CVMar 2, 2023
Measuring axiomatic soundness of counterfactual image modelsMiguel Monteiro, Fabio De Sousa Ribeiro, Nick Pawlowski et al. · microsoft-research
We present a general framework for evaluating image counterfactuals. The power and flexibility of deep generative models make them valuable tools for learning mechanisms in structural causal models. However, their flexibility makes counterfactual identifiability impossible in the general case. Motivated by these issues, we revisit Pearl's axiomatic definition of counterfactuals to determine the necessary constraints of any counterfactual inference model: composition, reversibility, and effectiveness. We frame counterfactuals as functions of an input variable, its parents, and counterfactual parents and use the axiomatic constraints to restrict the set of functions that could represent the counterfactual, thus deriving distance metrics between the approximate and ideal functions. We demonstrate how these metrics can be used to compare and choose between different approximate counterfactual inference models and to provide insight into a model's shortcomings and trade-offs.
CVAug 23, 2022
Deep Structural Causal Shape ModelsRajat Rasal, Daniel C. Castro, Nick Pawlowski et al. · microsoft-research
Causal reasoning provides a language to ask important interventional and counterfactual questions beyond purely statistical association. In medical imaging, for example, we may want to study the causal effect of genetic, environmental, or lifestyle factors on the normal and pathological variation of anatomical phenotypes. However, while anatomical shape models of 3D surface meshes, extracted from automated image segmentation, can be reliably constructed, there is a lack of computational tooling to enable causal reasoning about morphological variations. To tackle this problem, we propose deep structural causal shape models (CSMs), which utilise high-quality mesh generation techniques, from geometric deep learning, within the expressive framework of deep structural causal models. CSMs enable subject-specific prognoses through counterfactual mesh generation ("How would this patient's brain structure change if they were ten years older?"), which is in contrast to most current works on purely population-level statistical shape modelling. We demonstrate the capabilities of CSMs at all levels of Pearl's causal hierarchy through a number of qualitative and quantitative experiments leveraging a large dataset of 3D brain structures.
LGApr 11, 2023
Understanding Causality with Large Language Models: Feasibility and OpportunitiesCheng Zhang, Stefan Bauer, Paul Bennett et al.
We assess the ability of large language models (LLMs) to answer causal questions by analyzing their strengths and weaknesses against three types of causal question. We believe that current LLMs can answer causal questions with existing causal knowledge as combined domain experts. However, they are not yet able to provide satisfactory answers for discovering new knowledge or for high-stakes decision-making tasks with high precision. We discuss possible future directions and opportunities, such as enabling explicit and implicit causal modules as well as deep causal-aware LLMs. These will not only enable LLMs to answer many different types of causal questions for greater impact but also enable LLMs to be more trustworthy and efficient in general.
LGJun 27, 2023
High Fidelity Image Counterfactuals with Probabilistic Causal ModelsFabio De Sousa Ribeiro, Tian Xia, Miguel Monteiro et al.
We present a general causal generative modelling framework for accurate estimation of high fidelity image counterfactuals with deep structural causal models. Estimation of interventional and counterfactual queries for high-dimensional structured variables, such as images, remains a challenging task. We leverage ideas from causal mediation analysis and advances in generative modelling to design new deep causal mechanisms for structured variables in causal models. Our experiments demonstrate that our proposed mechanisms are capable of accurate abduction and estimation of direct, indirect and total effects as measured by axiomatic soundness of counterfactuals.
LGJul 26, 2023
BayesDAG: Gradient-Based Posterior Inference for Causal DiscoveryYashas Annadani, Nick Pawlowski, Joel Jennings et al.
