IVJun 13, 2022Code
RPLHR-CT Dataset and Transformer Baseline for Volumetric Super-Resolution from CT ScansPengxin Yu, Haoyue Zhang, Han Kang et al.
In clinical practice, anisotropic volumetric medical images with low through-plane resolution are commonly used due to short acquisition time and lower storage cost. Nevertheless, the coarse resolution may lead to difficulties in medical diagnosis by either physicians or computer-aided diagnosis algorithms. Deep learning-based volumetric super-resolution (SR) methods are feasible ways to improve resolution, with convolutional neural networks (CNN) at their core. Despite recent progress, these methods are limited by inherent properties of convolution operators, which ignore content relevance and cannot effectively model long-range dependencies. In addition, most of the existing methods use pseudo-paired volumes for training and evaluation, where pseudo low-resolution (LR) volumes are generated by a simple degradation of their high-resolution (HR) counterparts. However, the domain gap between pseudo- and real-LR volumes leads to the poor performance of these methods in practice. In this paper, we build the first public real-paired dataset RPLHR-CT as a benchmark for volumetric SR, and provide baseline results by re-implementing four state-of-the-art CNN-based methods. Considering the inherent shortcoming of CNN, we also propose a transformer volumetric super-resolution network (TVSRN) based on attention mechanisms, dispensing with convolutions entirely. This is the first research to use a pure transformer for CT volumetric SR. The experimental results show that TVSRN significantly outperforms all baselines on both PSNR and SSIM. Moreover, the TVSRN method achieves a better trade-off between the image quality, the number of parameters, and the running time. Data and code are available at https://github.com/smilenaxx/RPLHR-CT.
CVJun 13, 2022Code
Transformer Lesion TrackerWen Tang, Han Kang, Haoyue Zhang et al.
Evaluating lesion progression and treatment response via longitudinal lesion tracking plays a critical role in clinical practice. Automated approaches for this task are motivated by prohibitive labor costs and time consumption when lesion matching is done manually. Previous methods typically lack the integration of local and global information. In this work, we propose a transformer-based approach, termed Transformer Lesion Tracker (TLT). Specifically, we design a Cross Attention-based Transformer (CAT) to capture and combine both global and local information to enhance feature extraction. We also develop a Registration-based Anatomical Attention Module (RAAM) to introduce anatomical information to CAT so that it can focus on useful feature knowledge. A Sparse Selection Strategy (SSS) is presented for selecting features and reducing memory footprint in Transformer training. In addition, we use a global regression to further improve model performance. We conduct experiments on a public dataset to show the superiority of our method and find that our model performance has improved the average Euclidean center error by at least 14.3% (6mm vs. 7mm) compared with the state-of-the-art (SOTA). Code is available at https://github.com/TangWen920812/TLT.
IVMar 10, 2023
Multi-site, Multi-domain Airway Tree Modeling (ATM'22): A Public Benchmark for Pulmonary Airway SegmentationMinghui Zhang, Yangqian Wu, Hanxiao Zhang et al. · harvard
Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and clinical drive for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage.
LGSep 16, 2022Code
A Comprehensive Benchmark for COVID-19 Predictive Modeling Using Electronic Health Records in Intensive CareJunyi Gao, Yinghao Zhu, Wenqing Wang et al.
The COVID-19 pandemic has posed a heavy burden to the healthcare system worldwide and caused huge social disruption and economic loss. Many deep learning models have been proposed to conduct clinical predictive tasks such as mortality prediction for COVID-19 patients in intensive care units using Electronic Health Record (EHR) data. Despite their initial success in certain clinical applications, there is currently a lack of benchmarking results to achieve a fair comparison so that we can select the optimal model for clinical use. Furthermore, there is a discrepancy between the formulation of traditional prediction tasks and real-world clinical practice in intensive care. To fill these gaps, we propose two clinical prediction tasks, Outcome-specific length-of-stay prediction and Early mortality prediction for COVID-19 patients in intensive care units. The two tasks are adapted from the naive length-of-stay and mortality prediction tasks to accommodate the clinical practice for COVID-19 patients. We propose fair, detailed, open-source data-preprocessing pipelines and evaluate 17 state-of-the-art predictive models on two tasks, including 5 machine learning models, 6 basic deep learning models and 6 deep learning predictive models specifically designed for EHR data. We provide benchmarking results using data from two real-world COVID-19 EHR datasets. One dataset is publicly available without needing any inquiry and another dataset can be accessed on request. We provide fair, reproducible benchmarking results for two tasks. We deploy all experiment results and models on an online platform. We also allow clinicians and researchers to upload their data to the platform and get quick prediction results using our trained models. We hope our efforts can further facilitate deep learning and machine learning research for COVID-19 predictive modeling.
