Search

Automatic subphenotyping from electronic health records (EHRs)provides numerous opportunities to understand diseases with unique subgroups and enhance personalized medicine for patients. However, existing machine learning algorithms either focus on specific diseases for better interpretability or produce coarse-grained phenotype topics without considering nuanced disease patterns. In this study, we propose a guided topic model, MixEHR-Nest, to infer sub-phenotype topics from thousands of disease using multi-modal EHR data. Specifically, MixEHR-Nest detects multiple subtopics from each phenotype topic, whose prior is guided by the expert-curated phenotype concepts such as Phenotype Codes (PheCodes) or Clinical Classification Software (CCS) codes. We evaluated MixEHR-Nest on two EHR datasets: (1) the MIMIC-III dataset consisting of over 38 thousand patients from intensive care unit (ICU) from Beth Israel Deaconess Medical Center (BIDMC) in Boston, USA; (2) the healthcare administrative database PopHR, comprising 1.3 million patients from Montreal, Canada. Experimental results demonstrate that MixEHR-Nest can identify subphenotypes with distinct patterns within each phenotype, which are predictive for disease progression and severity. Consequently, MixEHR-Nest distinguishes between type 1 and type 2 diabetes by inferring subphenotypes using CCS codes, which do not differentiate these two subtype concepts. Additionally, MixEHR-Nest not only improved the prediction accuracy of short-term mortality of ICU patients and initial insulin treatment in diabetic patients but also revealed the contributions of subphenotypes. For longitudinal analysis, MixEHR-Nest identified subphenotypes of distinct age prevalence under the same phenotypes, such as asthma, leukemia, epilepsy, and depression. The MixEHR-Nest software is available at GitHub: https://github.com/li-lab-mcgill/MixEHR-Nest.

In many domains, such as healthcare, time-series data is often irregularly sampled with varying intervals between observations. This poses challenges for classical time-series models that require equally spaced data. To address this, we propose a novel time-series Transformer called Trajectory Generative Pre-trained Transformer (TrajGPT). TrajGPT employs a novel Selective Recurrent Attention (SRA) mechanism, which utilizes a data-dependent decay to adaptively filter out irrelevant past information based on contexts. By interpreting TrajGPT as discretized ordinary differential equations (ODEs), it effectively captures the underlying continuous dynamics and enables time-specific inference for forecasting arbitrary target timesteps. Experimental results demonstrate that TrajGPT excels in trajectory forecasting, drug usage prediction, and phenotype classification without requiring task-specific fine-tuning. By evolving the learned continuous dynamics, TrajGPT can interpolate and extrapolate disease risk trajectories from partially-observed time series. The visualization of predicted health trajectories shows that TrajGPT forecasts unseen diseases based on the history of clinically relevant phenotypes (i.e., contexts)., Comment: 9 pages

Monocular depth estimation aims to infer a dense depth map from a single image, which is a fundamental and prevalent task in computer vision. Many previous works have shown impressive depth estimation results through carefully designed network structures, but they usually ignore the planar information and therefore perform poorly in low-texture areas of indoor scenes. In this paper, we propose Plane2Depth, which adaptively utilizes plane information to improve depth prediction within a hierarchical framework. Specifically, in the proposed plane guided depth generator (PGDG), we design a set of plane queries as prototypes to softly model planes in the scene and predict per-pixel plane coefficients. Then the predicted plane coefficients can be converted into metric depth values with the pinhole camera model. In the proposed adaptive plane query aggregation (APGA) module, we introduce a novel feature interaction approach to improve the aggregation of multi-scale plane features in a top-down manner. Extensive experiments show that our method can achieve outstanding performance, especially in low-texture or repetitive areas. Furthermore, under the same backbone network, our method outperforms the state-of-the-art methods on the NYU-Depth-v2 dataset, achieves competitive results with state-of-the-art methods KITTI dataset and can be generalized to unseen scenes effectively., Comment: 14 pages, 12 figures, 8 tables

Estimating depth from a single image is a challenging visual task. Compared to relative depth estimation, metric depth estimation attracts more attention due to its practical physical significance and critical applications in real-life scenarios. However, existing metric depth estimation methods are typically trained on specific datasets with similar scenes, facing challenges in generalizing across scenes with significant scale variations. To address this challenge, we propose a novel monocular depth estimation method called ScaleDepth. Our method decomposes metric depth into scene scale and relative depth, and predicts them through a semantic-aware scale prediction (SASP) module and an adaptive relative depth estimation (ARDE) module, respectively. The proposed ScaleDepth enjoys several merits. First, the SASP module can implicitly combine structural and semantic features of the images to predict precise scene scales. Second, the ARDE module can adaptively estimate the relative depth distribution of each image within a normalized depth space. Third, our method achieves metric depth estimation for both indoor and outdoor scenes in a unified framework, without the need for setting the depth range or fine-tuning model. Extensive experiments demonstrate that our method attains state-of-the-art performance across indoor, outdoor, unconstrained, and unseen scenes. Project page: https://ruijiezhu94.github.io/ScaleDepth, Comment: 14 pages, 11 figure, 13 tables