Bayesian causal discovery aims to infer the posterior distribution over causal models from observed data, quantifying epistemic uncertainty and benefiting downstream tasks. However, computational challenges arise due to joint inference over combinatorial space of Directed Acyclic Graphs (DAGs) and nonlinear functions. Despite recent progress towards efficient posterior inference over DAGs, existing methods are either limited to variational inference on node permutation matrices for linear causal models, leading to compromised inference accuracy, or continuous relaxation of adjacency matrices constrained by a DAG regularizer, which cannot ensure resulting graphs are DAGs. In this work, we introduce a scalable Bayesian causal discovery framework based on a combination of stochastic gradient Markov Chain Monte Carlo (SG-MCMC) and Variational Inference (VI) that overcomes these limitations. Our approach directly samples DAGs from the posterior without requiring any DAG regularization, simultaneously draws function parameter samples and is applicable to both linear and nonlinear causal models. To enable our approach, we derive a novel equivalence to the permutation-based DAG learning, which opens up possibilities of using any relaxed gradient estimator defined over permutations. To our knowledge, this is the first framework applying gradient-based MCMC sampling for causal discovery. Empirical evaluation on synthetic and real-world datasets demonstrate our approach's effectiveness compared to state-of-the-art baselines.
LGOct 26, 2022
Rhino: Deep Causal Temporal Relationship Learning With History-dependent NoiseWenbo Gong, Joel Jennings, Cheng Zhang et al.
Discovering causal relationships between different variables from time series data has been a long-standing challenge for many domains such as climate science, finance, and healthcare. Given the complexity of real-world relationships and the nature of observations in discrete time, causal discovery methods need to consider non-linear relations between variables, instantaneous effects and history-dependent noise (the change of noise distribution due to past actions). However, previous works do not offer a solution addressing all these problems together. In this paper, we propose a novel causal relationship learning framework for time-series data, called Rhino, which combines vector auto-regression, deep learning and variational inference to model non-linear relationships with instantaneous effects while allowing the noise distribution to be modulated by historical observations. Theoretically, we prove the structural identifiability of Rhino. Our empirical results from extensive synthetic experiments and two real-world benchmarks demonstrate better discovery performance compared to relevant baselines, with ablation studies revealing its robustness under model misspecification.
LGMay 25, 2022
Structured Uncertainty in the Observation Space of Variational AutoencodersJames Langley, Miguel Monteiro, Charles Jones et al.
Variational autoencoders (VAEs) are a popular class of deep generative models with many variants and a wide range of applications. Improvements upon the standard VAE mostly focus on the modelling of the posterior distribution over the latent space and the properties of the neural network decoder. In contrast, improving the model for the observational distribution is rarely considered and typically defaults to a pixel-wise independent categorical or normal distribution. In image synthesis, sampling from such distributions produces spatially-incoherent results with uncorrelated pixel noise, resulting in only the sample mean being somewhat useful as an output prediction. In this paper, we aim to stay true to VAE theory by improving the samples from the observational distribution. We propose SOS-VAE, an alternative model for the observation space, encoding spatial dependencies via a low-rank parameterisation. We demonstrate that this new observational distribution has the ability to capture relevant covariance between pixels, resulting in spatially-coherent samples. In contrast to pixel-wise independent distributions, our samples seem to contain semantically-meaningful variations from the mean allowing the prediction of multiple plausible outputs with a single forward pass.
CYAug 17, 2022
NeurIPS Competition Instructions and Guide: Causal Insights for Learning Paths in EducationWenbo Gong, Digory Smith, Zichao Wang et al.
In this competition, participants will address two fundamental causal challenges in machine learning in the context of education using time-series data. The first is to identify the causal relationships between different constructs, where a construct is defined as the smallest element of learning. The second challenge is to predict the impact of learning one construct on the ability to answer questions on other constructs. Addressing these challenges will enable optimisation of students' knowledge acquisition, which can be deployed in a real edtech solution impacting millions of students. Participants will run these tasks in an idealised environment with synthetic data and a real-world scenario with evaluation data collected from a series of A/B tests.
LGOct 1, 2023
Towards Causal Foundation Model: on Duality between Causal Inference and AttentionJiaqi Zhang, Joel Jennings, Agrin Hilmkil et al.