IVJun 13, 2022Code
MMMNA-Net for Overall Survival Time Prediction of Brain Tumor PatientsWen Tang, Haoyue Zhang, Pengxin Yu et al.
Overall survival (OS) time is one of the most important evaluation indices for gliomas situations. Multimodal Magnetic Resonance Imaging (MRI) scans play an important role in the study of glioma prognosis OS time. Several deep learning-based methods are proposed for the OS time prediction on multi-modal MRI problems. However, these methods usually fuse multi-modal information at the beginning or at the end of the deep learning networks and lack the fusion of features from different scales. In addition, the fusion at the end of networks always adapts global with global (eg. fully connected after concatenation of global average pooling output) or local with local (eg. bilinear pooling), which loses the information of local with global. In this paper, we propose a novel method for multi-modal OS time prediction of brain tumor patients, which contains an improved nonlocal features fusion module introduced on different scales. Our method obtains a relative 8.76% improvement over the current state-of-art method (0.6989 vs. 0.6426 on accuracy). Extensive testing demonstrates that our method could adapt to situations with missing modalities. The code is available at https://github.com/TangWen920812/mmmna-net.
LGOct 11, 2023Code
Domain-invariant Clinical Representation Learning by Bridging Data Distribution Shift across EMR DatasetsZhongji Zhang, Yuhang Wang, Yinghao Zhu et al.
Emerging diseases present challenges in symptom recognition and timely clinical intervention due to limited available information. An effective prognostic model could assist physicians in making accurate diagnoses and designing personalized treatment plans to prevent adverse outcomes. However, in the early stages of disease emergence, several factors hamper model development: limited data collection, insufficient clinical experience, and privacy and ethical concerns restrict data availability and complicate accurate label assignment. Furthermore, Electronic Medical Record (EMR) data from different diseases or sources often exhibit significant cross-dataset feature misalignment, severely impacting the effectiveness of deep learning models. We present a domain-invariant representation learning method that constructs a transition model between source and target datasets. By constraining the distribution shift of features generated across different domains, we capture domain-invariant features specifically relevant to downstream tasks, developing a unified domain-invariant encoder that achieves better feature representation across various task domains. Experimental results across multiple target tasks demonstrate that our proposed model surpasses competing baseline methods and achieves faster training convergence, particularly when working with limited data. Extensive experiments validate our method's effectiveness in providing more accurate predictions for emerging pandemics and other diseases. Code is publicly available at https://github.com/wang1yuhang/domain_invariant_network.
LGJun 7, 2023
M$^3$Fair: Mitigating Bias in Healthcare Data through Multi-Level and Multi-Sensitive-Attribute Reweighting MethodYinghao Zhu, Jingkun An, Enshen Zhou et al. · tencent-ai
In the data-driven artificial intelligence paradigm, models heavily rely on large amounts of training data. However, factors like sampling distribution imbalance can lead to issues of bias and unfairness in healthcare data. Sensitive attributes, such as race, gender, age, and medical condition, are characteristics of individuals that are commonly associated with discrimination or bias. In healthcare AI, these attributes can play a significant role in determining the quality of care that individuals receive. For example, minority groups often receive fewer procedures and poorer-quality medical care than white individuals in US. Therefore, detecting and mitigating bias in data is crucial to enhancing health equity. Bias mitigation methods include pre-processing, in-processing, and post-processing. Among them, Reweighting (RW) is a widely used pre-processing method that performs well in balancing machine learning performance and fairness performance. RW adjusts the weights for samples within each (group, label) combination, where these weights are utilized in loss functions. However, RW is limited to considering only a single sensitive attribute when mitigating bias and assumes that each sensitive attribute is equally important. This may result in potential inaccuracies when addressing intersectional bias. To address these limitations, we propose M3Fair, a multi-level and multi-sensitive-attribute reweighting method by extending the RW method to multiple sensitive attributes at multiple levels. Our experiments on real-world datasets show that the approach is effective, straightforward, and generalizable in addressing the healthcare fairness issues.
LGJan 17, 2023
Mortality Prediction with Adaptive Feature Importance Recalibration for Peritoneal Dialysis Patients: a deep-learning-based study on a real-world longitudinal follow-up datasetLiantao Ma, Chaohe Zhang, Junyi Gao et al.
