problem by using a set of temporally-extended actions, or options, each of which has its own subgoal. These subgoals are normally handcrafted for specific tasks. Here, though, we introduce a generic class of subgoals with broad applicability in the visual domain. Underlying our approach (in common with work using "auxiliary tasks") is the hypothesis that the ability to control aspects of the environment is an inherently useful skill to have. We incorporate such subgoals in an end-to-end hierarchical reinforcement learning system and test two variants of our algorithm on a number of games from the Atari suite. We highlight the advantage of our approach in one of the hardest games -- Montezuma's revenge -- for which the ability to handle sparse rewards is key. Our agent learns several times faster than the current state-of-the-art HRL agent in this game, reaching a similar level of performance. UPDATE 22/11/17: We found that a standard A3C agent with a simple shaped reward, i.e. extrinsic reward + feature control intrinsic reward, has comparable performance to our agent in Montezuma Revenge. In light of the new experiments performed, the advantage of our HRL approach can be attributed more to its ability to learn useful features from intrinsic rewards rather than its ability to explore and reuse abstracted skills with hierarchical components. This has led us to a new conclusion about the result.

cs.LG↗

arXiv2017

DLTK: State of the Art Reference Implementations for Deep Learning on Medical Images

We present DLTK, a toolkit providing baseline implementations for efficient experimentation with deep learning methods on biomedical images. It builds on top of TensorFlow and its high modularity and easy-to-use examples allow for a low-threshold access to state-of-the-art implementations for typical medical imaging problems. A comparison of DLTK's reference implementations of popular network architectures for image segmentation demonstrates new top performance on the publicly available challenge data "Multi-Atlas Labeling Beyond the Cranial Vault". The average test Dice similarity coefficient of $81.5$ exceeds the previously best performing CNN ($75.7$) and the accuracy of the challenge winning method ($79.0$).

cs.CV↗

arXiv2017

Ensembles of Multiple Models and Architectures for Robust Brain Tumour Segmentation

Deep learning approaches such as convolutional neural nets have consistently outperformed previous methods on challenging tasks such as dense, semantic segmentation. However, the various proposed networks perform differently, with behaviour largely influenced by architectural choices and training settings. This paper explores Ensembles of Multiple Models and Architectures (EMMA) for robust performance through aggregation of predictions from a wide range of methods. The approach reduces the influence of the meta-parameters of individual models and the risk of overfitting the configuration to a particular database. EMMA can be seen as an unbiased, generic deep learning model which is shown to yield excellent performance, winning the first position in the BRATS 2017 competition among 50+ participating teams.

cs.CV↗

arXiv2017

Efficient variational Bayesian neural network ensembles for outlier detection

In this work we perform outlier detection using ensembles of neural networks obtained by variational approximation of the posterior in a Bayesian neural network setting. The variational parameters are obtained by sampling from the true posterior by gradient descent. We show our outlier detection results are comparable to those obtained using other efficient ensembling methods.

stat.ML↗

arXiv2016

A Portable Diagnostic Device for Cardiac Magnetic Field Mapping

In this paper we present a portable magnetocardiography device. The focus of this development was delivering a rapid assessment of chest pain in an emergency department. The aim was therefore to produce an inexpensive device that could be rapidly deployed in a noisy unshielded ward environment. We found that induction coil magnetometers with a coil design optimized for magnetic field mapping possess sufficient sensitivity ($104fT/\sqrt{Hz}$ noise floor at 10Hz) and response ($813fT/μV$ at 10Hz) for cycle averaged magnetocardiography and are able to measure depolarisation signals in an unshielded environment. We were unable to observe repolarisation signals to a reasonable fidelity. We present the design of the induction coil sensor array and signal processing routine along with data demonstrating performance in a hospital environment.

physics.med-ph↗