Foundation models have brought changes to the landscape of machine learning, demonstrating sparks of human-level intelligence across a diverse array of tasks. However, a gap persists in complex tasks such as causal inference, primarily due to challenges associated with intricate reasoning steps and high numerical precision requirements. In this work, we take a first step towards building causally-aware foundation models for treatment effect estimations. We propose a novel, theoretically justified method called Causal Inference with Attention (CInA), which utilizes multiple unlabeled datasets to perform self-supervised causal learning, and subsequently enables zero-shot causal inference on unseen tasks with new data. This is based on our theoretical results that demonstrate the primal-dual connection between optimal covariate balancing and self-attention, facilitating zero-shot causal inference through the final layer of a trained transformer-type architecture. We demonstrate empirically that CInA effectively generalizes to out-of-distribution datasets and various real-world datasets, matching or even surpassing traditional per-dataset methodologies. These results provide compelling evidence that our method has the potential to serve as a stepping stone for the development of causal foundation models.
MLJun 11, 2020Code
Deep Structural Causal Models for Tractable Counterfactual InferenceNick Pawlowski, Daniel C. Castro, Ben Glocker
We formulate a general framework for building structural causal models (SCMs) with deep learning components. The proposed approach employs normalising flows and variational inference to enable tractable inference of exogenous noise variables - a crucial step for counterfactual inference that is missing from existing deep causal learning methods. Our framework is validated on a synthetic dataset built on MNIST as well as on a real-world medical dataset of brain MRI scans. Our experimental results indicate that we can successfully train deep SCMs that are capable of all three levels of Pearl's ladder of causation: association, intervention, and counterfactuals, giving rise to a powerful new approach for answering causal questions in imaging applications and beyond. The code for all our experiments is available at https://github.com/biomedia-mira/deepscm.
CVJan 24, 2020Code
An Explicit Local and Global Representation Disentanglement Framework with Applications in Deep Clustering and Unsupervised Object DetectionRujikorn Charakorn, Yuttapong Thawornwattana, Sirawaj Itthipuripat et al.
Visual data can be understood at different levels of granularity, where global features correspond to semantic-level information and local features correspond to texture patterns. In this work, we propose a framework, called SPLIT, which allows us to disentangle local and global information into two separate sets of latent variables within the variational autoencoder (VAE) framework. Our framework adds generative assumption to the VAE by requiring a subset of the latent variables to generate an auxiliary set of observable data. This additional generative assumption primes the latent variables to local information and encourages the other latent variables to represent global information. We examine three different flavours of VAEs with different generative assumptions. We show that the framework can effectively disentangle local and global information within these models leads to improved representation, with better clustering and unsupervised object detection benchmarks. Finally, we establish connections between SPLIT and recent research in cognitive neuroscience regarding the disentanglement in human visual perception. The code for our experiments is at https://github.com/51616/split-vae .
CLDec 14, 2017Code
Rasa: Open Source Language Understanding and Dialogue ManagementTom Bocklisch, Joey Faulkner, Nick Pawlowski et al.
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/
AIFeb 6, 2024
The Essential Role of Causality in Foundation World Models for Embodied AITarun Gupta, Wenbo Gong, Chao Ma et al.
Recent advances in foundation models, especially in large multi-modal models and conversational agents, have ignited interest in the potential of generally capable embodied agents. Such agents will require the ability to perform new tasks in many different real-world environments. However, current foundation models fail to accurately model physical interactions and are therefore insufficient for Embodied AI. The study of causality lends itself to the construction of veridical world models, which are crucial for accurately predicting the outcomes of possible interactions. This paper focuses on the prospects of building foundation world models for the upcoming generation of embodied agents and presents a novel viewpoint on the significance of causality within these. We posit that integrating causal considerations is vital to facilitating meaningful physical interactions with the world. Finally, we demystify misconceptions about causality in this context and present our outlook for future research.
AIJun 18, 2024
Probabilistic Temporal Prediction of Continuous Disease Trajectories and Treatment Effects Using Neural SDEsJoshua Durso-Finley, Berardino Barile, Jean-Pierre Falet et al.