Objective: Peritoneal Dialysis (PD) is one of the most widely used life-supporting therapies for patients with End-Stage Renal Disease (ESRD). Predicting mortality risk and identifying modifiable risk factors based on the Electronic Medical Records (EMR) collected along with the follow-up visits are of great importance for personalized medicine and early intervention. Here, our objective is to develop a deep learning model for a real-time, individualized, and interpretable mortality prediction model - AICare. Method and Materials: Our proposed model consists of a multi-channel feature extraction module and an adaptive feature importance recalibration module. AICare explicitly identifies the key features that strongly indicate the outcome prediction for each patient to build the health status embedding individually. This study has collected 13,091 clinical follow-up visits and demographic data of 656 PD patients. To verify the application universality, this study has also collected 4,789 visits of 1,363 hemodialysis dialysis (HD) as an additional experiment dataset to test the prediction performance, which will be discussed in the Appendix. Results: 1) Experiment results show that AICare achieves 81.6%/74.3% AUROC and 47.2%/32.5% AUPRC for the 1-year mortality prediction task on PD/HD dataset respectively, which outperforms the state-of-the-art comparative deep learning models. 2) This study first provides a comprehensive elucidation of the relationship between the causes of mortality in patients with PD and clinical features based on an end-to-end deep learning model. 3) This study first reveals the pattern of variation in the importance of each feature in the mortality prediction based on built-in interpretability. 4) We develop a practical AI-Doctor interaction system to visualize the trajectory of patients' health status and risk indicators.
LGApr 21, 2022
MedFACT: Modeling Medical Feature Correlations in Patient Health Representation Learning via Feature ClusteringXinyu Ma, Xu Chu, Yasha Wang et al.
In healthcare prediction tasks, it is essential to exploit the correlations between medical features and learn better patient health representations. Existing methods try to estimate feature correlations only from data, or increase the quality of estimation by introducing task-specific medical knowledge. However, such methods either are difficult to estimate the feature correlations due to insufficient training samples, or cannot be generalized to other tasks due to reliance on specific knowledge. There are medical research revealing that not all the medical features are strongly correlated. Thus, to address the issues, we expect to group up strongly correlated features and learn feature correlations in a group-wise manner to reduce the learning complexity without losing generality. In this paper, we propose a general patient health representation learning framework MedFACT. We estimate correlations via measuring similarity between temporal patterns of medical features with kernel methods, and cluster features with strong correlations into groups. The feature group is further formulated as a correlation graph, and we employ graph convolutional networks to conduct group-wise feature interactions for better representation learning. Experiments on two real-world datasets demonstrate the superiority of MedFACT. The discovered medical findings are also confirmed by literature, providing valuable medical insights and explanations.
LGDec 18, 2023Code
Predict and Interpret Health Risk using EHR through Typical PatientsZhihao Yu, Chaohe Zhang, Yasha Wang et al.
Predicting health risks from electronic health records (EHR) is a topic of recent interest. Deep learning models have achieved success by modeling temporal and feature interaction. However, these methods learn insufficient representations and lead to poor performance when it comes to patients with few visits or sparse records. Inspired by the fact that doctors may compare the patient with typical patients and make decisions from similar cases, we propose a Progressive Prototypical Network (PPN) to select typical patients as prototypes and utilize their information to enhance the representation of the given patient. In particular, a progressive prototype memory and two prototype separation losses are proposed to update prototypes. Besides, a novel integration is introduced for better fusing information from patients and prototypes. Experiments on three real-world datasets demonstrate that our model brings improvement on all metrics. To make our results better understood by physicians, we developed an application at http://ppn.ai-care.top. Our code is released at https://github.com/yzhHoward/PPN.
IVDec 21, 2023
Hunting imaging biomarkers in pulmonary fibrosis: Benchmarks of the AIIB23 challengeYang Nan, Xiaodan Xing, Shiyi Wang et al.
Airway-related quantitative imaging biomarkers are crucial for examination, diagnosis, and prognosis in pulmonary diseases. However, the manual delineation of airway trees remains prohibitively time-consuming. While significant efforts have been made towards enhancing airway modelling, current public-available datasets concentrate on lung diseases with moderate morphological variations. The intricate honeycombing patterns present in the lung tissues of fibrotic lung disease patients exacerbate the challenges, often leading to various prediction errors. To address this issue, the 'Airway-Informed Quantitative CT Imaging Biomarker for Fibrotic Lung Disease 2023' (AIIB23) competition was organized in conjunction with the official 2023 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). The airway structures were meticulously annotated by three experienced radiologists. Competitors were encouraged to develop automatic airway segmentation models with high robustness and generalization abilities, followed by exploring the most correlated QIB of mortality prediction. A training set of 120 high-resolution computerised tomography (HRCT) scans were publicly released with expert annotations and mortality status. The online validation set incorporated 52 HRCT scans from patients with fibrotic lung disease and the offline test set included 140 cases from fibrosis and COVID-19 patients. The results have shown that the capacity of extracting airway trees from patients with fibrotic lung disease could be enhanced by introducing voxel-wise weighted general union loss and continuity loss. In addition to the competitive image biomarkers for prognosis, a strong airway-derived biomarker (Hazard ratio>1.5, p<0.0001) was revealed for survival prognostication compared with existing clinical measurements, clinician assessment and AI-based biomarkers.
