On the Fairness of Swarm Learning in Skin Lesion Classification

in healthcare. However, the existing AI model may be biased in its decision marking. The bias induced by data itself, such as collecting data in subgroups only, can be mitigated by including more diversified data. Distributed and collaborative learning is an approach to involve training models in massive, heterogeneous, and distributed data sources, also known as nodes. In this work, we target on examining the fairness issue in Swarm Learning (SL), a recent edge-computing based decentralized machine learning approach, which is designed for heterogeneous illnesses detection in precision medicine. SL has achieved high performance in clinical applications, but no attempt has been made to evaluate if SL can improve fairness. To address the problem, we present an empirical study by comparing the fairness among single (node) training, SL, centralized training. Specifically, we evaluate on large public available skin lesion dataset, which contains samples from various subgroups. The experiments demonstrate that SL does not exacerbate the fairness problem compared to centralized training and improves both performance and fairness compared to single training. However, there still exists biases in SL model and the implementation of SL is more complex than the alternative two strategies.

Deformable Image Registration using Neural ODEs

Deformable image registration, aiming to find spatial correspondence between a given image pair, is one of the most critical problems in the domain of medical image analysis. In this paper, we present a generic, fast, and accurate diffeomorphic image registration framework that leverages neural ordinary differential equations (NODEs). We model each voxel as a moving particle and consider the set of all voxels in a 3D image as a high-dimensional dynamical system whose trajectory determines the targeted deformation field. Compared with traditional optimization-based methods, our framework reduces the running time from tens of minutes to tens of seconds. Compared with recent data-driven deep learning methods, our framework is more accessible since it does not require large amounts of training data. Our experiments show that the registration results of our method outperform state-of-the-arts under various metrics, indicating that our modeling approach is well fitted for the task of deformable image registration.

A Pseudo Label-wise Attention Network for Automatic ICD Coding

Automatic International Classification of Diseases (ICD) coding is defined as a kind of text multi-label classification problem, which is difficult because the number of labels is very large and the distribution of labels is unbalanced. The label-wise attention mechanism is widely used in automatic ICD coding because it can assign weights to every word in full Electronic Medical Records (EMR) for different ICD codes. However, the label-wise attention mechanism is computational redundant and costly. In this paper, we propose a pseudo label-wise attention mechanism to tackle the problem. Instead of computing different attention modes for different ICD codes, the pseudo label-wise attention mechanism automatically merges similar ICD codes and computes only one attention mode for the similar ICD codes, which greatly compresses the number of attention modes and improves the predicted accuracy. In addition, we apply a more convenient and effective way to obtain the ICD vectors, and thus our model can predict new ICD codes by calculating the similarities between EMR vectors and ICD vectors. Extensive experiments show the superior performance of our model. On the public MIMIC-III dataset and private Xiangya dataset, our model achieves micro f1 of 0.583 and 0.806, respectively, which outperforms other competing models. Furthermore, we verify the ability of our model in predicting new ICD codes. The case study shows how pseudo label-wise attention works, and demonstrates the effectiveness of pseudo label-wise attention mechanism.

Unsupervised Learning of Multi-level Structures for Anomaly Detection

The main difficulty in high-dimensional anomaly detection tasks is the lack of anomalous data for training. And simply collecting anomalous data from the real world, common distributions, or the boundary of normal data manifold may face the problem of missing anomaly modes. This paper first introduces a novel method to generate anomalous data by breaking up global structures while preserving local structures of normal data at multiple levels. It can efficiently expose local abnormal structures of various levels. To fully exploit the exposed multi-level abnormal structures, we propose to train multiple level-specific patch-based detectors with contrastive losses. Each detector learns to detect local abnormal structures of corresponding level at all locations and outputs patchwise anomaly scores. By aggregating the outputs of all level-specific detectors, we obtain a model that can detect all potential anomalies. The effectiveness is evaluated on MNIST, CIFAR10, and ImageNet10 dataset, where the results surpass the accuracy of state-of-the-art methods. Qualitative experiments demonstrate our model is robust that it unbiasedly detects all anomaly modes.

On the Optimality of Batch Policy Optimization Algorithms

Batch policy optimization considers leveraging existing data for policy construction before interacting with an environment. Although interest in this problem has grown significantly in recent years, its theoretical foundations remain under-developed. To advance the understanding of this problem, we provide three results that characterize the limits and possibilities of batch policy optimization in the finite-armed stochastic bandit setting. First, we introduce a class of confidence-adjusted index algorithms that unifies optimistic and pessimistic principles in a common framework, which enables a general analysis. For this family, we show that any confidence-adjusted index algorithm is minimax optimal, whether it be optimistic, pessimistic or neutral. Our analysis reveals that instance-dependent optimality, commonly used to establish optimality of on-line stochastic bandit algorithms, cannot be achieved by any algorithm in the batch setting. In particular, for any algorithm that performs optimally in some environment, there exists another environment where the same algorithm suffers arbitrarily larger regret. Therefore, to establish a framework for distinguishing algorithms, we introduce a new weighted-minimax criterion that considers the inherent difficulty of optimal value prediction. We demonstrate how this criterion can be used to justify commonly used pessimistic principles for batch policy optimization.

