Hypoxemia, a medical condition that occurs when the blood is not carrying enough oxygen to adequately supply the tissues, is a leading indicator for dangerous complications of respiratory diseases like asthma, COPD, and COVID-19. While purpose-built pulse oximeters can provide accurate blood-oxygen saturation (SpO$_2$) readings that allow for diagnosis of hypoxemia, enabling this capability in unmodified smartphone cameras via a software update could give more people access to important information about their health, as well as improve physicians' ability to remotely diagnose and treat respiratory conditions. In this work, we take a step towards this goal by performing the first clinical development validation on a smartphone-based SpO$_2$ sensing system using a varied fraction of inspired oxygen (FiO$_2$) protocol, creating a clinically relevant validation dataset for solely smartphone-based methods on a wide range of SpO$_2$ values (70%-100%) for the first time. This contrasts with previous studies, which evaluated performance on a far smaller range (85%-100%). We build a deep learning model using this data to demonstrate accurate reporting of SpO$_2$ level with an overall MAE=5.00% SpO$_2$ and identifying positive cases of low SpO$_2$<90% with 81% sensitivity and 79% specificity. We ground our analysis with a summary of recent literature in smartphone-based SpO2 monitoring, and we provide the data from the FiO$_2$ study in open-source format, so that others may build on this work.
Connecting multiple machine learning models into a pipeline is effective for handling complex problems. By breaking down the problem into steps, each tackled by a specific component model of the pipeline, the overall solution can be made accurate and explainable. This paper describes an enhancement of object detection based on this multi-step concept, where a post-processing step called the calibration model is introduced. The calibration model consists of a convolutional neural network, and utilizes rich contextual information based on the domain knowledge of the input. Improvements of object detection performance by 0.8-1.9 in average precision metric over existing object detectors have been observed using the new model.
Automatic and accurate lung nodule detection from 3D Computed Tomography scans plays a vital role in efficient lung cancer screening. Despite the state-of-the-art performance obtained by recent anchor-based detectors using Convolutional Neural Networks, they require predetermined anchor parameters such as the size, number, and aspect ratio of anchors, and have limited robustness when dealing with lung nodules with a massive variety of sizes. We propose a 3D sphere representation-based center-points matching detection network (SCPM-Net) that is anchor-free and automatically predicts the position, radius, and offset of nodules without the manual design of nodule/anchor parameters. The SCPM-Net consists of two novel pillars: sphere representation and center points matching. To mimic the nodule annotation in clinical practice, we replace the conventional bounding box with the newly proposed bounding sphere. A compatible sphere-based intersection over-union loss function is introduced to train the lung nodule detection network stably and efficiently.We empower the network anchor-free by designing a positive center-points selection and matching (CPM) process, which naturally discards pre-determined anchor boxes. An online hard example mining and re-focal loss subsequently enable the CPM process more robust, resulting in more accurate point assignment and the mitigation of class imbalance. In addition, to better capture spatial information and 3D context for the detection, we propose to fuse multi-level spatial coordinate maps with the feature extractor and combine them with 3D squeeze-and-excitation attention modules. Experimental results on the LUNA16 dataset showed that our proposed SCPM-Net framework achieves superior performance compared with existing used anchor-based and anchor-free methods for lung nodule detection.
Tables are widely used with various structures to organize and present data. Recent attempts on table understanding mainly focus on relational tables, yet overlook to other common table structures. In this paper, we propose TUTA, a unified pre-training architecture for understanding generally structured tables. Since understanding a table needs to leverage both spatial, hierarchical, and semantic information, we adapt the self-attention strategy with several key structure-aware mechanisms. First, we propose a novel tree-based structure called a bi-dimensional coordinate tree, to describe both the spatial and hierarchical information in tables. Upon this, we extend the pre-training architecture with two core mechanisms, namely the tree-based attention and tree-based position embedding. Moreover, to capture table information in a progressive manner, we devise three pre-training objectives to enable representations at the token, cell, and table levels. TUTA pre-trains on a wide range of unlabeled tables and fine-tunes on a critical task in the field of table structure understanding, i.e. cell type classification. Experiment results show that TUTA is highly effective, achieving state-of-the-art on four well-annotated cell type classification datasets.
The brain tumor segmentation task aims to classify tissue into the whole tumor (WT), tumor core (TC), and enhancing tumor (ET) classes using multimodel MRI images. Quantitative analysis of brain tumors is critical for clinical decision making. While manual segmentation is tedious, time-consuming, and subjective, this task is at the same time very challenging to automatic segmentation methods. Thanks to the powerful learning ability, convolutional neural networks (CNNs), mainly fully convolutional networks, have shown promising brain tumor segmentation. This paper further boosts the performance of brain tumor segmentation by proposing hyperdense inception 3D UNet (HI-Net), which captures multi-scale information by stacking factorization of 3D weighted convolutional layers in the residual inception block. We use hyper dense connections among factorized convolutional layers to extract more contexual information, with the help of features reusability. We use a dice loss function to cope with class imbalances. We validate the proposed architecture on the multi-modal brain tumor segmentation challenges (BRATS) 2020 testing dataset. Preliminary results on the BRATS 2020 testing set show that achieved by our proposed approach, the dice (DSC) scores of ET, WT, and TC are 0.79457, 0.87494, and 0.83712, respectively.
