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Jun 19

Graph-Aware Isomorphic Attention for Adaptive Dynamics in Transformers

We present an approach to modifying Transformer architectures by integrating graph-aware relational reasoning into the attention mechanism, merging concepts from graph neural networks and language modeling. Building on the inherent connection between attention and graph theory, we reformulate the Transformer's attention mechanism as a graph operation and propose Graph-Aware Isomorphic Attention. This method leverages advanced graph modeling strategies, including Graph Isomorphism Networks (GIN) and Principal Neighborhood Aggregation (PNA), to enrich the representation of relational structures. Our approach captures complex dependencies and generalizes across tasks, as evidenced by a reduced generalization gap and improved learning performance. Additionally, we expand the concept of graph-aware attention to introduce Sparse GIN-Attention, a fine-tuning approach that employs sparse GINs. By interpreting attention matrices as sparse adjacency graphs, this technique enhances the adaptability of pre-trained foundational models with minimal computational overhead, endowing them with graph-aware capabilities. Sparse GIN-Attention fine-tuning achieves improved training dynamics and better generalization compared to alternative methods like low-rank adaption (LoRA). We discuss latent graph-like structures within traditional attention mechanisms, offering a new lens through which Transformers can be understood. By evolving Transformers as hierarchical GIN models for relational reasoning. This perspective suggests profound implications for foundational model development, enabling the design of architectures that dynamically adapt to both local and global dependencies. Applications in bioinformatics, materials science, language modeling, and beyond could benefit from this synthesis of relational and sequential data modeling, setting the stage for interpretable and generalizable modeling strategies.

  • 1 authors
·
Jan 4, 2025 2

Neighbor Embedding for High-Dimensional Sparse Poisson Data

Across many scientific fields, measurements often represent the number of times an event occurs. For example, a document can be represented by word occurrence counts, neural activity by spike counts per time window, or online communication by daily email counts. These measurements yield high-dimensional count data that often approximate a Poisson distribution, frequently with low rates that produce substantial sparsity and complicate downstream analysis. A useful approach is to embed the data into a low-dimensional space that preserves meaningful structure, commonly termed dimensionality reduction. Yet existing dimensionality reduction methods, including both linear (e.g., PCA) and nonlinear approaches (e.g., t-SNE), often assume continuous Euclidean geometry, thereby misaligning with the discrete, sparse nature of low-rate count data. Here, we propose p-SNE (Poisson Stochastic Neighbor Embedding), a nonlinear neighbor embedding method designed around the Poisson structure of count data, using KL divergence between Poisson distributions to measure pairwise dissimilarity and Hellinger distance to optimize the embedding. We test p-SNE on synthetic Poisson data and demonstrate its ability to recover meaningful structure in real-world count datasets, including weekday patterns in email communication, research area clusters in OpenReview papers, and temporal drift and stimulus gradients in neural spike recordings.

  • 2 authors
·
Apr 17

Local Augmentation for Graph Neural Networks

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node features of the neighbors conditioned on the central node's feature and enhance GNN's expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3.4\% and 1.6\% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https://github.com/SongtaoLiu0823/LAGNN.

  • 9 authors
·
Sep 8, 2021

PA&DA: Jointly Sampling PAth and DAta for Consistent NAS

Based on the weight-sharing mechanism, one-shot NAS methods train a supernet and then inherit the pre-trained weights to evaluate sub-models, largely reducing the search cost. However, several works have pointed out that the shared weights suffer from different gradient descent directions during training. And we further find that large gradient variance occurs during supernet training, which degrades the supernet ranking consistency. To mitigate this issue, we propose to explicitly minimize the gradient variance of the supernet training by jointly optimizing the sampling distributions of PAth and DAta (PA&DA). We theoretically derive the relationship between the gradient variance and the sampling distributions, and reveal that the optimal sampling probability is proportional to the normalized gradient norm of path and training data. Hence, we use the normalized gradient norm as the importance indicator for path and training data, and adopt an importance sampling strategy for the supernet training. Our method only requires negligible computation cost for optimizing the sampling distributions of path and data, but achieves lower gradient variance during supernet training and better generalization performance for the supernet, resulting in a more consistent NAS. We conduct comprehensive comparisons with other improved approaches in various search spaces. Results show that our method surpasses others with more reliable ranking performance and higher accuracy of searched architectures, showing the effectiveness of our method. Code is available at https://github.com/ShunLu91/PA-DA.