It has long been challenging to recover the underlying dynamic 3D scene representations from a monocular RGB video. Existing works formulate this problem into finding a single most plausible solution by adding various constraints such as depth priors and strong geometry constraints, ignoring the fact that there could be infinitely many 3D scene representations corresponding to a single dynamic video. In this paper, we aim to learn all plausible 3D scene configurations that match the input video, instead of just inferring a specific one. To achieve this ambitious goal, we introduce a new framework, called OSN. The key to our approach is a simple yet innovative object scale network together with a joint optimization module to learn an accurate scale range for every dynamic 3D object. This allows us to sample as many faithful 3D scene configurations as possible. Extensive experiments show that our method surpasses all baselines and achieves superior accuracy in dynamic novel view synthesis on multiple synthetic and real-world datasets. Most notably, our method demonstrates a clear advantage in learning fine-grained 3D scene geometry. Our code and data are available at https://github.com/vLAR-group/OSN, Comment: ICML 2024. Code and data are available at: https://github.com/vLAR-group/OSN

Sequential decision-making refers to algorithms that take into account the dynamics of the environment, where early decisions affect subsequent decisions. With large language models (LLMs) demonstrating powerful capabilities between tasks, we can't help but ask: Can Current LLMs Effectively Make Sequential Decisions? In order to answer this question, we propose the UNO Arena based on the card game UNO to evaluate the sequential decision-making capability of LLMs and explain in detail why we choose UNO. In UNO Arena, We evaluate the sequential decision-making capability of LLMs dynamically with novel metrics based Monte Carlo methods. We set up random players, DQN-based reinforcement learning players, and LLM players (e.g. GPT-4, Gemini-pro) for comparison testing. Furthermore, in order to improve the sequential decision-making capability of LLMs, we propose the TUTRI player, which can involves having LLMs reflect their own actions wtih the summary of game history and the game strategy. Numerous experiments demonstrate that the TUTRI player achieves a notable breakthrough in the performance of sequential decision-making compared to the vanilla LLM player.

Learning time-series representations for discriminative tasks, such as classification and regression, has been a long-standing challenge in the healthcare domain. Current pre-training methods are limited in either unidirectional next-token prediction or randomly masked token prediction. We propose a novel architecture called Bidirectional Timely Generative Pre-trained Transformer (BiTimelyGPT), which pre-trains on biosignals and longitudinal clinical records by both next-token and previous-token prediction in alternating transformer layers. This pre-training task preserves original distribution and data shapes of the time-series. Additionally, the full-rank forward and backward attention matrices exhibit more expressive representation capabilities. Using biosignals and longitudinal clinical records, BiTimelyGPT demonstrates superior performance in predicting neurological functionality, disease diagnosis, and physiological signs. By visualizing the attention heatmap, we observe that the pre-trained BiTimelyGPT can identify discriminative segments from biosignal time-series sequences, even more so after fine-tuning on the task.

This report describes the solution that secured the first place in the "View Synthesis Challenge for Human Heads (VSCHH)" at the ICCV 2023 workshop. Given the sparse view images of human heads, the objective of this challenge is to synthesize images from novel viewpoints. Due to the complexity of textures on the face and the impact of lighting, the baseline method TensoRF yields results with significant artifacts, seriously affecting facial reconstruction. To address this issue, we propose TI-Face, which improves facial reconstruction through tensorial radiance fields (T-Face) and implicit surfaces (I-Face), respectively. Specifically, we employ an SAM-based approach to obtain the foreground mask, thereby filtering out intense lighting in the background. Additionally, we design mask-based constraints and sparsity constraints to eliminate rendering artifacts effectively. The experimental results demonstrate the effectiveness of the proposed improvements and superior performance of our method on face reconstruction. The code will be available at https://github.com/RuijieZhu94/TI-Face., Comment: 1st place solution in the View Synthesis Challenge for Human Heads (VSCHH) at the ICCV 2023 workshop

