Yue Wang

Lu Bai, Lixin Cui, Yue Wang et al.

In this work, we propose a family of novel quantum kernels, namely the Hierarchical Aligned Quantum Jensen-Shannon Kernels (HAQJSK), for un-attributed graphs. Different from most existing classical graph kernels, the proposed HAQJSK kernels can incorporate hierarchical aligned structure information between graphs and transform graphs of random sizes into fixed-sized aligned graph structures, i.e., the Hierarchical Transitive Aligned Adjacency Matrix of vertices and the Hierarchical Transitive Aligned Density Matrix of the Continuous-Time Quantum Walk (CTQW). For a pair of graphs to hand, the resulting HAQJSK kernels are defined by measuring the Quantum Jensen-Shannon Divergence (QJSD) between their transitive aligned graph structures. We show that the proposed HAQJSK kernels not only reflect richer intrinsic global graph characteristics in terms of the CTQW, but also address the drawback of neglecting structural correspondence information arising in most existing R-convolution kernels. Furthermore, unlike the previous Quantum Jensen-Shannon Kernels associated with the QJSD and the CTQW, the proposed HAQJSK kernels can simultaneously guarantee the properties of permutation invariant and positive definiteness, explaining the theoretical advantages of the HAQJSK kernels. Experiments indicate the effectiveness of the proposed kernels.

Lixin Cui, Ming Li, Yue Wang et al.

In this work, we develop an Aligned Entropic Reproducing Kernel (AERK) for graph classification. We commence by performing the Continuous-time Quantum Walk (CTQW) on each graph structure, and computing the Averaged Mixing Matrix (AMM) to describe how the CTQW visit all vertices from a starting vertex. More specifically, we show how this AMM matrix allows us to compute a quantum Shannon entropy for each vertex of a graph. For pairwise graphs, the proposed AERK kernel is defined by computing a reproducing kernel based similarity between the quantum Shannon entropies of their each pair of aligned vertices. The analysis of theoretical properties reveals that the proposed AERK kernel cannot only address the shortcoming of neglecting the structural correspondence information between graphs arising in most existing R-convolution graph kernels, but also overcome the problem of neglecting the structural differences between pairs of aligned vertices arising in existing vertex-based matching kernels. Moreover, unlike existing classical graph kernels that only focus on the global or local structural information of graphs, the proposed AERK kernel can simultaneously capture both global and local structural information through the quantum Shannon entropies, reflecting more precise kernel based similarity measures between pairs of graphs. The above theoretical properties explain the effectiveness of the proposed kernel. The experimental evaluation on standard graph datasets demonstrates that the proposed AERK kernel is able to outperform state-of-the-art graph kernels for graph classification tasks.

Yi Fang, Haoran Xu, Jiaxin Han et al.

Foundation models have revolutionized various fields such as natural language processing (NLP) and computer vision (CV). While efforts have been made to transfer the success of the foundation models in general AI domains to biology, existing works focus on directly adopting the existing foundation model architectures from general machine learning domains without a systematic design considering the unique physicochemical and structural properties of each biological data modality. This leads to suboptimal performance, as these repurposed architectures struggle to capture the long-range dependencies, sparse information, and complex underlying ``grammars'' inherent to biological data. To address this gap, we introduce BioArc, a novel framework designed to move beyond intuition-driven architecture design towards principled, automated architecture discovery for biological foundation models. Leveraging Neural Architecture Search (NAS), BioArc systematically explores a vast architecture design space, evaluating architectures across multiple biological modalities while rigorously analyzing the interplay between architecture, tokenization, and training strategies. This large-scale analysis identifies novel, high-performance architectures, allowing us to distill a set of empirical design principles to guide future model development. Furthermore, to make the best of this set of discovered principled architectures, we propose and compare several architecture prediction methods that effectively and efficiently predict optimal architectures for new biological tasks. Overall, our work provides a foundational resource and a principled methodology to guide the creation of the next generation of task-specific and foundation models for biology.

Jingyi Xu, Xieyuanli Chen, Junyi Ma et al.