  • 7 authors
·
Feb 28, 2023

Robust Collaborative Learning with Linear Gradient Overhead

Collaborative learning algorithms, such as distributed SGD (or D-SGD), are prone to faulty machines that may deviate from their prescribed algorithm because of software or hardware bugs, poisoned data or malicious behaviors. While many solutions have been proposed to enhance the robustness of D-SGD to such machines, previous works either resort to strong assumptions (trusted server, homogeneous data, specific noise model) or impose a gradient computational cost that is several orders of magnitude higher than that of D-SGD. We present MoNNA, a new algorithm that (a) is provably robust under standard assumptions and (b) has a gradient computation overhead that is linear in the fraction of faulty machines, which is conjectured to be tight. Essentially, MoNNA uses Polyak's momentum of local gradients for local updates and nearest-neighbor averaging (NNA) for global mixing, respectively. While MoNNA is rather simple to implement, its analysis has been more challenging and relies on two key elements that may be of independent interest. Specifically, we introduce the mixing criterion of (alpha, lambda)-reduction to analyze the non-linear mixing of non-faulty machines, and present a way to control the tension between the momentum and the model drifts. We validate our theory by experiments on image classification and make our code available at https://github.com/LPD-EPFL/robust-collaborative-learning.

  • 6 authors
·
Sep 22, 2022

Graphlets correct for the topological information missed by random walks

Random walks are widely used for mining networks due to the computational efficiency of computing them. For instance, graph representation learning learns a d-dimensional embedding space, so that the nodes that tend to co-occur on random walks (a proxy of being in the same network neighborhood) are close in the embedding space. Specific local network topology (i.e., structure) influences the co-occurrence of nodes on random walks, so random walks of limited length capture only partial topological information, hence diminishing the performance of downstream methods. We explicitly capture all topological neighborhood information and improve performance by introducing orbit adjacencies that quantify the adjacencies of two nodes as co-occurring on a given pair of graphlet orbits, which are symmetric positions on graphlets (small, connected, non-isomorphic, induced subgraphs of a large network). Importantly, we mathematically prove that random walks on up to k nodes capture only a subset of all the possible orbit adjacencies for up to k-node graphlets. Furthermore, we enable orbit adjacency-based analysis of networks by developing an efficient GRaphlet-orbit ADjacency COunter (GRADCO), which exhaustively computes all 28 orbit adjacency matrices for up to four-node graphlets. Note that four-node graphlets suffice, because real networks are usually small-world. In large networks on around 20,000 nodes, GRADCOcomputesthe28matricesinminutes. Onsixrealnetworksfromvarious domains, we compare the performance of node-label predictors obtained by using the network embeddings based on our orbit adjacencies to those based on random walks. We find that orbit adjacencies, which include those unseen by random walks, outperform random walk-based adjacencies, demonstrating the importance of the inclusion of the topological neighborhood information that is unseen by random walks.

  • 3 authors
·
May 23, 2024

I Know What I Don't Know: Latent Posterior Factor Models for Multi-Evidence Probabilistic Reasoning

Real-world decision-making, from tax compliance assessment to medical diagnosis, requires aggregating multiple noisy and potentially contradictory evidence sources. Existing approaches either lack explicit uncertainty quantification (neural aggregation methods) or rely on manually engineered discrete predicates (probabilistic logic frameworks), limiting scalability to unstructured data. We introduce Latent Posterior Factors (LPF), a framework that transforms Variational Autoencoder (VAE) latent posteriors into soft likelihood factors for Sum-Product Network (SPN) inference, enabling tractable probabilistic reasoning over unstructured evidence while preserving calibrated uncertainty estimates. We instantiate LPF as LPF-SPN (structured factor-based inference) and LPF-Learned (end-to-end learned aggregation), enabling a principled comparison between explicit probabilistic reasoning and learned aggregation under a shared uncertainty representation. Across eight domains (seven synthetic and the FEVER benchmark), LPF-SPN achieves high accuracy (up to 97.8%), low calibration error (ECE 1.4%), and strong probabilistic fit, substantially outperforming evidential deep learning, LLMs and graph-based baselines over 15 random seeds. Contributions: (1) A framework bridging latent uncertainty representations with structured probabilistic reasoning. (2) Dual architectures enabling controlled comparison of reasoning paradigms. (3) Reproducible training methodology with seed selection. (4) Evaluation against EDL, BERT, R-GCN, and large language model baselines. (5) Cross-domain validation. (6) Formal guarantees in a companion paper.

