MSNGO: multi-species protein function annotation based on 3D protein structure and network propagation

Motivation: In recent years, protein function prediction has broken through the bottleneck of sequence features, significantly improving prediction accuracy using high-precision protein structures predicted by AlphaFold2. While single-species protein function prediction methods have achieved remarkable success, multi-species protein function prediction methods are still in the stage of using PPI networks and sequence features. Providing effective cross-species label propagation for species with sparse protein annotations remains a challenging issue. To address this problem, we propose the MSNGO model, which integrates structural features and network propagation methods. Our validation shows that using structural features can significantly improve the accuracy of multi-species protein function prediction. Results: We employ graph representation learning techniques to extract amino acid representations from protein structure contact maps and train a structural model using a graph convolution pooling module to derive protein-level structural features. After incorporating the sequence features from ESM-2, we apply a network propagation algorithm to aggregate information and update node representations within a heterogeneous network. The results demonstrate that MSNGO outperforms previous multi-species protein function prediction methods that rely on sequence features and PPI networks. Availability: https://github.com/blingbell/MSNGO.

Reliable and Compact Graph Fine-tuning via GraphSparse Prompting

Recently, graph prompt learning has garnered increasing attention in adapting pre-trained GNN models for downstream graph learning tasks. However, existing works generally conduct prompting over all graph elements (e.g., nodes, edges, node attributes, etc.), which is suboptimal and obviously redundant. To address this issue, we propose exploiting sparse representation theory for graph prompting and present Graph Sparse Prompting (GSP). GSP aims to adaptively and sparsely select the optimal elements (e.g., certain node attributes) to achieve compact prompting for downstream tasks. Specifically, we propose two kinds of GSP models, termed Graph Sparse Feature Prompting (GSFP) and Graph Sparse multi-Feature Prompting (GSmFP). Both GSFP and GSmFP provide a general scheme for tuning any specific pre-trained GNNs that can achieve attribute selection and compact prompt learning simultaneously. A simple yet effective algorithm has been designed for solving GSFP and GSmFP models. Experiments on 16 widely-used benchmark datasets validate the effectiveness and advantages of the proposed GSFPs.

RNG: Relightable Neural Gaussians

3D Gaussian Splatting (3DGS) has shown its impressive power in novel view synthesis. However, creating relightable 3D assets, especially for objects with ill-defined shapes (e.g., fur), is still a challenging task. For these scenes, the decomposition between the light, geometry, and material is more ambiguous, as neither the surface constraints nor the analytical shading model hold. To address this issue, we propose RNG, a novel representation of relightable neural Gaussians, enabling the relighting of objects with both hard surfaces or fluffy boundaries. We avoid any assumptions in the shading model but maintain feature vectors, which can be further decoded by an MLP into colors, in each Gaussian point. Following prior work, we utilize a point light to reduce the ambiguity and introduce a shadow-aware condition to the network. We additionally propose a depth refinement network to help the shadow computation under the 3DGS framework, leading to better shadow effects under point lights. Furthermore, to avoid the blurriness brought by the alpha-blending in 3DGS, we design a hybrid forward-deferred optimization strategy. As a result, we achieve about $20\times$ faster in training and about $600\times$ faster in rendering than prior work based on neural radiance fields, with $60$ frames per second on an RTX4090.

Graph Edge Representation via Tensor Product Graph Convolutional Representation

Graph Convolutional Networks (GCNs) have been widely studied. The core of GCNs is the definition of convolution operators on graphs. However, existing Graph Convolution (GC) operators are mainly defined on adjacency matrix and node features and generally focus on obtaining effective node embeddings which cannot be utilized to address the graphs with (high-dimensional) edge features. To address this problem, by leveraging tensor contraction representation and tensor product graph diffusion theories, this paper analogously defines an effective convolution operator on graphs with edge features which is named as Tensor Product Graph Convolution (TPGC). The proposed TPGC aims to obtain effective edge embeddings. It provides a complementary model to traditional graph convolutions (GCs) to address the more general graph data analysis with both node and edge features. Experimental results on several graph learning tasks demonstrate the effectiveness of the proposed TPGC.

A Unified Graph Selective Prompt Learning for Graph Neural Networks

In recent years, graph prompt learning/tuning has garnered increasing attention in adapting pre-trained models for graph representation learning. As a kind of universal graph prompt learning method, Graph Prompt Feature (GPF) has achieved remarkable success in adapting pre-trained models for Graph Neural Networks (GNNs). By fixing the parameters of a pre-trained GNN model, the aim of GPF is to modify the input graph data by adding some (learnable) prompt vectors into graph node features to better align with the downstream tasks on the smaller dataset. However, existing GPFs generally suffer from two main limitations. First, GPFs generally focus on node prompt learning which ignore the prompting for graph edges. Second, existing GPFs generally conduct the prompt learning on all nodes equally which fails to capture the importances of different nodes and may perform sensitively w.r.t noisy nodes in aligning with the downstream tasks. To address these issues, in this paper, we propose a new unified Graph Selective Prompt Feature learning (GSPF) for GNN fine-tuning. The proposed GSPF integrates the prompt learning on both graph node and edge together, which thus provides a unified prompt model for the graph data. Moreover, it conducts prompt learning selectively on nodes and edges by concentrating on the important nodes and edges for prompting which thus make our model be more reliable and compact. Experimental results on many benchmark datasets demonstrate the effectiveness and advantages of the proposed GSPF method.