The task of occupancy forecasting (OCF) involves utilizing past and present perception data to predict future occupancy states of autonomous vehicle surrounding environments, which is critical for downstream tasks such as obstacle avoidance and path planning. Existing 3D OCF approaches struggle to predict plausible spatial details for movable objects and suffer from slow inference speeds due to neglecting the bias and uneven distribution of changing occupancy states in both space and time. In this paper, we propose a novel spatiotemporal decoupling vision-based paradigm to explicitly tackle the bias and achieve both effective and efficient 3D OCF. To tackle spatial bias in empty areas, we introduce a novel spatial representation that decouples the conventional dense 3D format into 2D bird's-eye view (BEV) occupancy with corresponding height values, enabling 3D OCF derived only from 2D predictions thus enhancing efficiency. To reduce temporal bias on static voxels, we design temporal decoupling to improve end-to-end OCF by temporally associating instances via predicted flows. We develop an efficient multi-head network EfficientOCF to achieve 3D OCF with our devised spatiotemporally decoupled representation. A new metric, conditional IoU (C-IoU), is also introduced to provide a robust 3D OCF performance assessment, especially in datasets with missing or incomplete annotations. The experimental results demonstrate that EfficientOCF surpasses existing baseline methods on accuracy and efficiency, achieving state-of-the-art performance with a fast inference time of 82.33ms with a single GPU. Our code will be released as open source.

Zhuo Xu, Lu Bai, Lixin Cui et al.

Graph Auto-Encoders (GAEs) are powerful tools for graph representation learning. In this paper, we develop a novel Hierarchical Cluster-based GAE (HC-GAE), that can learn effective structural characteristics for graph data analysis. To this end, during the encoding process, we commence by utilizing the hard node assignment to decompose a sample graph into a family of separated subgraphs. We compress each subgraph into a coarsened node, transforming the original graph into a coarsened graph. On the other hand, during the decoding process, we adopt the soft node assignment to reconstruct the original graph structure by expanding the coarsened nodes. By hierarchically performing the above compressing procedure during the decoding process as well as the expanding procedure during the decoding process, the proposed HC-GAE can effectively extract bidirectionally hierarchical structural features of the original sample graph. Furthermore, we re-design the loss function that can integrate the information from either the encoder or the decoder. Since the associated graph convolution operation of the proposed HC-GAE is restricted in each individual separated subgraph and cannot propagate the node information between different subgraphs, the proposed HC-GAE can significantly reduce the over-smoothing problem arising in the classical convolution-based GAEs. The proposed HC-GAE can generate effective representations for either node classification or graph classification, and the experiments demonstrate the effectiveness on real-world datasets.

Zhehan Zhao, Lu Bai, Lixin Cui et al.

Graph Neural Networks (GNNs) are powerful tools for graph classification. One important operation for GNNs is the downsampling or pooling that can learn effective embeddings from the node representations. In this paper, we propose a new hierarchical pooling operation, namely the Edge-Node Attention-based Differentiable Pooling (ENADPool), for GNNs to learn effective graph representations. Unlike the classical hierarchical pooling operation that is based on the unclear node assignment and simply computes the averaged feature over the nodes of each cluster, the proposed ENADPool not only employs a hard clustering strategy to assign each node into an unique cluster, but also compress the node features as well as their edge connectivity strengths into the resulting hierarchical structure based on the attention mechanism after each pooling step. As a result, the proposed ENADPool simultaneously identifies the importance of different nodes within each separated cluster and edges between corresponding clusters, that significantly addresses the shortcomings of the uniform edge-node based structure information aggregation arising in the classical hierarchical pooling operation. Moreover, to mitigate the over-smoothing problem arising in existing GNNs, we propose a Multi-distance GNN (MD-GNN) model associated with the proposed ENADPool operation, allowing the nodes to actively and directly receive the feature information from neighbors at different random walk steps. Experiments demonstrate the effectiveness of the MD-GNN associated with the proposed ENADPool.

Zhuo Xu, Lixin Cui, Ming Li et al.

In this paper, we develop a novel local graph pooling method, namely the Separated Subgraph-based Hierarchical Pooling (SSHPool), for graph classification. We commence by assigning the nodes of a sample graph into different clusters, resulting in a family of separated subgraphs. We individually employ the local graph convolution units as the local structure to further compress each subgraph into a coarsened node, transforming the original graph into a coarsened graph. Since these subgraphs are separated by different clusters and the structural information cannot be propagated between them, the local convolution operation can significantly avoid the over-smoothing problem caused by message passing through edges in most existing Graph Neural Networks (GNNs). By hierarchically performing the proposed procedures on the resulting coarsened graph, the proposed SSHPool can effectively extract the hierarchical global features of the original graph structure, encapsulating rich intrinsic structural characteristics. Furthermore, we develop an end-to-end GNN framework associated with the SSHPool module for graph classification. Experimental results demonstrate the superior performance of the proposed model on real-world datasets.

