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Abstract BackgroundLung cancer is the deadliest and second most common cancer in the United States due to the lack of symptoms for early diagnosis. Pulmonary nodules are small abnormal regions that can be potentially correlated to the occurrence of lung cancer. Early detection of these nodules is critical because it can significantly improve the patient's survival rates. Thoracic thin‐sliced computed tomography (CT) scanning has emerged as a widely used method for diagnosing and prognosis lung abnormalities. PurposeThe standard clinical workflow of detecting pulmonary nodules relies on radiologists to analyze CT images to assess the risk factors of cancerous nodules. However, this approach can be error‐prone due to the various nodule formation causes, such as pollutants and infections. Deep learning (DL) algorithms have recently demonstrated remarkable success in medical image classification and segmentation. As an ever more important assistant to radiologists in nodule detection, it is imperative ensure the DL algorithm and radiologist to better understand the decisions from each other. This study aims to develop a framework integrating explainable AI methods to achieve accurate pulmonary nodule detection. MethodsA robust and explainable detection (RXD) framework is proposed, focusing on reducing false positives in pulmonary nodule detection. Its implementation is based on an explanation supervision method, which uses nodule contours of radiologists as supervision signals to force the model to learn nodule morphologies, enabling improved learning ability on small dataset, and enable small dataset learning ability. In addition, two imputation methods are applied to the nodule region annotations to reduce the noise within human annotations and allow the model to have robust attributions that meet human expectations. The 480, 265, and 265 CT image sets from the public Lung Image Database Consortium and Image Database Resource Initiative (LIDC‐IDRI) dataset are used for training, validation, and testing. ResultsUsing only 10, 30, 50, and 100 training samples sequentially, our method constantly improves the classification performance and explanation quality of baseline in terms of Area Under the Curve (AUC) and Intersection over Union (IoU). In particular, our framework with a learnable imputation kernel improves IoU from baseline by 24.0% to 80.0%. A pre‐defined Gaussian imputation kernel achieves an even greater improvement, from 38.4% to 118.8% from baseline. Compared to the baseline trained on 100 samples, our method shows less drop in AUC when trained on fewer samples. A comprehensive comparison of interpretability shows that our method aligns better with expert opinions. ConclusionsA pulmonary nodule detection framework was demonstrated using public thoracic CT image datasets. The framework integrates the robust explanation supervision (RES) technique to ensure the performance of nodule classification and morphology. The method can reduce the workload of radiologists and enable them to focus on the diagnosis and prognosis of the potential cancerous pulmonary nodules at the early stage to improve the outcomes for lung cancer patients. 

Abstract MotivationExpanding our knowledge of small molecules beyond what is known in nature or designed in wet laboratories promises to significantly advance cheminformatics, drug discovery, biotechnology and material science. In silico molecular design remains challenging, primarily due to the complexity of the chemical space and the non-trivial relationship between chemical structures and biological properties. Deep generative models that learn directly from data are intriguing, but they have yet to demonstrate interpretability in the learned representation, so we can learn more about the relationship between the chemical and biological space. In this article, we advance research on disentangled representation learning for small molecule generation. We build on recent work by us and others on deep graph generative frameworks, which capture atomic interactions via a graph-based representation of a small molecule. The methodological novelty is how we leverage the concept of disentanglement in the graph variational autoencoder framework both to generate biologically relevant small molecules and to enhance model interpretability. ResultsExtensive qualitative and quantitative experimental evaluation in comparison with state-of-the-art models demonstrate the superiority of our disentanglement framework. We believe this work is an important step to address key challenges in small molecule generation with deep generative frameworks. Availability and implementationTraining and generated data are made available at https://ieee-dataport.org/documents/dataset-disentangled-representation-learning-interpretable-molecule-generation. All code is made available at https://anonymous.4open.science/r/D-MolVAE-2799/. Supplementary informationSupplementary data are available at Bioinformatics online. 

Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation. Recently, the advancement of deep learning has created the opportunity for expressive methods to learn the underlying representation and properties of data. Such capability provides new ways of determining the mutual relationship between the structural patterns and functional properties of the data and leveraging such relationships to generate structural data, given the desired properties. This article is a systematic review that explains this promising research area, commonly known as controllable deep data generation. First, the article raises the potential challenges and provides preliminaries. Then the article formally defines controllable deep data generation, proposes a taxonomy on various techniques and summarizes the evaluation metrics in this specific domain. After that, the article introduces exciting applications of controllable deep data generation, experimentally analyzes and compares existing works. Finally, this article highlights the promising future directions of controllable deep data generation and identifies five potential challenges. 

As the societal impact of Deep Neural Networks (DNNs) grows, the goals for advancing DNNs become more complex and diverse, ranging from improving a conventional model accuracy metric to infusing advanced human virtues such as fairness, accountability, transparency, and unbiasedness. Recently, techniques in Explainable Artificial Intelligence (XAI) have been attracting considerable attention and have tremendously helped Machine Learning (ML) engineers in understand AI models. However, at the same time, we started to witness the emerging need beyond XAI among AI communities; based on the insights learned from XAI, how can we better empower ML engineers in steering their DNNs so that the model’s reasonableness and performance can be improved as intended? This article provides a timely and extensive literature overview of the field Explanation-Guided Learning (EGL), a domain of techniques that steer the DNNs’ reasoning process by adding regularization, supervision, or intervention on model explanations. In doing so, we first provide a formal definition of EGL and its general learning paradigm. Second, an overview of the key factors for EGL evaluation, as well as summarization and categorization of existing evaluation procedures and metrics for EGL are provided. Finally, the current and potential future application areas and directions of EGL are discussed, and an extensive experimental study is presented aiming at providing comprehensive comparative studies among existing EGL models in various popular application domains, such as Computer Vision and Natural Language Processing domains. Additional resources related to event prediction are included in the article website:https://kugaoyang.github.io/EGL/