Personalized medicine based on medical images, including predicting future individualized clinical disease progression and treatment response, would have an enormous impact on healthcare and drug development, particularly for diseases (e.g. multiple sclerosis (MS)) with long term, complex, heterogeneous evolutions and no cure. In this work, we present the first stochastic causal temporal framework to model the continuous temporal evolution of disease progression via Neural Stochastic Differential Equations (NSDE). The proposed causal inference model takes as input the patient's high dimensional images (MRI) and tabular data, and predicts both factual and counterfactual progression trajectories on different treatments in latent space. The NSDE permits the estimation of high-confidence personalized trajectories and treatment effects. Extensive experiments were performed on a large, multi-centre, proprietary dataset of patient 3D MRI and clinical data acquired during several randomized clinical trials for MS treatments. Our results present the first successful uncertainty-based causal Deep Learning (DL) model to: (a) accurately predict future patient MS disability evolution (e.g. EDSS) and treatment effects leveraging baseline MRI, and (b) permit the discovery of subgroups of patients for which the model has high confidence in their response to treatment even in clinical trials which did not reach their clinical endpoints.
LGMay 5, 2023
Improving Image-Based Precision Medicine with Uncertainty-Aware Causal ModelsJoshua Durso-Finley, Jean-Pierre Falet, Raghav Mehta et al.
Image-based precision medicine aims to personalize treatment decisions based on an individual's unique imaging features so as to improve their clinical outcome. Machine learning frameworks that integrate uncertainty estimation as part of their treatment recommendations would be safer and more reliable. However, little work has been done in adapting uncertainty estimation techniques and validation metrics for precision medicine. In this paper, we use Bayesian deep learning for estimating the posterior distribution over factual and counterfactual outcomes on several treatments. This allows for estimating the uncertainty for each treatment option and for the individual treatment effects (ITE) between any two treatments. We train and evaluate this model to predict future new and enlarging T2 lesion counts on a large, multi-center dataset of MR brain images of patients with multiple sclerosis, exposed to several treatments during randomized controlled trials. We evaluate the correlation of the uncertainty estimate with the factual error, and, given the lack of ground truth counterfactual outcomes, demonstrate how uncertainty for the ITE prediction relates to bounds on the ITE error. Lastly, we demonstrate how knowledge of uncertainty could modify clinical decision-making to improve individual patient and clinical trial outcomes.
MLFeb 4, 2022
Deep End-to-end Causal InferenceTomas Geffner, Javier Antoran, Adam Foster et al.
Causal inference is essential for data-driven decision making across domains such as business engagement, medical treatment and policy making. However, research on causal discovery has evolved separately from inference methods, preventing straight-forward combination of methods from both fields. In this work, we develop Deep End-to-end Causal Inference (DECI), a single flow-based non-linear additive noise model that takes in observational data and can perform both causal discovery and inference, including conditional average treatment effect (CATE) estimation. We provide a theoretical guarantee that DECI can recover the ground truth causal graph under standard causal discovery assumptions. Motivated by application impact, we extend this model to heterogeneous, mixed-type data with missing values, allowing for both continuous and discrete treatment decisions. Our results show the competitive performance of DECI when compared to relevant baselines for both causal discovery and (C)ATE estimation in over a thousand experiments on both synthetic datasets and causal machine learning benchmarks across data-types and levels of missingness.
LGOct 15, 2021
Simultaneous Missing Value Imputation and Structure Learning with GroupsPablo Morales-Alvarez, Wenbo Gong, Angus Lamb et al.
Learning structures between groups of variables from data with missing values is an important task in the real world, yet difficult to solve. One typical scenario is discovering the structure among topics in the education domain to identify learning pathways. Here, the observations are student performances for questions under each topic which contain missing values. However, most existing methods focus on learning structures between a few individual variables from the complete data. In this work, we propose VISL, a novel scalable structure learning approach that can simultaneously infer structures between groups of variables under missing data and perform missing value imputations with deep learning. Particularly, we propose a generative model with a structured latent space and a graph neural network-based architecture, scaling to a large number of variables. Empirically, we conduct extensive experiments on synthetic, semi-synthetic, and real-world education data sets. We show improved performances on both imputation and structure learning accuracy compared to popular and recent approaches.
CVApr 8, 2021
Does Your Dermatology Classifier Know What It Doesn't Know? Detecting the Long-Tail of Unseen ConditionsAbhijit Guha Roy, Jie Ren, Shekoofeh Azizi et al.