In this paper, we aim to model 3D scene dynamics from multi-view videos. Unlike the majority of existing works which usually focus on the common task of novel view synthesis within the training time period, we propose to simultaneously learn the geometry, appearance, and physical velocity of 3D scenes only from video frames, such that multiple desirable applications can be supported, including future frame extrapolation, unsupervised 3D semantic scene decomposition, and dynamic motion transfer. Our method consists of three major components, 1) the keyframe dynamic radiance field, 2) the interframe velocity field, and 3) a joint keyframe and interframe optimization module which is the core of our framework to effectively train both networks. To validate our method, we further introduce two dynamic 3D datasets: 1) Dynamic Object dataset, and 2) Dynamic Indoor Scene dataset. We conduct extensive experiments on multiple datasets, demonstrating the superior performance of our method over all baselines, particularly in the critical tasks of future frame extrapolation and unsupervised 3D semantic scene decomposition., Comment: NeurIPS 2023. Code and data are available at: https://github.com/vLAR-group/NVFi

Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success in Natural Language Processing and Computer Vision domains. However, the development of PTMs on healthcare time-series data is lagging behind.This underscores the limitations of the existing transformer-based architectures, particularly their scalability to handle large-scale time series and ability to capture long-term temporal dependencies. In this study, we present Timely Generative Pre-trained Transformer (TimelyGPT). TimelyGPT employs an extrapolatable position (xPos) embedding to encode trend and periodic patterns into time-series representations. It also integrates recurrent attention and temporal convolution modules to effectively capture global-local temporal dependencies. We evaluated TimelyGPT on two large-scale healthcare time series datasets corresponding to continuous biosignals and irregularly-sampled time series, respectively. Our experiments show that during pre-training, TimelyGPT excels in learning time-series representations from continuously monitored biosignals and irregularly-sampled time series data commonly observed in longitudinal electronic health records (EHRs). In forecasting continuous biosignals, TimelyGPT achieves accurate extrapolation up to 6,000 timesteps of body temperature during the sleep stage transition, given a short look-up window (i.e., prompt) containing only 2,000 timesteps. For irregularly-sampled time series, TimelyGPT with a proposed time-specific inference demonstrates high top recall scores in predicting future diagnoses using early diagnostic records, effectively handling irregular intervals between clinical records. Together, we envision TimelyGPT to be useful in a broad spectrum of health domains, including long-term patient health state forecasting and patient risk trajectory prediction., Comment: 17 pages

Self-supervised monocular depth estimation holds significant importance in the fields of autonomous driving and robotics. However, existing methods are typically trained and tested on standard datasets, overlooking the impact of various adverse conditions prevalent in real-world applications, such as rainy days. As a result, it is commonly observed that these methods struggle to handle these challenging scenarios. To address this issue, we present EC-Depth, a novel self-supervised two-stage framework to achieve a robust depth estimation. In the first stage, we propose depth consistency regularization to propagate reliable supervision from standard to challenging scenes. In the second stage, we adopt the Mean Teacher paradigm and propose a novel consistency-based pseudo-label filtering strategy to improve the quality of pseudo-labels, further improving both the accuracy and robustness of our model. Extensive experiments demonstrate that our method achieves accurate and consistent depth predictions in both standard and challenging scenarios, surpassing existing state-of-the-art methods on KITTI, KITTI-C, DrivingStereo, and NuScenes-Night benchmarks., Comment: Project page: https://ruijiezhu94.github.io/ECDepth_page

Terahertz (THz) communication is one of the most promising candidates to accommodate high-speed mobile data services. This paper proposes a secure hybrid automatic repeat request with incremental redundancy (HARQ-IR) aided THz communication scheme, where the transmission secrecy is ensured by confusing the eavesdropper with dummy messages. The connection and secrecy outage probabilities are then derived in closed-form. Besides, the tail behaviour of the connection outage probability in high signal-to-noise ratio (SNR) is examined by carrying out the asymptotic analysis, and the upper bound of the secrecy outage probability is obtained in a simple form by capitalizing on large deviations. With these results, we take a step further to investigate the secrecy long term average throughput (LTAT). By noticing that HARQ-IR not only improves the reliability of the legitimate user, but also increases the probability of being eavesdropped, a robust rate adaption policy is finally proposed to maximize the LTAT while restricting the connection and secrecy outage probabilities within satisfactory requirements.