AIFeb 19, 2025
Proving Olympiad Inequalities by Synergizing LLMs and Symbolic ReasoningZenan Li, Zhaoyu Li, Wen Tang et al. · utoronto
Large language models (LLMs) can prove mathematical theorems formally by generating proof steps (\textit{a.k.a.} tactics) within a proof system. However, the space of possible tactics is vast and complex, while the available training data for formal proofs is limited, posing a significant challenge to LLM-based tactic generation. To address this, we introduce a neuro-symbolic tactic generator that synergizes the mathematical intuition learned by LLMs with domain-specific insights encoded by symbolic methods. The key aspect of this integration is identifying which parts of mathematical reasoning are best suited to LLMs and which to symbolic methods. While the high-level idea of neuro-symbolic integration is broadly applicable to various mathematical problems, in this paper, we focus specifically on Olympiad inequalities (Figure~1). We analyze how humans solve these problems and distill the techniques into two types of tactics: (1) scaling, handled by symbolic methods, and (2) rewriting, handled by LLMs. In addition, we combine symbolic tools with LLMs to prune and rank the proof goals for efficient proof search. We evaluate our framework on 161 challenging inequalities from multiple mathematics competitions, achieving state-of-the-art performance and significantly outperforming existing LLM and symbolic approaches without requiring additional training data.
CLOct 31, 2024
The Potential of LLMs in Medical Education: Generating Questions and Answers for Qualification ExamsYunqi Zhu, Wen Tang, Huayu Yang et al.
In this work, we leverage LLMs to produce medical qualification exam questions and the corresponding answers through few-shot prompts, investigating in-depth how LLMs meet the requirements in terms of coherence, evidence of statement, factual consistency, and professionalism etc. Utilizing a multicenter bidirectional anonymized database with respect to comorbid chronic diseases, named Elderly Comorbidity Medical Database (CECMed), we tasked LLMs with generating open-ended questions and answers based on a subset of sampled admission reports. For CECMed, the retrospective cohort includes patients enrolled from January 2010 to January 2022 while the prospective cohort from January 2023 to November 2023, with participants sourced from selected tertiary and community hospitals across the southern, northern, and central regions of China. A total of 8 widely used LLMs were used, including ERNIE 4, ChatGLM 4, Doubao, Hunyuan, Spark 4, Qwen, Conventional medical education requires sophisticated clinicians to formulate questions and answers based on prototypes from EHRs, which is heuristic and time-consuming. We found that mainstream LLMs could generate questions and answers with real-world EHRs at levels close to clinicians. Although current LLMs performed dissatisfactory in some aspects, medical students, interns and residents could reasonably make use of LLMs to facilitate understanding.
CLOct 11, 2025
MedAgentAudit: Diagnosing and Quantifying Collaborative Failure Modes in Medical Multi-Agent SystemsLei Gu, Yinghao Zhu, Haoran Sang et al.
While large language model (LLM)-based multi-agent systems show promise in simulating medical consultations, their evaluation is often confined to final-answer accuracy. This practice treats their internal collaborative processes as opaque "black boxes" and overlooks a critical question: is a diagnostic conclusion reached through a sound and verifiable reasoning pathway? The inscrutable nature of these systems poses a significant risk in high-stakes medical applications, potentially leading to flawed or untrustworthy conclusions. To address this, we conduct a large-scale empirical study of 3,600 cases from six medical datasets and six representative multi-agent frameworks. Through a rigorous, mixed-methods approach combining qualitative analysis with quantitative auditing, we develop a comprehensive taxonomy of collaborative failure modes. Our quantitative audit reveals four dominant failure patterns: flawed consensus driven by shared model deficiencies, suppression of correct minority opinions, ineffective discussion dynamics, and critical information loss during synthesis. This study demonstrates that high accuracy alone is an insufficient measure of clinical or public trust. It highlights the urgent need for transparent and auditable reasoning processes, a cornerstone for the responsible development and deployment of medical AI.
CVJul 13, 2021
eProduct: A Million-Scale Visual Search Benchmark to Address Product Recognition ChallengesJiangbo Yuan, An-Ti Chiang, Wen Tang et al.
