A Field Guide to Scientific XAI: Transparent and Interpretable Deep Learning for Bioinformatics Research

Deep learning has become popular because of its potential to achieve high accuracy in prediction tasks. However, accuracy is not always the only goal of statistical modelling, especially for models developed as part of scientific research. Rather, many scientific models are developed to facilitate scientific discovery, by which we mean to abstract a human-understandable representation of the natural world. Unfortunately, the opacity of deep neural networks limit their role in scientific discovery, creating a new demand for models that are transparently interpretable. This article is a field guide to transparent model design. It provides a taxonomy of transparent model design concepts, a practical workflow for putting design concepts into practice, and a general template for reporting design choices. We hope this field guide will help researchers more effectively design transparently interpretable models, and thus enable them to use deep learning for scientific discovery.

Plug and Play, Model-Based Reinforcement Learning

Sample-efficient generalisation of reinforcement learning approaches have always been a challenge, especially, for complex scenes with many components. In this work, we introduce Plug and Play Markov Decision Processes, an object-based representation that allows zero-shot integration of new objects from known object classes. This is achieved by representing the global transition dynamics as a union of local transition functions, each with respect to one active object in the scene. Transition dynamics from an object class can be pre-learnt and thus would be ready to use in a new environment. Each active object is also endowed with its reward function. Since there is no central reward function, addition or removal of objects can be handled efficiently by only updating the reward functions of objects involved. A new transfer learning mechanism is also proposed to adapt reward function in such cases. Experiments show that our representation can achieve sample-efficiency in a variety of set-ups.

Clustering by Maximizing Mutual Information Across Views

We propose a novel framework for image clustering that incorporates joint representation learning and clustering. Our method consists of two heads that share the same backbone network - a "representation learning" head and a "clustering" head. The "representation learning" head captures fine-grained patterns of objects at the instance level which serve as clues for the "clustering" head to extract coarse-grain information that separates objects into clusters. The whole model is trained in an end-to-end manner by minimizing the weighted sum of two sample-oriented contrastive losses applied to the outputs of the two heads. To ensure that the contrastive loss corresponding to the "clustering" head is optimal, we introduce a novel critic function called "log-of-dot-product". Extensive experimental results demonstrate that our method significantly outperforms state-of-the-art single-stage clustering methods across a variety of image datasets, improving over the best baseline by about 5-7% in accuracy on CIFAR10/20, STL10, and ImageNet-Dogs. Further, the "two-stage" variant of our method also achieves better results than baselines on three challenging ImageNet subsets.

Combining Online Learning and Offline Learning for Contextual Bandits with Deficient Support

We address policy learning with logged data in contextual bandits. Current offline-policy learning algorithms are mostly based on inverse propensity score (IPS) weighting requiring the logging policy to have \emph{full support} i.e. a non-zero probability for any context/action of the evaluation policy. However, many real-world systems do not guarantee such logging policies, especially when the action space is large and many actions have poor or missing rewards. With such \emph{support deficiency}, the offline learning fails to find optimal policies. We propose a novel approach that uses a hybrid of offline learning with online exploration. The online exploration is used to explore unsupported actions in the logged data whilst offline learning is used to exploit supported actions from the logged data avoiding unnecessary explorations. Our approach determines an optimal policy with theoretical guarantees using the minimal number of online explorations. We demonstrate our algorithms' effectiveness empirically on a diverse collection of datasets.

A New Representation of Successor Features for Transfer across Dissimilar Environments

Transfer in reinforcement learning is usually achieved through generalisation across tasks. Whilst many studies have investigated transferring knowledge when the reward function changes, they have assumed that the dynamics of the environments remain consistent. Many real-world RL problems require transfer among environments with different dynamics. To address this problem, we propose an approach based on successor features in which we model successor feature functions with Gaussian Processes permitting the source successor features to be treated as noisy measurements of the target successor feature function. Our theoretical analysis proves the convergence of this approach as well as the bounded error on modelling successor feature functions with Gaussian Processes in environments with both different dynamics and rewards. We demonstrate our method on benchmark datasets and show that it outperforms current baselines.

A Spatio-temporal Attention-based Model for Infant Movement Assessment from Videos

The absence or abnormality of fidgety movements of joints or limbs is strongly indicative of cerebral palsy in infants. Developing computer-based methods for assessing infant movements in videos is pivotal for improved cerebral palsy screening. Most existing methods use appearance-based features and are thus sensitive to strong but irrelevant signals caused by background clutter or a moving camera. Moreover, these features are computed over the whole frame, thus they measure gross whole body movements rather than specific joint/limb motion. Addressing these challenges, we develop and validate a new method for fidgety movement assessment from consumer-grade videos using human poses extracted from short clips. Human poses capture only relevant motion profiles of joints and limbs and are thus free from irrelevant appearance artifacts. The dynamics and coordination between joints are modeled using spatio-temporal graph convolutional networks. Frames and body parts that contain discriminative information about fidgety movements are selected through a spatio-temporal attention mechanism. We validate the proposed model on the cerebral palsy screening task using a real-life consumer-grade video dataset collected at an Australian hospital through the Cerebral Palsy Alliance, Australia. Our experiments show that the proposed method achieves the ROC-AUC score of 81.87%, significantly outperforming existing competing methods with better interpretability.

