An explainable Transformer-based deep learning model for the prediction of incident heart failure

Predicting the incidence of complex chronic conditions such as heart failure is challenging. Deep learning models applied to rich electronic health records may improve prediction but remain unexplainable hampering their wider use in medical practice. We developed a novel Transformer deep-learning model for more accurate and yet explainable prediction of incident heart failure involving 100,071 patients from longitudinal linked electronic health records across the UK. On internal 5-fold cross validation and held-out external validation, our model achieved 0.93 and 0.93 area under the receiver operator curve and 0.69 and 0.70 area under the precision-recall curve, respectively and outperformed existing deep learning models. Predictor groups included all community and hospital diagnoses and medications contextualised within the age and calendar year for each patient's clinical encounter. The importance of contextualised medical information was revealed in a number of sensitivity analyses, and our perturbation method provided a way of identifying factors contributing to risk. Many of the identified risk factors were consistent with existing knowledge from clinical and epidemiological research but several new associations were revealed which had not been considered in expert-driven risk prediction models.

Learning from the Best: Rationalizing Prediction by Adversarial Information Calibration

Explaining the predictions of AI models is paramount in safety-critical applications, such as in legal or medical domains. One form of explanation for a prediction is an extractive rationale, i.e., a subset of features of an instance that lead the model to give its prediction on the instance. Previous works on generating extractive rationales usually employ a two-phase model: a selector that selects the most important features (i.e., the rationale) followed by a predictor that makes the prediction based exclusively on the selected features. One disadvantage of these works is that the main signal for learning to select features comes from the comparison of the answers given by the predictor and the ground-truth answers. In this work, we propose to squeeze more information from the predictor via an information calibration method. More precisely, we train two models jointly: one is a typical neural model that solves the task at hand in an accurate but black-box manner, and the other is a selector-predictor model that additionally produces a rationale for its prediction. The first model is used as a guide to the second model. We use an adversarial-based technique to calibrate the information extracted by the two models such that the difference between them is an indicator of the missed or over-selected features. In addition, for natural language tasks, we propose to use a language-model-based regularizer to encourage the extraction of fluent rationales. Experimental results on a sentiment analysis task as well as on three tasks from the legal domain show the effectiveness of our approach to rationale extraction.

Multi-type Disentanglement without Adversarial Training

Controlling the style of natural language by disentangling the latent space is an important step towards interpretable machine learning. After the latent space is disentangled, the style of a sentence can be transformed by tuning the style representation without affecting other features of the sentence. Previous works usually use adversarial training to guarantee that disentangled vectors do not affect each other. However, adversarial methods are difficult to train. Especially when there are multiple features (e.g., sentiment, or tense, which we call style types in this paper), each feature requires a separate discriminator for extracting a disentangled style vector corresponding to that feature. In this paper, we propose a unified distribution-controlling method, which provides each specific style value (the value of style types, e.g., positive sentiment, or past tense) with a unique representation. This method contributes a solid theoretical basis to avoid adversarial training in multi-type disentanglement. We also propose multiple loss functions to achieve a style-content disentanglement as well as a disentanglement among multiple style types. In addition, we observe that if two different style types always have some specific style values that occur together in the dataset, they will affect each other when transferring the style values. We call this phenomenon training bias, and we propose a loss function to alleviate such training bias while disentangling multiple types. We conduct experiments on two datasets (Yelp service reviews and Amazon product reviews) to evaluate the style-disentangling effect and the unsupervised style transfer performance on two style types: sentiment and tense. The experimental results show the effectiveness of our model.

Reinforced Medical Report Generation with X-Linear Attention and Repetition Penalty

To reduce doctors' workload, deep-learning-based automatic medical report generation has recently attracted more and more research efforts, where attention mechanisms and reinforcement learning are integrated with the classic encoder-decoder architecture to enhance the performance of deep models. However, these state-of-the-art solutions mainly suffer from two shortcomings: (i) their attention mechanisms cannot utilize high-order feature interactions, and (ii) due to the use of TF-IDF-based reward functions, these methods are fragile with generating repeated terms. Therefore, in this work, we propose a reinforced medical report generation solution with x-linear attention and repetition penalty mechanisms (ReMRG-XR) to overcome these problems. Specifically, x-linear attention modules are used to explore high-order feature interactions and achieve multi-modal reasoning, while repetition penalty is used to apply penalties to repeated terms during the model's training process. Extensive experimental studies have been conducted on two public datasets, and the results show that ReMRG-XR greatly outperforms the state-of-the-art baselines in terms of all metrics.