Zhuoyuan Wu, Xurui Yang, Jiahui Huang et al.

Estimating accurate camera poses, 3D scene geometry, and object motion from in-the-wild videos is a long-standing challenge for classical structure from motion pipelines due to the presence of dynamic objects. Recent learning-based methods attempt to overcome this challenge by training motion estimators to filter dynamic objects and focus on the static background. However, their performance is largely limited by the availability of large-scale motion segmentation datasets, resulting in inaccurate segmentation and, therefore, inferior structural 3D understanding. In this work, we introduce the Dynamic Prior (\ourmodel) to robustly identify dynamic objects without task-specific training, leveraging the powerful reasoning capabilities of Vision-Language Models (VLMs) and the fine-grained spatial segmentation capacity of SAM2. \ourmodel can be seamlessly integrated into state-of-the-art pipelines for camera pose optimization, depth reconstruction, and 4D trajectory estimation. Extensive experiments on both synthetic and real-world videos demonstrate that \ourmodel not only achieves state-of-the-art performance on motion segmentation, but also significantly improves accuracy and robustness for structural 3D understanding.

Haodong Feng, Peiyan Hu, Yue Wang et al.

Control in fluid environments is an important research area with numerous applications across various domains, including underwater robotics, aerospace engineering, and biomedical systems. However, in practice, control methods often face challenges due to sparse or missing observations, stemming from sensor limitations and faults. These issues result in observations that are not only sparse but also inconsistent in their number and modalities (e.g., velocity and pressure sensors). In this work, we propose a Physics-Informed Representation (PIR) algorithm for multi-modal policies of control to leverage the sparse and random observations in complex fluid environments. PIR integrates sparse observational data with the Partial Differential Equation (PDE) information to distill a unified representation of fluid systems. The main idea is that PDE solutions are determined by three elements: the equation, initial conditions, and boundary conditions. Given the equation, we only need to learn the representation of the initial and boundary conditions, which define a trajectory of a specific fluid system. Specifically, it leverages PDE loss to fit the neural network and data loss calculated on the observations with random quantities and multi-modalities to propagate the information with initial and boundary conditions into the representations. The representations are the learnable parameters or the output of the encoder. In the experiments, the PIR illustrates the superior consistency with the features of the ground truth compared with baselines, even when there are missing modalities. Furthermore, PIR combined with Reinforcement Learning has been successfully applied in control tasks where the robot leverages the learned state by PIR faster and more accurately, passing through the complex vortex street from a random starting location to reach a random target.

Feifei Qian, Lixin Cui, Ming Li et al.

In this paper, we propose a new model to learn Adaptive Kernel-based Representations (AKBR) for graph classification. Unlike state-of-the-art R-convolution graph kernels that are defined by merely counting any pair of isomorphic substructures between graphs and cannot provide an end-to-end learning mechanism for the classifier, the proposed AKBR approach aims to define an end-to-end representation learning model to construct an adaptive kernel matrix for graphs. To this end, we commence by leveraging a novel feature-channel attention mechanism to capture the interdependencies between different substructure invariants of original graphs. The proposed AKBR model can thus effectively identify the structural importance of different substructures, and compute the R-convolution kernel between pairwise graphs associated with the more significant substructures specified by their structural attentions. Since each row of the resulting kernel matrix can be theoretically seen as the embedding vector of a sample graph, the proposed AKBR model is able to directly employ the resulting kernel matrix as the graph feature matrix and input it into the classifier for classification (i.e., the SoftMax layer), naturally providing an end-to-end learning architecture between the kernel computation as well as the classifier. Experimental results show that the proposed AKBR model outperforms existing state-of-the-art graph kernels and deep learning methods on standard graph benchmarks.

Niya Wang, Eric P. Hoffman, Robert Clarke et al.

Tissue heterogeneity is a major confounding factor in studying individual populations that cannot be resolved directly by global profiling. Experimental solutions to mitigate tissue heterogeneity are expensive, time consuming, inapplicable to existing data, and may alter the original gene expression patterns. Here we ask whether it is possible to deconvolute two-source mixed expressions (estimating both proportions and cell-specific profiles) from two or more heterogeneous samples without requiring any prior knowledge. Supported by a well-grounded mathematical framework, we argue that both constituent proportions and cell-specific expressions can be estimated in a completely unsupervised mode when cell-specific marker genes exist, which do not have to be known a priori, for each of constituent cell types. We demonstrate the performance of unsupervised deconvolution on both simulation and real gene expression data, together with perspective discussions.