P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching

Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow.

MixEHR-Nest: Identifying Subphenotypes within Electronic Health Records through Hierarchical Guided-Topic Modeling

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.

TrajGPT: Irregular Time-Series Representation Learning for Health Trajectory Analysis

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).

Plane2Depth: Hierarchical Adaptive Plane Guidance for Monocular Depth Estimation

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.

ScaleDepth: Decomposing Metric Depth Estimation into Scale Prediction and Relative Depth Estimation

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

OSN: Infinite Representations of Dynamic 3D Scenes from Monocular Videos

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

UNO Arena for Evaluating Sequential Decision-Making Capability of Large Language Models

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.

Bidirectional Generative Pre-training for Improving Time Series Representation Learning

Learning time-series representations for discriminative tasks has been a long-standing challenge. 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 time-series data by both next-token and previous-token predictions 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 biosignal data, 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 time-series sequences, even more so after fine-tuning on the task.

TIFace: Improving Facial Reconstruction through Tensorial Radiance Fields and Implicit Surfaces

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.

NVFi: Neural Velocity Fields for 3D Physics Learning from Dynamic Videos

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.