Accurate depth estimation under out-of-distribution (OoD) scenarios, such as adverse weather conditions, sensor failure, and noise contamination, is desirable for safety-critical applications. Existing depth estimation systems, however, suffer inevitably from real-world corruptions and perturbations and are struggled to provide reliable depth predictions under such cases. In this paper, we summarize the winning solutions from the RoboDepth Challenge -- an academic competition designed to facilitate and advance robust OoD depth estimation. This challenge was developed based on the newly established KITTI-C and NYUDepth2-C benchmarks. We hosted two stand-alone tracks, with an emphasis on robust self-supervised and robust fully-supervised depth estimation, respectively. Out of more than two hundred participants, nine unique and top-performing solutions have appeared, with novel designs ranging from the following aspects: spatial- and frequency-domain augmentations, masked image modeling, image restoration and super-resolution, adversarial training, diffusion-based noise suppression, vision-language pre-training, learned model ensembling, and hierarchical feature enhancement. Extensive experimental analyses along with insightful observations are drawn to better understand the rationale behind each design. We hope this challenge could lay a solid foundation for future research on robust and reliable depth estimation and beyond. The datasets, competition toolkit, workshop recordings, and source code from the winning teams are publicly available on the challenge website., Comment: Technical Report; 65 pages, 34 figures, 24 tables; Code at https://github.com/ldkong1205/RoboDepth

Terahertz (THz) communications are envisioned to be a promising technology for 6G thanks to its broad bandwidth. However, the large path loss, antenna misalignment, and atmospheric influence of THz communications severely deteriorate its reliability. To address this, hybrid automatic repeat request (HARQ) is recognized as an effective technique to ensure reliable THz communications. This paper delves into the performance analysis of HARQ with incremental redundancy (HARQ-IR)-aided THz communications in the presence/absence of blockage. More specifically, the analytical expression of the outage probability of HARQ-IR-aided THz communications is derived, with which the asymptotic outage analysis is enabled to gain meaningful insights, including diversity order, power allocation gain, modulation and coding gain, etc. Then the long term average throughput (LTAT) is expressed in terms of the outage probability based on renewal theory. Moreover, to combat the blockage effects, a multi-hop HARQ-IR-aided THz communication scheme is proposed and its performance is examined. To demonstrate the superiority of the proposed scheme, the other two HARQ-aided schemes, i.e., Type-I HARQ and HARQ with chase combining (HARQ-CC), are used for benchmarking in the simulations. In addition, a deep neural network (DNN) based outage evaluation framework with low computational complexity is devised to reap the benefits of using both asymptotic and simulation results in low and high outage regimes, respectively. This novel outage evaluation framework is finally employed for the optimal rate selection, which outperforms the asymptotic based optimization., Comment: Blockage, hybrid automatic repeat request (HARQ), outage probability, terahertz (THz) communications

In this paper, we study the problem of 3D object segmentation from raw point clouds. Unlike all existing methods which usually require a large amount of human annotations for full supervision, we propose the first unsupervised method, called OGC, to simultaneously identify multiple 3D objects in a single forward pass, without needing any type of human annotations. The key to our approach is to fully leverage the dynamic motion patterns over sequential point clouds as supervision signals to automatically discover rigid objects. Our method consists of three major components, 1) the object segmentation network to directly estimate multi-object masks from a single point cloud frame, 2) the auxiliary self-supervised scene flow estimator, and 3) our core object geometry consistency component. By carefully designing a series of loss functions, we effectively take into account the multi-object rigid consistency and the object shape invariance in both temporal and spatial scales. This allows our method to truly discover the object geometry even in the absence of annotations. We extensively evaluate our method on five datasets, demonstrating the superior performance for object part instance segmentation and general object segmentation in both indoor and the challenging outdoor scenarios., Comment: NeurIPS 2022. Code and data are available at: https://github.com/vLAR-group/OGC

Although terahertz (THz) communications can provide mobile broadband services, it usually has a large path loss and is vulnerable to antenna misalignment. This significantly degrades the reception reliability. To address this issue, the hybrid automatic repeat request (HARQ) is proposed to further enhance the reliability of THz communications. This paper provides an in-depth investigation on the outage performance of two different types of HARQ-aided THz communications, including Type-I HARQ and HARQ with chase combining (HARQ-CC). Moreover, the effects of both fading and stochastic antenna misalignment are considered in this paper. The exact outage probabilities of HARQ-aided THz communications are derived in closed-form, with which the asymptotic outage analysis is enabled to explore helpful insights. In particular, it is revealed that full time diversity can be achieved by using HARQ assisted schemes. Besides, the HARQ-CC-aided scheme performs better than the Type-I HARQ-aided one due to its high diversity combining gain. The analytical results are eventually validated via Monte-Carlo simulations.