We develop and rigorously evaluate a deep learning based system that can accurately classify skin conditions while detecting rare conditions for which there is not enough data available for training a confident classifier. We frame this task as an out-of-distribution (OOD) detection problem. Our novel approach, hierarchical outlier detection (HOD) assigns multiple abstention classes for each training outlier class and jointly performs a coarse classification of inliers vs. outliers, along with fine-grained classification of the individual classes. We demonstrate the effectiveness of the HOD loss in conjunction with modern representation learning approaches (BiT, SimCLR, MICLe) and explore different ensembling strategies for further improving the results. We perform an extensive subgroup analysis over conditions of varying risk levels and different skin types to investigate how the OOD detection performance changes over each subgroup and demonstrate the gains of our framework in comparison to baselines. Finally, we introduce a cost metric to approximate downstream clinical impact. We use this cost metric to compare the proposed method against a baseline system, thereby making a stronger case for the overall system effectiveness in a real-world deployment scenario.
CVJun 10, 2020
Stochastic Segmentation Networks: Modelling Spatially Correlated Aleatoric UncertaintyMiguel Monteiro, Loïc Le Folgoc, Daniel Coelho de Castro et al.
In image segmentation, there is often more than one plausible solution for a given input. In medical imaging, for example, experts will often disagree about the exact location of object boundaries. Estimating this inherent uncertainty and predicting multiple plausible hypotheses is of great interest in many applications, yet this ability is lacking in most current deep learning methods. In this paper, we introduce stochastic segmentation networks (SSNs), an efficient probabilistic method for modelling aleatoric uncertainty with any image segmentation network architecture. In contrast to approaches that produce pixel-wise estimates, SSNs model joint distributions over entire label maps and thus can generate multiple spatially coherent hypotheses for a single image. By using a low-rank multivariate normal distribution over the logit space to model the probability of the label map given the image, we obtain a spatially consistent probability distribution that can be efficiently computed by a neural network without any changes to the underlying architecture. We tested our method on the segmentation of real-world medical data, including lung nodules in 2D CT and brain tumours in 3D multimodal MRI scans. SSNs outperform state-of-the-art for modelling correlated uncertainty in ambiguous images while being much simpler, more flexible, and more efficient.
LGAug 21, 2019
Representation Disentanglement for Multi-task Learning with application to Fetal UltrasoundQingjie Meng, Nick Pawlowski, Daniel Rueckert et al.
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.
CVAug 16, 2019
Needles in Haystacks: On Classifying Tiny Objects in Large ImagesNick Pawlowski, Suvrat Bhooshan, Nicolas Ballas et al.
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.
IVJul 25, 2019
Is Texture Predictive for Age and Sex in Brain MRI?Nick Pawlowski, Ben Glocker
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.
CVNov 5, 2018
Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS ChallengeSpyridon Bakas, Mauricio Reyes, Andras Jakab et al.
Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset.
CVJun 14, 2018
Deep Generative Models in the Real-World: An Open Challenge from Medical ImagingXiaoran Chen, Nick Pawlowski, Martin Rajchl et al.
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.
CVJun 11, 2018
NeuroNet: Fast and Robust Reproduction of Multiple Brain Image Segmentation PipelinesMartin Rajchl, Nick Pawlowski, Daniel Rueckert et al.
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.
CVNov 18, 2017
DLTK: State of the Art Reference Implementations for Deep Learning on Medical ImagesNick Pawlowski, Sofia Ira Ktena, Matthew C. H. Lee et al.
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 ($79.0$).
CVNov 4, 2017
Ensembles of Multiple Models and Architectures for Robust Brain Tumour SegmentationKonstantinos Kamnitsas, Wenjia Bai, Enzo Ferrante et al.
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.
MLNov 3, 2017
Implicit Weight Uncertainty in Neural NetworksNick Pawlowski, Andrew Brock, Matthew C. H. Lee et al.
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.
LGMay 18, 2017
Feature Control as Intrinsic Motivation for Hierarchical Reinforcement LearningNat Dilokthanakul, Christos Kaplanis, Nick Pawlowski et al.
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.
MLMar 20, 2017
Efficient variational Bayesian neural network ensembles for outlier detectionNick Pawlowski, Miguel Jaques, Ben Glocker
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.