SAG-GAN: Semi-Supervised Attention-Guided GANs for Data Augmentation on Medical Images

Recently deep learning methods, in particular, convolutional neural networks (CNNs), have led to a massive breakthrough in the range of computer vision. Also, the large-scale annotated dataset is the essential key to a successful training procedure. However, it is a huge challenge to get such datasets in the medical domain. Towards this, we present a data augmentation method for generating synthetic medical images using cycle-consistency Generative Adversarial Networks (GANs). We add semi-supervised attention modules to generate images with convincing details. We treat tumor images and normal images as two domains. The proposed GANs-based model can generate a tumor image from a normal image, and in turn, it can also generate a normal image from a tumor image. Furthermore, we show that generated medical images can be used for improving the performance of ResNet18 for medical image classification. Our model is applied to three limited datasets of tumor MRI images. We first generate MRI images on limited datasets, then we trained three popular classification models to get the best model for tumor classification. Finally, we train the classification model using real images with classic data augmentation methods and classification models using synthetic images. The classification results between those trained models showed that the proposed SAG-GAN data augmentation method can boost Accuracy and AUC compare with classic data augmentation methods. We believe the proposed data augmentation method can apply to other medical image domains, and improve the accuracy of computer-assisted diagnosis.

w-Net: Dual Supervised Medical Image Segmentation Model with Multi-Dimensional Attention and Cascade Multi-Scale Convolution

Deep learning-based medical image segmentation technology aims at automatic recognizing and annotating objects on the medical image. Non-local attention and feature learning by multi-scale methods are widely used to model network, which drives progress in medical image segmentation. However, those attention mechanism methods have weakly non-local receptive fields' strengthened connection for small objects in medical images. Then, the features of important small objects in abstract or coarse feature maps may be deserted, which leads to unsatisfactory performance. Moreover, the existing multi-scale methods only simply focus on different sizes of view, whose sparse multi-scale features collected are not abundant enough for small objects segmentation. In this work, a multi-dimensional attention segmentation model with cascade multi-scale convolution is proposed to predict accurate segmentation for small objects in medical images. As the weight function, multi-dimensional attention modules provide coefficient modification for significant/informative small objects features. Furthermore, The cascade multi-scale convolution modules in each skip-connection path are exploited to capture multi-scale features in different semantic depth. The proposed method is evaluated on three datasets: KiTS19, Pancreas CT of Decathlon-10, and MICCAI 2018 LiTS Challenge, demonstrating better segmentation performances than the state-of-the-art baselines.

Efficient Medical Image Segmentation with Intermediate Supervision Mechanism

Because the expansion path of U-Net may ignore the characteristics of small targets, intermediate supervision mechanism is proposed. The original mask is also entered into the network as a label for intermediate output. However, U-Net is mainly engaged in segmentation, and the extracted features are also targeted at segmentation location information, and the input and output are different. The label we need is that the input and output are both original masks, which is more similar to the refactoring process, so we propose another intermediate supervision mechanism. However, the features extracted by the contraction path of this intermediate monitoring mechanism are not necessarily consistent. For example, U-Net's contraction path extracts transverse features, while auto-encoder extracts longitudinal features, which may cause the output of the expansion path to be inconsistent with the label. Therefore, we put forward the intermediate supervision mechanism of shared-weight decoder module. Although the intermediate supervision mechanism improves the segmentation accuracy, the training time is too long due to the extra input and multiple loss functions. For one of these problems, we have introduced tied-weight decoder. To reduce the redundancy of the model, we combine shared-weight decoder module with tied-weight decoder module.

The Gap on GAP: Tackling the Problem of Differing Data Distributions in Bias-Measuring Datasets

Diagnostic datasets that can detect biased models are an important prerequisite for bias reduction within natural language processing. However, undesired patterns in the collected data can make such tests incorrect. For example, if the feminine subset of a gender-bias-measuring coreference resolution dataset contains sentences with a longer average distance between the pronoun and the correct candidate, an RNN-based model may perform worse on this subset due to long-term dependencies. In this work, we introduce a theoretically grounded method for weighting test samples to cope with such patterns in the test data. We demonstrate the method on the GAP dataset for coreference resolution. We annotate GAP with spans of all personal names and show that examples in the female subset contain more personal names and a longer distance between pronouns and their referents, potentially affecting the bias score in an undesired way. Using our weighting method, we find the set of weights on the test instances that should be used for coping with these correlations, and we re-evaluate 16 recently released coreference models.