Bayesian Optimistic Optimisation with Exponentially Decaying Regret

Bayesian optimisation (BO) is a well-known efficient algorithm for finding the global optimum of expensive, black-box functions. The current practical BO algorithms have regret bounds ranging from $\mathcal{O}(\frac{logN}{\sqrt{N}})$ to $\mathcal O(e^{-\sqrt{N}})$, where $N$ is the number of evaluations. This paper explores the possibility of improving the regret bound in the noiseless setting by intertwining concepts from BO and tree-based optimistic optimisation which are based on partitioning the search space. We propose the BOO algorithm, a first practical approach which can achieve an exponential regret bound with order $\mathcal O(N^{-\sqrt{N}})$ under the assumption that the objective function is sampled from a Gaussian process with a Mat\'ern kernel with smoothness parameter $\nu > 4 +\frac{D}{2}$, where $D$ is the number of dimensions. We perform experiments on optimisation of various synthetic functions and machine learning hyperparameter tuning tasks and show that our algorithm outperforms baselines.

Intuitive Physics Guided Exploration for Sample Efficient Sim2real Transfer

Physics-based reinforcement learning tasks can benefit from simplified physics simulators as they potentially allow near-optimal policies to be learned in simulation. However, such simulators require the latent factors (e.g. mass, friction coefficient etc.) of the associated objects and other environment-specific factors (e.g. wind speed, air density etc.) to be accurately specified, without which, it could take considerable additional learning effort to adapt the learned simulation policy to the real environment. As such a complete specification can be impractical, in this paper, we instead, focus on learning task-specific estimates of latent factors which allow the approximation of real world trajectories in an ideal simulation environment. Specifically, we propose two new concepts: a) action grouping - the idea that certain types of actions are closely associated with the estimation of certain latent factors, and; b) partial grounding - the idea that simulation of task-specific dynamics may not need precise estimation of all the latent factors. We first introduce intuitive action groupings based on human physics knowledge and experience, which is then used to design novel strategies for interacting with the real environment. Next, we describe how prior knowledge of a task in a given environment can be used to extract the relative importance of different latent factors, and how this can be used to inform partial grounding, which enables efficient learning of the task in any arbitrary environment. We demonstrate our approach in a range of physics based tasks, and show that it achieves superior performance relative to other baselines, using only a limited number of real-world interactions.

ALT-MAS: A Data-Efficient Framework for Active Testing of Machine Learning Algorithms

Machine learning models are being used extensively in many important areas, but there is no guarantee a model will always perform well or as its developers intended. Understanding the correctness of a model is crucial to prevent potential failures that may have significant detrimental impact in critical application areas. In this paper, we propose a novel framework to efficiently test a machine learning model using only a small amount of labeled test data. The idea is to estimate the metrics of interest for a model-under-test using Bayesian neural network (BNN). We develop a novel data augmentation method helping to train the BNN to achieve high accuracy. We also devise a theoretic information based sampling strategy to sample data points so as to achieve accurate estimations for the metrics of interest. Finally, we conduct an extensive set of experiments to test various machine learning models for different types of metrics. Our experiments show that the metrics estimations by our method are significantly better than existing baselines.

On Finite-Sample Analysis of Offline Reinforcement Learning with Deep ReLU Networks

This paper studies the statistical theory of offline reinforcement learning with deep ReLU networks. We consider the off-policy evaluation (OPE) problem where the goal is to estimate the expected discounted reward of a target policy given the logged data generated by unknown behaviour policies. We study a regression-based fitted Q evaluation (FQE) method using deep ReLU networks and characterize a finite-sample bound on the estimation error of this method under mild assumptions. The prior works in OPE with either general function approximation or deep ReLU networks ignore the data-dependent structure in the algorithm, dodging the technical bottleneck of OPE, while requiring a rather restricted regularity assumption. In this work, we overcome these limitations and provide a comprehensive analysis of OPE with deep ReLU networks. In particular, we precisely quantify how the distribution shift of the offline data, the dimension of the input space, and the regularity of the system control the OPE estimation error. Consequently, we provide insights into the interplay between offline reinforcement learning and deep learning.