Large-scale product recognition is one of the major applications of computer vision and machine learning in the e-commerce domain. Since the number of products is typically much larger than the number of categories of products, image-based product recognition is often cast as a visual search rather than a classification problem. It is also one of the instances of super fine-grained recognition, where there are many products with slight or subtle visual differences. It has always been a challenge to create a benchmark dataset for training and evaluation on various visual search solutions in a real-world setting. This motivated creation of eProduct, a dataset consisting of 2.5 million product images towards accelerating development in the areas of self-supervised learning, weakly-supervised learning, and multimodal learning, for fine-grained recognition. We present eProduct as a training set and an evaluation set, where the training set contains 1.3M+ listing images with titles and hierarchical category labels, for model development, and the evaluation set includes 10,000 query and 1.1 million index images for visual search evaluation. We will present eProduct's construction steps, provide analysis about its diversity and cover the performance of baseline models trained on it.
AIJun 22, 2021
De Re UpdatesMichael Cohen, Wen Tang, Yanjing Wang
In this paper, we propose a lightweight yet powerful dynamic epistemic logic that captures not only the distinction between de dicto and de re knowledge but also the distinction between de dicto and de re updates. The logic is based on the dynamified version of an epistemic language extended with the assignment operator borrowed from dynamic logic, following the work of Wang and Seligman (Proc. AiML 2018). We obtain complete axiomatizations for the counterparts of public announcement logic and event-model-based DEL based on new reduction axioms taking care of the interactions between dynamics and assignments.
LGApr 21, 2021
Deep Transform and Metric Learning NetworksWen Tang, Emilie Chouzenoux, Jean-Christophe Pesquet et al.
Based on its great successes in inference and denosing tasks, Dictionary Learning (DL) and its related sparse optimization formulations have garnered a lot of research interest. While most solutions have focused on single layer dictionaries, the recently improved Deep DL methods have also fallen short on a number of issues. We hence propose a novel Deep DL approach where each DL layer can be formulated and solved as a combination of one linear layer and a Recurrent Neural Network, where the RNN is flexibly regraded as a layer-associated learned metric. Our proposed work unveils new insights between the Neural Networks and Deep DL, and provides a novel, efficient and competitive approach to jointly learn the deep transforms and metrics. Extensive experiments are carried out to demonstrate that the proposed method can not only outperform existing Deep DL, but also state-of-the-art generic Convolutional Neural Networks.
LGJul 17, 2020
CovidCare: Transferring Knowledge from Existing EMR to Emerging Epidemic for Interpretable PrognosisLiantao Ma, Xinyu Ma, Junyi Gao et al.
Due to the characteristics of COVID-19, the epidemic develops rapidly and overwhelms health service systems worldwide. Many patients suffer from systemic life-threatening problems and need to be carefully monitored in ICUs. Thus the intelligent prognosis is in an urgent need to assist physicians to take an early intervention, prevent the adverse outcome, and optimize the medical resource allocation. However, in the early stage of the epidemic outbreak, the data available for analysis is limited due to the lack of effective diagnostic mechanisms, rarity of the cases, and privacy concerns. In this paper, we propose a deep-learning-based approach, CovidCare, which leverages the existing electronic medical records to enhance the prognosis for inpatients with emerging infectious diseases. It learns to embed the COVID-19-related medical features based on massive existing EMR data via transfer learning. The transferred parameters are further trained to imitate the teacher model's representation behavior based on knowledge distillation, which embeds the health status more comprehensively in the source dataset. We conduct the length of stay prediction experiments for patients on a real-world COVID-19 dataset. The experiment results indicate that our proposed model consistently outperforms the comparative baseline methods. CovidCare also reveals that, 1) hs-cTnI, hs-CRP and Platelet Counts are the most fatal biomarkers, whose abnormal values usually indicate emergency adverse outcome. 2) Normal values of gamma-GT, AP and eGFR indicate the overall improvement of health. The medical findings extracted by CovidCare are empirically confirmed by human experts and medical literatures.
LGFeb 18, 2020
Deep Transform and Metric Learning Network: Wedding Deep Dictionary Learning and Neural NetworksWen Tang, Emilie Chouzenoux, Jean-Christophe Pesquet et al.
On account of its many successes in inference tasks and denoising applications, Dictionary Learning (DL) and its related sparse optimization problems have garnered a lot of research interest. While most solutions have focused on single layer dictionaries, the improved recently proposed Deep DL (DDL) methods have also fallen short on a number of issues. We propose herein, a novel DDL approach where each DL layer can be formulated as a combination of one linear layer and a Recurrent Neural Network (RNN). The RNN is shown to flexibly account for the layer-associated and learned metric. Our proposed work unveils new insights into Neural Networks and DDL and provides a new, efficient and competitive approach to jointly learn a deep transform and a metric for inference applications. Extensive experiments are carried out to demonstrate that the proposed method can not only outperform existing DDL but also state-of-the-art generic CNNs.
LGJan 24, 2020
StageNet: Stage-Aware Neural Networks for Health Risk PredictionJunyi Gao, Cao Xiao, Yasha Wang et al.