  • 1 authors
·
Mar 13 2

Manifold k-NN: Accelerated k-NN Queries for Manifold Point Clouds

k-nearest neighbor (k-NN) search is a fundamental primitive in geometry processing and computer graphics. While spatial partitioning structures such as kd-trees are standard, they are often manifold-blind, failing to exploit the intrinsic low-dimensional structure of points sampled from 2-manifolds. Recent advances in dynamic programming-based nearest neighbor search (DP-NNS) leverage incrementally constructed Voronoi diagrams to accelerate queries, where each site p maintains a list of successors that progressively refine its Voronoi cell. However, DP-NNS is restricted to single nearest neighbor (k=1) searches, precluding their adoption in applications that require local neighborhood statistics. In this paper, we generalize the DP-NNS framework to support arbitrary k-NN queries for manifold-aligned data. Our approach is founded on the geometric observation that if p_i is the nearest neighbor of a query q in P, then the second nearest neighbor of q must reside either within the prefix set P_{1:i-1} = {p_1, \dots, p_{i-1}} or within p_i's successor list. By recursively extending this principle, we introduce Manifold k-NN, a recursive algorithmic scheme that significantly outperforms conventional kd-trees for manifold-aligned data. Our method achieves a 1\times--10\times speedup in volume-to-surface query scenarios and inherently supports dynamic prefix queries -- enabling k-NN searches within any subset P_{1:m} (m \leq n) with zero overhead. Furthermore, we extend the framework to support point deletion via local Delaunay updates, providing a complete suite of dynamic operations for point set modification. Comprehensive experiments on diverse geometric datasets demonstrate the efficiency and broad applicability of our approach for modern graphics pipelines. Source code is available at https://github.com/sssomeone/manifold-knn.

  • 7 authors
·
May 3

Do logarithmic proximity measures outperform plain ones in graph clustering?

We consider a number of graph kernels and proximity measures including commute time kernel, regularized Laplacian kernel, heat kernel, exponential diffusion kernel (also called "communicability"), etc., and the corresponding distances as applied to clustering nodes in random graphs and several well-known datasets. The model of generating random graphs involves edge probabilities for the pairs of nodes that belong to the same class or different predefined classes of nodes. It turns out that in most cases, logarithmic measures (i.e., measures resulting after taking logarithm of the proximities) perform better while distinguishing underlying classes than the "plain" measures. A comparison in terms of reject curves of inter-class and intra-class distances confirms this conclusion. A similar conclusion can be made for several well-known datasets. A possible origin of this effect is that most kernels have a multiplicative nature, while the nature of distances used in cluster algorithms is an additive one (cf. the triangle inequality). The logarithmic transformation is a tool to transform the first nature to the second one. Moreover, some distances corresponding to the logarithmic measures possess a meaningful cutpoint additivity property. In our experiments, the leader is usually the logarithmic Communicability measure. However, we indicate some more complicated cases in which other measures, typically, Communicability and plain Walk, can be the winners.

  • 2 authors
·
May 3, 2016

Federated PCA on Grassmann Manifold for Anomaly Detection in IoT Networks

In the era of Internet of Things (IoT), network-wide anomaly detection is a crucial part of monitoring IoT networks due to the inherent security vulnerabilities of most IoT devices. Principal Components Analysis (PCA) has been proposed to separate network traffics into two disjoint subspaces corresponding to normal and malicious behaviors for anomaly detection. However, the privacy concerns and limitations of devices' computing resources compromise the practical effectiveness of PCA. We propose a federated PCA-based Grassmannian optimization framework that coordinates IoT devices to aggregate a joint profile of normal network behaviors for anomaly detection. First, we introduce a privacy-preserving federated PCA framework to simultaneously capture the profile of various IoT devices' traffic. Then, we investigate the alternating direction method of multipliers gradient-based learning on the Grassmann manifold to guarantee fast training and the absence of detecting latency using limited computational resources. Empirical results on the NSL-KDD dataset demonstrate that our method outperforms baseline approaches. Finally, we show that the Grassmann manifold algorithm is highly adapted for IoT anomaly detection, which permits drastically reducing the analysis time of the system. To the best of our knowledge, this is the first federated PCA algorithm for anomaly detection meeting the requirements of IoT networks.