Robust Proximity Detection using On-Device Gait Monitoring

Proximity detection in indoor environments based on WiFi signals has gained significant attention in recent years. Existing works rely on the dynamic signal reflections and their extracted features are dependent on motion strength. To address this issue, we design a robust WiFi-based proximity detector by considering gait monitoring. Specifically, we propose a gait score that accurately evaluates gait presence by leveraging the speed estimated from the autocorrelation function (ACF) of channel state information (CSI). By combining this gait score with a proximity feature, our approach effectively distinguishes different transition patterns, enabling more reliable proximity detection. In addition, to enhance the stability of the detection process, we employ a state machine and extract temporal information, ensuring continuous proximity detection even during subtle movements. Extensive experiments conducted in different environments demonstrate an overall detection rate of 92.5% and a low false alarm rate of 1.12% with a delay of 0.825s.

CORP: A Multi-Modal Dataset for Campus-Oriented Roadside Perception Tasks

Numerous roadside perception datasets have been introduced to propel advancements in autonomous driving and intelligent transportation systems research and development. However, it has been observed that the majority of their concentrates is on urban arterial roads, inadvertently overlooking residential areas such as parks and campuses that exhibit entirely distinct characteristics. In light of this gap, we propose CORP, which stands as the first public benchmark dataset tailored for multi-modal roadside perception tasks under campus scenarios. Collected in a university campus, CORP consists of over 205k images plus 102k point clouds captured from 18 cameras and 9 LiDAR sensors. These sensors with different configurations are mounted on roadside utility poles to provide diverse viewpoints within the campus region. The annotations of CORP encompass multi-dimensional information beyond 2D and 3D bounding boxes, providing extra support for 3D seamless tracking and instance segmentation with unique IDs and pixel masks for identifying targets, to enhance the understanding of objects and their behaviors distributed across the campus premises. Unlike other roadside datasets about urban traffic, CORP extends the spectrum to highlight the challenges for multi-modal perception in campuses and other residential areas.

mmID: High-Resolution mmWave Imaging for Human Identification

Achieving accurate human identification through RF imaging has been a persistent challenge, primarily attributed to the limited aperture size and its consequent impact on imaging resolution. The existing imaging solution enables tasks such as pose estimation, activity recognition, and human tracking based on deep neural networks by estimating skeleton joints. In contrast to estimating joints, this paper proposes to improve imaging resolution by estimating the human figure as a whole using conditional generative adversarial networks (cGAN). In order to reduce training complexity, we use an estimated spatial spectrum using the MUltiple SIgnal Classification (MUSIC) algorithm as input to the cGAN. Our system generates environmentally independent, high-resolution images that can extract unique physical features useful for human identification. We use a simple convolution layers-based classification network to obtain the final identification result. From the experimental results, we show that resolution of the image produced by our trained generator is high enough to enable human identification. Our finding indicates high-resolution accuracy with 5% mean silhouette difference to the Kinect device. Extensive experiments in different environments on multiple testers demonstrate that our system can achieve 93% overall test accuracy in unseen environments for static human target identification.

Trustworthy Edge Machine Learning: A Survey

The convergence of Edge Computing (EC) and Machine Learning (ML), known as Edge Machine Learning (EML), has become a highly regarded research area by utilizing distributed network resources to perform joint training and inference in a cooperative manner. However, EML faces various challenges due to resource constraints, heterogeneous network environments, and diverse service requirements of different applications, which together affect the trustworthiness of EML in the eyes of its stakeholders. This survey provides a comprehensive summary of definitions, attributes, frameworks, techniques, and solutions for trustworthy EML. Specifically, we first emphasize the importance of trustworthy EML within the context of Sixth-Generation (6G) networks. We then discuss the necessity of trustworthiness from the perspective of challenges encountered during deployment and real-world application scenarios. Subsequently, we provide a preliminary definition of trustworthy EML and explore its key attributes. Following this, we introduce fundamental frameworks and enabling technologies for trustworthy EML systems, and provide an in-depth literature review of the latest solutions to enhance trustworthiness of EML. Finally, we discuss corresponding research challenges and open issues.

EdgeCalib: Multi-Frame Weighted Edge Features for Automatic Targetless LiDAR-Camera Calibration

In multimodal perception systems, achieving precise extrinsic calibration between LiDAR and camera is of critical importance. Previous calibration methods often required specific targets or manual adjustments, making them both labor-intensive and costly. Online calibration methods based on features have been proposed, but these methods encounter challenges such as imprecise feature extraction, unreliable cross-modality associations, and high scene-specific requirements. To address this, we introduce an edge-based approach for automatic online calibration of LiDAR and cameras in real-world scenarios. The edge features, which are prevalent in various environments, are aligned in both images and point clouds to determine the extrinsic parameters. Specifically, stable and robust image edge features are extracted using a SAM-based method and the edge features extracted from the point cloud are weighted through a multi-frame weighting strategy for feature filtering. Finally, accurate extrinsic parameters are optimized based on edge correspondence constraints. We conducted evaluations on both the KITTI dataset and our dataset. The results show a state-of-the-art rotation accuracy of 0.086{\deg} and a translation accuracy of 0.977 cm, outperforming existing edge-based calibration methods in both precision and robustness.