Deep learning has demonstrated success in health risk prediction especially for patients with chronic and progressing conditions. Most existing works focus on learning disease Network (StageNet) model to extract disease stage information from patient data and integrate it into risk prediction. StageNet is enabled by (1) a stage-aware long short-term memory (LSTM) module that extracts health stage variations unsupervisedly; (2) a stage-adaptive convolutional module that incorporates stage-related progression patterns into risk prediction. We evaluate StageNet on two real-world datasets and show that StageNet outperforms state-of-the-art models in risk prediction task and patient subtyping task. Compared to the best baseline model, StageNet achieves up to 12% higher AUPRC for risk prediction task on two real-world patient datasets. StageNet also achieves over 58% higher Calinski-Harabasz score (a cluster quality metric) for a patient subtyping task.
LGNov 27, 2019
ConCare: Personalized Clinical Feature Embedding via Capturing the Healthcare ContextLiantao Ma, Chaohe Zhang, Yasha Wang et al.
Predicting the patient's clinical outcome from the historical electronic medical records (EMR) is a fundamental research problem in medical informatics. Most deep learning-based solutions for EMR analysis concentrate on learning the clinical visit embedding and exploring the relations between visits. Although those works have shown superior performances in healthcare prediction, they fail to explore the personal characteristics during the clinical visits thoroughly. Moreover, existing works usually assume that the more recent record weights more in the prediction, but this assumption is not suitable for all conditions. In this paper, we propose ConCare to handle the irregular EMR data and extract feature interrelationship to perform individualized healthcare prediction. Our solution can embed the feature sequences separately by modeling the time-aware distribution. ConCare further improves the multi-head self-attention via the cross-head decorrelation, so that the inter-dependencies among dynamic features and static baseline information can be effectively captured to form the personal health context. Experimental results on two real-world EMR datasets demonstrate the effectiveness of ConCare. The medical findings extracted by ConCare are also empirically confirmed by human experts and medical literature.
LGNov 27, 2019
AdaCare: Explainable Clinical Health Status Representation Learning via Scale-Adaptive Feature Extraction and RecalibrationLiantao Ma, Junyi Gao, Yasha Wang et al.
Deep learning-based health status representation learning and clinical prediction have raised much research interest in recent years. Existing models have shown superior performance, but there are still several major issues that have not been fully taken into consideration. First, the historical variation pattern of the biomarker in diverse time scales plays a vital role in indicating the health status, but it has not been explicitly extracted by existing works. Second, key factors that strongly indicate the health risk are different among patients. It is still challenging to adaptively make use of the features for patients in diverse conditions. Third, using prediction models as the black box will limit the reliability in clinical practice. However, none of the existing works can provide satisfying interpretability and meanwhile achieve high prediction performance. In this work, we develop a general health status representation learning model, named AdaCare. It can capture the long and short-term variations of biomarkers as clinical features to depict the health status in multiple time scales. It also models the correlation between clinical features to enhance the ones which strongly indicate the health status and thus can maintain a state-of-the-art performance in terms of prediction accuracy while providing qualitative interpretability. We conduct a health risk prediction experiment on two real-world datasets. Experiment results indicate that AdaCare outperforms state-of-the-art approaches and provides effective interpretability, which is verifiable by clinical experts.
CVJun 13, 2019
Joint Concept Matching based Learning for Zero-Shot RecognitionWen Tang, Ashkan Panahi, Hamid Krim
Zero-shot learning (ZSL) which aims to recognize unseen object classes by only training on seen object classes, has increasingly been of great interest in Machine Learning, and has registered with some successes. Most existing ZSL methods typically learn a projection map between the visual feature space and the semantic space and mainly suffer which is prone to a projection domain shift primarily due to a large domain gap between seen and unseen classes. In this paper, we propose a novel inductive ZSL model based on projecting both visual and semantic features into a common distinct latent space with class-specific knowledge, and on reconstructing both visual and semantic features by such a distinct common space to narrow the domain shift gap. We show that all these constraints on the latent space, class-specific knowledge, reconstruction of features and their combinations enhance the robustness against the projection domain shift problem, and improve the generalization ability to unseen object classes. Comprehensive experiments on four benchmark datasets demonstrate that our proposed method is superior to state-of-the-art algorithms.
CVMar 18, 2019
MUSEFood: Multi-sensor-based Food Volume Estimation on SmartphonesJunyi Gao, Weihao Tan, Liantao Ma et al.