Instabilities of Offline RL with Pre-Trained Neural Representation

In offline reinforcement learning (RL), we seek to utilize offline data to evaluate (or learn) policies in scenarios where the data are collected from a distribution that substantially differs from that of the target policy to be evaluated. Recent theoretical advances have shown that such sample-efficient offline RL is indeed possible provided certain strong representational conditions hold, else there are lower bounds exhibiting exponential error amplification (in the problem horizon) unless the data collection distribution has only a mild distribution shift relative to the target policy. This work studies these issues from an empirical perspective to gauge how stable offline RL methods are. In particular, our methodology explores these ideas when using features from pre-trained neural networks, in the hope that these representations are powerful enough to permit sample efficient offline RL. Through extensive experiments on a range of tasks, we see that substantial error amplification does occur even when using such pre-trained representations (trained on the same task itself); we find offline RL is stable only under extremely mild distribution shift. The implications of these results, both from a theoretical and an empirical perspective, are that successful offline RL (where we seek to go beyond the low distribution shift regime) requires substantially stronger conditions beyond those which suffice for successful supervised learning.

Estimating and Improving Fairness with Adversarial Learning

Fairness and accountability are two essential pillars for trustworthy Artificial Intelligence (AI) in healthcare. However, the existing AI model may be biased in its decision marking. To tackle this issue, we propose an adversarial multi-task training strategy to simultaneously mitigate and detect bias in the deep learning-based medical image analysis system. Specifically, we propose to add a discrimination module against bias and a critical module that predicts unfairness within the base classification model. We further impose an orthogonality regularization to force the two modules to be independent during training. Hence, we can keep these deep learning tasks distinct from one another, and avoid collapsing them into a singular point on the manifold. Through this adversarial training method, the data from the underprivileged group, which is vulnerable to bias because of attributes such as sex and skin tone, are transferred into a domain that is neutral relative to these attributes. Furthermore, the critical module can predict fairness scores for the data with unknown sensitive attributes. We evaluate our framework on a large-scale public-available skin lesion dataset under various fairness evaluation metrics. The experiments demonstrate the effectiveness of our proposed method for estimating and improving fairness in the deep learning-based medical image analysis system.

BridgeDPI: A Novel Graph Neural Network for Predicting Drug-Protein Interactions

Motivation: Exploring drug-protein interactions (DPIs) work as a pivotal step in drug discovery. The fast expansion of available biological data enables computational methods effectively assist in experimental methods. Among them, deep learning methods extract features only from basic characteristics, such as protein sequences, molecule structures. Others achieve significant improvement by learning from not only sequences/molecules but the protein-protein and drug-drug associations (PPAs and DDAs). The PPAs and DDAs are generally obtained by using computational methods. However, existing computational methods have some limitations, resulting in low-quality PPAs and DDAs that hamper the prediction performance. Therefore, we hope to develop a novel supervised learning method to learn the PPAs and DDAs effectively and thereby improve the prediction performance of the specific task of DPI. Results: In this research, we propose a novel deep learning framework, namely BridgeDPI. BridgeDPI introduces a class of nodes named hyper-nodes, which bridge different proteins/drugs to work as PPAs and DDAs. The hyper-nodes can be supervised learned for the specific task of DPI since the whole process is an end-to-end learning. Consequently, such a model would improve prediction performance of DPI. In three real-world datasets, we further demonstrate that BridgeDPI outperforms state-of-the-art methods. Moreover, ablation studies verify the effectiveness of the hyper-nodes. Last, in an independent verification, BridgeDPI explores the candidate bindings among COVID-19's proteins and various antiviral drugs. And the predictive results accord with the statement of the World Health Organization and Food and Drug Administration, showing the validity and reliability of BridgeDPI.

Quantization in Relative Gradient Angle Domain For Building Polygon Estimation

Building footprint extraction in remote sensing data benefits many important applications, such as urban planning and population estimation. Recently, rapid development of Convolutional Neural Networks (CNNs) and open-sourced high resolution satellite building image datasets have pushed the performance boundary further for automated building extractions. However, CNN approaches often generate imprecise building morphologies including noisy edges and round corners. In this paper, we leverage the performance of CNNs, and propose a module that uses prior knowledge of building corners to create angular and concise building polygons from CNN segmentation outputs. We describe a new transform, Relative Gradient Angle Transform (RGA Transform) that converts object contours from time vs. space to time vs. angle. We propose a new shape descriptor, Boundary Orientation Relation Set (BORS), to describe angle relationship between edges in RGA domain, such as orthogonality and parallelism. Finally, we develop an energy minimization framework that makes use of the angle relationship in BORS to straighten edges and reconstruct sharp corners, and the resulting corners create a polygon. Experimental results demonstrate that our method refines CNN output from a rounded approximation to a more clear-cut angular shape of the building footprint.