We present a GAN-based Transformer for general action-conditioned 3D human motion generation, including not only single-person actions but also multi-person interactive actions. Our approach consists of a powerful Action-conditioned motion TransFormer (ActFormer) under a GAN training scheme, equipped with a Gaussian Process latent prior. Such a design combines the strong spatio-temporal representation capacity of Transformer, superiority in generative modeling of GAN, and inherent temporal correlations from the latent prior. Furthermore, ActFormer can be naturally extended to multi-person motions by alternately modeling temporal correlations and human interactions with Transformer encoders. To further facilitate research on multi-person motion generation, we introduce a new synthetic dataset of complex multi-person combat behaviors. Extensive experiments on NTU-13, NTU RGB+D 120, BABEL and the proposed combat dataset show that our method can adapt to various human motion representations and achieve superior performance over the state-of-the-art methods on both single-person and multi-person motion generation tasks, demonstrating a promising step towards a general human motion generator.

Deep features have been proven powerful in building accurate dense semantic correspondences in various previous works. However, the multi-scale and pyramidal hierarchy of convolutional neural networks has not been well studied to learn discriminative pixel-level features for semantic correspondence. In this paper, we propose a multi-scale matching network that is sensitive to tiny semantic differences between neighboring pixels. We follow the coarse-to-fine matching strategy and build a top-down feature and matching enhancement scheme that is coupled with the multi-scale hierarchy of deep convolutional neural networks. During feature enhancement, intra-scale enhancement fuses same-resolution feature maps from multiple layers together via local self-attention and cross-scale enhancement hallucinates higher-resolution feature maps along the top-down hierarchy. Besides, we learn complementary matching details at different scales thus the overall matching score is refined by features of different semantic levels gradually. Our multi-scale matching network can be trained end-to-end easily with few additional learnable parameters. Experimental results demonstrate that the proposed method achieves state-of-the-art performance on three popular benchmarks with high computational efficiency., Comment: Accepted to appear in ICCV 2021

Motivation: Electronic health record (EHR) data provides a new venue to elucidate disease comorbidities and latent phenotypes for precision medicine. To fully exploit its potential, a realistic data generative process of the EHR data needs to be modelled. We present MixEHR-S to jointly infer specialist-disease topics from the EHR data. As the key contribution, we model the specialist assignments and ICD-coded diagnoses as the latent topics based on patient's underlying disease topic mixture in a novel unified supervised hierarchical Bayesian topic model. For efficient inference, we developed a closed-form collapsed variational inference algorithm to learn the model distributions of MixEHR-S. We applied MixEHR-S to two independent large-scale EHR databases in Quebec with three targeted applications: (1) Congenital Heart Disease (CHD) diagnostic prediction among 154,775 patients; (2) Chronic obstructive pulmonary disease (COPD) diagnostic prediction among 73,791 patients; (3) future insulin treatment prediction among 78,712 patients diagnosed with diabetes as a mean to assess the disease exacerbation. In all three applications, MixEHR-S conferred clinically meaningful latent topics among the most predictive latent topics and achieved superior target prediction accuracy compared to the existing methods, providing opportunities for prioritizing high-risk patients for healthcare services. MixEHR-S source code and scripts of the experiments are freely available at https://github.com/li-lab-mcgill/mixehrS

In recognition-based action interaction, robots' responses to human actions are often pre-designed according to recognized categories and thus stiff. In this paper, we specify a new Interactive Action Translation (IAT) task which aims to learn end-to-end action interaction from unlabeled interactive pairs, removing explicit action recognition. To enable learning on small-scale data, we propose a Paired-Embedding (PE) method for effective and reliable data augmentation. Specifically, our method first utilizes paired relationships to cluster individual actions in an embedding space. Then two actions originally paired can be replaced with other actions in their respective neighborhood, assembling into new pairs. An Act2Act network based on conditional GAN follows to learn from augmented data. Besides, IAT-test and IAT-train scores are specifically proposed for evaluating methods on our task. Experimental results on two datasets show impressive effects and broad application prospects of our method., Comment: 16 pages, 7 figures

Despite the notable progress made in action recognition tasks, not much work has been done in action recognition specifically for human-robot interaction. In this paper, we deeply explore the characteristics of the action recognition task in interaction scenarios and propose an attention-oriented multi-level network framework to meet the need for real-time interaction. Specifically, a Pre-Attention network is employed to roughly focus on the interactor in the scene at low resolution firstly and then perform fine-grained pose estimation at high resolution. The other compact CNN receives the extracted skeleton sequence as input for action recognition, utilizing attention-like mechanisms to capture local spatial-temporal patterns and global semantic information effectively. To evaluate our approach, we construct a new action dataset specially for the recognition task in interaction scenarios. Experimental results on our dataset and high efficiency (112 fps at 640 x 480 RGBD) on the mobile computing platform (Nvidia Jetson AGX Xavier) demonstrate excellent applicability of our method on action recognition in real-time human-robot interaction., Comment: 8 pages, 8 figures