Researches have shown that diet recording can help people increase awareness of food intake and improve nutrition management, and thereby maintain a healthier life. Recently, researchers have been working on smartphone-based diet recording methods and applications that help users accomplish two tasks: record what they eat and how much they eat. Although the former task has made great progress through adopting image recognition technology, it is still a challenge to estimate the volume of foods accurately and conveniently. In this paper, we propose a novel method, named MUSEFood, for food volume estimation. MUSEFood uses the camera to capture photos of the food, but unlike existing volume measurement methods, MUSEFood requires neither training images with volume information nor placing a reference object of known size while taking photos. In addition, considering the impact of different containers on the contour shape of foods, MUSEFood uses a multi-task learning framework to improve the accuracy of food segmentation, and uses a differential model applicable for various containers to further reduce the negative impact of container differences on volume estimation accuracy. Furthermore, MUSEFood uses the microphone and the speaker to accurately measure the vertical distance from the camera to the food in a noisy environment, thus scaling the size of food in the image to its actual size. The experiments on real foods indicate that MUSEFood outperforms state-of-the-art approaches, and highly improves the speed of food volume estimation.
LGMar 7, 2019
Analysis Dictionary Learning: An Efficient and Discriminative SolutionWen Tang, Ashkan Panahi, Hamid Krim et al.
Discriminative Dictionary Learning (DL) methods have been widely advocated for image classification problems. To further sharpen their discriminative capabilities, most state-of-the-art DL methods have additional constraints included in the learning stages. These various constraints, however, lead to additional computational complexity. We hence propose an efficient Discriminative Convolutional Analysis Dictionary Learning (DCADL) method, as a lower cost Discriminative DL framework, to both characterize the image structures and refine the interclass structure representations. The proposed DCADL jointly learns a convolutional analysis dictionary and a universal classifier, while greatly reducing the time complexity in both training and testing phases, and achieving a competitive accuracy, thus demonstrating great performance in many experiments with standard databases.
CVJul 13, 2018
Analysis Dictionary Learning based Classification: Structure for RobustnessWen Tang, Ashkan Panahi, Hamid Krim et al.
A discriminative structured analysis dictionary is proposed for the classification task. A structure of the union of subspaces (UoS) is integrated into the conventional analysis dictionary learning to enhance the capability of discrimination. A simple classifier is also simultaneously included into the formulated functional to ensure a more complete consistent classification. The solution of the algorithm is efficiently obtained by the linearized alternating direction method of multipliers. Moreover, a distributed structured analysis dictionary learning is also presented to address large scale datasets. It can group-(class-) independently train the structured analysis dictionaries by different machines/cores/threads, and therefore avoid a high computational cost. A consensus structured analysis dictionary and a global classifier are jointly learned in the distributed approach to safeguard the discriminative power and the efficiency of classification. Experiments demonstrate that our method achieves a comparable or better performance than the state-of-the-art algorithms in a variety of visual classification tasks. In addition, the training and testing computational complexity are also greatly reduced.
CVMay 2, 2018
Structured Analysis Dictionary Learning for Image ClassificationWen Tang, Ashkan Panahi, Hamid Krim et al.
We propose a computationally efficient and high-performance classification algorithm by incorporating class structural information in analysis dictionary learning. To achieve more consistent classification, we associate a class characteristic structure of independent subspaces and impose it on the classification error constrained analysis dictionary learning. Experiments demonstrate that our method achieves a comparable or better performance than the state-of-the-art algorithms in a variety of visual classification tasks. In addition, our method greatly reduces the training and testing computational complexity.
CVMar 14, 2018
Context-Aware Mixed Reality: A Framework for Ubiquitous InteractionLong Chen, Wen Tang, Nigel John et al.
Mixed Reality (MR) is a powerful interactive technology that yields new types of user experience. We present a semantic based interactive MR framework that exceeds the current geometry level approaches, a step change in generating high-level context-aware interactions. Our key insight is to build semantic understanding in MR that not only can greatly enhance user experience through object-specific behaviours, but also pave the way for solving complex interaction design challenges. The framework generates semantic properties of the real world environment through dense scene reconstruction and deep image understanding. We demonstrate our approach with a material-aware prototype system for generating context-aware physical interactions between the real and the virtual objects. Quantitative and qualitative evaluations are carried out and the results show that the framework delivers accurate and fast semantic information in interactive MR environment, providing effective semantic level interactions.
CVMar 14, 2018
Self-Supervised Monocular Image Depth Learning and Confidence EstimationLong Chen, Wen Tang, Nigel John
Convolutional Neural Networks (CNNs) need large amounts of data with ground truth annotation, which is a challenging problem that has limited the development and fast deployment of CNNs for many computer vision tasks. We propose a novel framework for depth estimation from monocular images with corresponding confidence in a self-supervised manner. A fully differential patch-based cost function is proposed by using the Zero-Mean Normalized Cross Correlation (ZNCC) that takes multi-scale patches as a matching strategy. This approach greatly increases the accuracy and robustness of the depth learning. In addition, the proposed patch-based cost function can provide a 0 to 1 confidence, which is then used to supervise the training of a parallel network for confidence map learning and estimation. Evaluation on KITTI dataset shows that our method outperforms the state-of-the-art results.
