Investigate Indistinguishable Points in Semantic Segmentation of 3D Point Cloud

This paper investigates the indistinguishable points (difficult to predict label) in semantic segmentation for large-scale 3D point clouds. The indistinguishable points consist of those located in complex boundary, points with similar local textures but different categories, and points in isolate small hard areas, which largely harm the performance of 3D semantic segmentation. To address this challenge, we propose a novel Indistinguishable Area Focalization Network (IAF-Net), which selects indistinguishable points adaptively by utilizing the hierarchical semantic features and enhances fine-grained features for points especially those indistinguishable points. We also introduce multi-stage loss to improve the feature representation in a progressive way. Moreover, in order to analyze the segmentation performances of indistinguishable areas, we propose a new evaluation metric called Indistinguishable Points Based Metric (IPBM). Our IAF-Net achieves the comparable results with state-of-the-art performance on several popular 3D point cloud datasets e.g. S3DIS and ScanNet, and clearly outperforms other methods on IPBM.Comment: AAAI202

Relational Learning between Multiple Pulmonary Nodules via Deep Set Attention Transformers

Diagnosis and treatment of multiple pulmonary nodules are clinically important but challenging. Prior studies on nodule characterization use solitary-nodule approaches on multiple nodular patients, which ignores the relations between nodules. In this study, we propose a multiple instance learning (MIL) approach and empirically prove the benefit to learn the relations between multiple nodules. By treating the multiple nodules from a same patient as a whole, critical relational information between solitary-nodule voxels is extracted. To our knowledge, it is the first study to learn the relations between multiple pulmonary nodules. Inspired by recent advances in natural language processing (NLP) domain, we introduce a self-attention transformer equipped with 3D CNN, named {NoduleSAT}, to replace typical pooling-based aggregation in multiple instance learning. Extensive experiments on lung nodule false positive reduction on LUNA16 database, and malignancy classification on LIDC-IDRI database, validate the effectiveness of the proposed method.Comment: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI 2020

MIA-Prognosis: A Deep Learning Framework to Predict Therapy Response

Predicting clinical outcome is remarkably important but challenging. Research efforts have been paid on seeking significant biomarkers associated with the therapy response or/and patient survival. However, these biomarkers are generally costly and invasive, and possibly dissatifactory for novel therapy. On the other hand, multi-modal, heterogeneous, unaligned temporal data is continuously generated in clinical practice. This paper aims at a unified deep learning approach to predict patient prognosis and therapy response, with easily accessible data, e.g., radiographics, laboratory and clinical information. Prior arts focus on modeling single data modality, or ignore the temporal changes. Importantly, the clinical time series is asynchronous in practice, i.e., recorded with irregular intervals. In this study, we formalize the prognosis modeling as a multi-modal asynchronous time series classification task, and propose a MIA-Prognosis framework with Measurement, Intervention and Assessment (MIA) information to predict therapy response, where a Simple Temporal Attention (SimTA) module is developed to process the asynchronous time series. Experiments on synthetic dataset validate the superiory of SimTA over standard RNN-based approaches. Furthermore, we experiment the proposed method on an in-house, retrospective dataset of real-world non-small cell lung cancer patients under anti-PD-1 immunotherapy. The proposed method achieves promising performance on predicting the immunotherapy response. Notably, our predictive model could further stratify low-risk and high-risk patients in terms of long-term survival.Comment: MICCAI 2020 (Early Accepted; Student Travel Award

Probabilistic Radiomics: Ambiguous Diagnosis with Controllable Shape Analysis

Radiomics analysis has achieved great success in recent years. However, conventional Radiomics analysis suffers from insufficiently expressive hand-crafted features. Recently, emerging deep learning techniques, e.g., convolutional neural networks (CNNs), dominate recent research in Computer-Aided Diagnosis (CADx). Unfortunately, as black-box predictors, we argue that CNNs are "diagnosing" voxels (or pixels), rather than lesions; in other words, visual saliency from a trained CNN is not necessarily concentrated on the lesions. On the other hand, classification in clinical applications suffers from inherent ambiguities: radiologists may produce diverse diagnosis on challenging cases. To this end, we propose a controllable and explainable {\em Probabilistic Radiomics} framework, by combining the Radiomics analysis and probabilistic deep learning. In our framework, 3D CNN feature is extracted upon lesion region only, then encoded into lesion representation, by a controllable Non-local Shape Analysis Module (NSAM) based on self-attention. Inspired from variational auto-encoders (VAEs), an Ambiguity PriorNet is used to approximate the ambiguity distribution over human experts. The final diagnosis is obtained by combining the ambiguity prior sample and lesion representation, and the whole network named $DenseSharp^{+}$ is end-to-end trainable. We apply the proposed method on lung nodule diagnosis on LIDC-IDRI database to validate its effectiveness.Comment: MICCAI 2019 (early accept), with supplementary material

Iterative SE(3)-Transformers

When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. Recent work in this area has successfully made use of an SE(3)-equivariant model, applying an iterative SE(3)-equivariant attention mechanism. Motivated by this application, we implement an iterative version of the SE(3)-Transformer, an SE(3)-equivariant attention-based model for graph data. We address the additional complications which arise when applying the SE(3)-Transformer in an iterative fashion, compare the iterative and single-pass versions on a toy problem, and consider why an iterative model may be beneficial in some problem settings. We make the code for our implementation available to the community

Neighbourhood-Insensitive Point Cloud Normal Estimation Network

We introduce a novel self-attention-based normal estimation network that is able to focus softly on relevant points and adjust the softness by learning a temperature parameter, making it able to work naturally and effectively within a large neighbourhood range. As a result, our model outperforms all existing normal estimation algorithms by a large margin, achieving 94.1% accuracy in comparison with the previous state of the art of 91.2%, with a 25x smaller model and 12x faster inference time. We also use point-to-plane Iterative Closest Point (ICP) as an application case to show that our normal estimations lead to faster convergence than normal estimations from other methods, without manually fine-tuning neighbourhood range parameters. Code available at https://code.active.vision.Comment: Accepted in BMVC 2020 as oral presentation. Code available at https://code.active.vision and project page at http://ninormal.active.visio