We consider the problem of sequential graph topology change-point detection from graph signals. We assume that signals on the nodes of the graph are regularized by the underlying graph structure via a graph filtering model, which we then leverage to distill the graph topology change-point detection problem to a subspace detection problem. We demonstrate how prior information on the spectral signature of the post-change graph can be incorporated to implicitly denoise the observed sequential data, thus leading to a natural CUSUM-based algorithm for change-point detection. Numerical experiments illustrate the performance of our proposed approach, particularly underscoring the benefits of (potentially noisy) prior information.
Traditional learning approaches for classification implicitly assume that each mistake has the same cost. In many real-world problems though, the utility of a decision depends on the underlying context $x$ and decision $y$. However, directly incorporating these utilities into the learning objective is often infeasible since these can be quite complex and difficult for humans to specify. We formally study this as agnostic learning with unknown utilities: given a dataset $S = \{x_1, \ldots, x_n\}$ where each data point $x_i \sim \mathcal{D}$, the objective of the learner is to output a function $f$ in some class of decision functions $\mathcal{F}$ with small excess risk. This risk measures the performance of the output predictor $f$ with respect to the best predictor in the class $\mathcal{F}$ on the unknown underlying utility $u^*$. This utility $u^*$ is not assumed to have any specific structure. This raises an interesting question whether learning is even possible in our setup, given that obtaining a generalizable estimate of utility $u^*$ might not be possible from finitely many samples. Surprisingly, we show that estimating the utilities of only the sampled points~$S$ suffices to learn a decision function which generalizes well. We study mechanisms for eliciting information which allow a learner to estimate the utilities $u^*$ on the set $S$. We introduce a family of elicitation mechanisms by generalizing comparisons, called the $k$-comparison oracle, which enables the learner to ask for comparisons across $k$ different inputs $x$ at once. We show that the excess risk in our agnostic learning framework decreases at a rate of $O\left(\frac{1}{k} \right)$. This result brings out an interesting accuracy-elicitation trade-off -- as the order $k$ of the oracle increases, the comparative queries become harder to elicit from humans but allow for more accurate learning.
This paper proposes a novel Ontology-based and user-focused Automatic Text Summarization (OATS) system, in the setting where the goal is to automatically generate text summarization from unstructured text by extracting sentences containing the information that aligns to the user's focus. OATS consists of two modules: ontology-based topic identification and user-focused text summarization; it first utilizes an ontology-based approach to identify relevant documents to user's interest, and then takes advantage of the answers extracted from a question answering model using questions specified from users for the generation of text summarization. To support the fight against the COVID-19 pandemic, we used COVID-19 risk factors as an example to demonstrate the proposed OATS system with the aim of helping the medical community accurately identify relevant scientific literature and efficiently review the information that addresses risk factors related to COVID-19.
Robust object tracking requires knowledge of tracked objects' appearance, motion and their evolution over time. Although motion provides distinctive and complementary information especially for fast moving objects, most of the recent tracking architectures primarily focus on the objects' appearance information. In this paper, we propose a two-stream deep neural network tracker that uses both spatial and temporal features. Our architecture is developed over ATOM tracker and contains two backbones: (i) 2D-CNN network to capture appearance features and (ii) 3D-CNN network to capture motion features. The features returned by the two networks are then fused with attention based Feature Aggregation Module (FAM). Since the whole architecture is unified, it can be trained end-to-end. The experimental results show that the proposed tracker TRAT (TRacking by ATtention) achieves state-of-the-art performance on most of the benchmarks and it significantly outperforms the baseline ATOM tracker.
Due to the strong correlation between visual attention and perceptual quality, many methods attempt to use human saliency information for image quality assessment. Although this mechanism can get good performance, the networks require human saliency labels, which is not easily accessible for omnidirectional images (ODI). To alleviate this issue, we propose a spatial attention-based perceptual quality prediction network for non-reference quality assessment on ODIs (SAP-net). To drive our SAP-net, we establish a large-scale IQA dataset of ODIs (IQA-ODI), which is composed of subjective scores of 200 subjects on 1,080 ODIs. In IQA-ODI, there are 120 high quality ODIs as reference, and 960 ODIs with impairments in both JPEG compression and map projection. Without any human saliency labels, our network can adaptively estimate human perceptual quality on impaired ODIs through a self-attention manner, which significantly promotes the prediction performance of quality scores. Moreover, our method greatly reduces the computational complexity in quality assessment task on ODIs. Extensive experiments validate that our network outperforms 9 state-of-the-art methods for quality assessment on ODIs. The dataset and code have been available on \url{ https://github.com/yanglixiaoshen/SAP-Net}.