CVAug 3, 2017
Real-time Geometry-Aware Augmented Reality in Minimally Invasive SurgeryLong Chen, Wen Tang, Nigel W. John
The potential of Augmented Reality (AR) technology to assist minimally invasive surgeries (MIS) lies in its computational performance and accuracy in dealing with challenging MIS scenes. Even with the latest hardware and software technologies, achieving both real-time and accurate augmented information overlay in MIS is still a formidable task. In this paper, we present a novel real-time AR framework for MIS that achieves interactive geometric aware augmented reality in endoscopic surgery with stereo views. Our framework tracks the movement of the endoscopic camera and simultaneously reconstructs a dense geometric mesh of the MIS scene. The movement of the camera is predicted by minimising the re-projection error to achieve a fast tracking performance, while the 3D mesh is incrementally built by a dense zero mean normalised cross correlation stereo matching method to improve the accuracy of the surface reconstruction. Our proposed system does not require any prior template or pre-operative scan and can infer the geometric information intra-operatively in real-time. With the geometric information available, our proposed AR framework is able to interactively add annotations, localisation of tumours and vessels, and measurement labelling with greater precision and accuracy compared with the state of the art approaches.
CVAug 3, 2017
Recent Developments and Future Challenges in Medical Mixed RealityLong Chen, Thomas Day, Wen Tang et al.
Mixed Reality (MR) is of increasing interest within technology-driven modern medicine but is not yet used in everyday practice. This situation is changing rapidly, however, and this paper explores the emergence of MR technology and the importance of its utility within medical applications. A classification of medical MR has been obtained by applying an unbiased text mining method to a database of 1,403 relevant research papers published over the last two decades. The classification results reveal a taxonomy for the development of medical MR research during this period as well as suggesting future trends. We then use the classification to analyse the technology and applications developed in the last five years. Our objective is to aid researchers to focus on the areas where technology advancements in medical MR are most needed, as well as providing medical practitioners with a useful source of reference.
CVAug 3, 2017
Semantic Augmented Reality Environment with Material-Aware Physical InteractionsLong Chen, Karl Francis, Wen Tang
In Augmented Reality (AR) environment, realistic interactions between the virtual and real objects play a crucial role in user experience. Much of recent advances in AR has been largely focused on developing geometry-aware environment, but little has been done in dealing with interactions at the semantic level. High-level scene understanding and semantic descriptions in AR would allow effective design of complex applications and enhanced user experience. In this paper, we present a novel approach and a prototype system that enables the deeper understanding of semantic properties of the real world environment, so that realistic physical interactions between the real and the virtual objects can be generated. A material-aware AR environment has been created based on the deep material learning using a fully convolutional network (FCN). The state-of-the-art dense Simultaneous Localisation and Mapping (SLAM) has been used for the semantic mapping. Together with efficient accelerated 3D ray casting, natural and realistic physical interactions are generated for interactive AR games. Our approach has significant impact on the future development of advanced AR systems and applications.
CVMar 1, 2017
Augmented Reality for Depth Cues in Monocular Minimally Invasive SurgeryLong Chen, Wen Tang, Nigel W. John et al.
One of the major challenges in Minimally Invasive Surgery (MIS) such as laparoscopy is the lack of depth perception. In recent years, laparoscopic scene tracking and surface reconstruction has been a focus of investigation to provide rich additional information to aid the surgical process and compensate for the depth perception issue. However, robust 3D surface reconstruction and augmented reality with depth perception on the reconstructed scene are yet to be reported. This paper presents our work in this area. First, we adopt a state-of-the-art visual simultaneous localization and mapping (SLAM) framework - ORB-SLAM - and extend the algorithm for use in MIS scenes for reliable endoscopic camera tracking and salient point mapping. We then develop a robust global 3D surface reconstruction frame- work based on the sparse point clouds extracted from the SLAM framework. Our approach is to combine an outlier removal filter within a Moving Least Squares smoothing algorithm and then employ Poisson surface reconstruction to obtain smooth surfaces from the unstructured sparse point cloud. Our proposed method has been quantitatively evaluated compared with ground-truth camera trajectories and the organ model surface we used to render the synthetic simulation videos. In vivo laparoscopic videos used in the tests have demonstrated the robustness and accuracy of our proposed framework on both camera tracking and surface reconstruction, illustrating the potential of our algorithm for depth augmentation and depth-corrected augmented reality in MIS with monocular endoscopes.