  • 5 authors
·
Dec 22, 2022

Towards Deeper Graph Neural Networks

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of these neighborhood aggregation methods only consider immediate neighbors, and the performance decreases when going deeper to enable larger receptive fields. Several recent studies attribute this performance deterioration to the over-smoothing issue, which states that repeated propagation makes node representations of different classes indistinguishable. In this work, we study this observation systematically and develop new insights towards deeper graph neural networks. First, we provide a systematical analysis on this issue and argue that the key factor compromising the performance significantly is the entanglement of representation transformation and propagation in current graph convolution operations. After decoupling these two operations, deeper graph neural networks can be used to learn graph node representations from larger receptive fields. We further provide a theoretical analysis of the above observation when building very deep models, which can serve as a rigorous and gentle description of the over-smoothing issue. Based on our theoretical and empirical analysis, we propose Deep Adaptive Graph Neural Network (DAGNN) to adaptively incorporate information from large receptive fields. A set of experiments on citation, co-authorship, and co-purchase datasets have confirmed our analysis and insights and demonstrated the superiority of our proposed methods.

  • 3 authors
·
Jul 17, 2020

Position-Sensing Graph Neural Networks: Proactively Learning Nodes Relative Positions

Most existing graph neural networks (GNNs) learn node embeddings using the framework of message passing and aggregation. Such GNNs are incapable of learning relative positions between graph nodes within a graph. To empower GNNs with the awareness of node positions, some nodes are set as anchors. Then, using the distances from a node to the anchors, GNNs can infer relative positions between nodes. However, P-GNNs arbitrarily select anchors, leading to compromising position-awareness and feature extraction. To eliminate this compromise, we demonstrate that selecting evenly distributed and asymmetric anchors is essential. On the other hand, we show that choosing anchors that can aggregate embeddings of all the nodes within a graph is NP-complete. Therefore, devising efficient optimal algorithms in a deterministic approach is practically not feasible. To ensure position-awareness and bypass NP-completeness, we propose Position-Sensing Graph Neural Networks (PSGNNs), learning how to choose anchors in a back-propagatable fashion. Experiments verify the effectiveness of PSGNNs against state-of-the-art GNNs, substantially improving performance on various synthetic and real-world graph datasets while enjoying stable scalability. Specifically, PSGNNs on average boost AUC more than 14% for pairwise node classification and 18% for link prediction over the existing state-of-the-art position-aware methods. Our source code is publicly available at: https://github.com/ZhenyueQin/PSGNN.

  • 6 authors
·
May 24, 2021

DAG: Deep Adaptive and Generative K-Free Community Detection on Attributed Graphs

Community detection on attributed graphs with rich semantic and topological information offers great potential for real-world network analysis, especially user matching in online games. Graph Neural Networks (GNNs) have recently enabled Deep Graph Clustering (DGC) methods to learn cluster assignments from semantic and topological information. However, their success depends on the prior knowledge related to the number of communities K, which is unrealistic due to the high costs and privacy issues of acquisition.In this paper, we investigate the community detection problem without prior K, referred to as K-Free Community Detection problem. To address this problem, we propose a novel Deep Adaptive and Generative model~(DAG) for community detection without specifying the prior K. DAG consists of three key components, i.e., a node representation learning module with masked attribute reconstruction, a community affiliation readout module, and a community number search module with group sparsity. These components enable DAG to convert the process of non-differentiable grid search for the community number, i.e., a discrete hyperparameter in existing DGC methods, into a differentiable learning process. In such a way, DAG can simultaneously perform community detection and community number search end-to-end. To alleviate the cost of acquiring community labels in real-world applications, we design a new metric, EDGE, to evaluate community detection methods even when the labels are not feasible. Extensive offline experiments on five public datasets and a real-world online mobile game dataset demonstrate the superiority of our DAG over the existing state-of-the-art (SOTA) methods. DAG has a relative increase of 7.35\% in teams in a Tencent online game compared with the best competitor.

  • 7 authors
·
Feb 20, 2025

Molt Dynamics: Emergent Social Phenomena in Autonomous AI Agent Populations

MoltBook is a large-scale multi-agent coordination environment where over 770,000 autonomous LLM agents interact without human participation, offering the first opportunity we are aware of to observe emergent multi-agent coordination dynamics at this population scale. We introduce Molt Dynamics: the emergent agent coordination behaviors, inter-agent communication dynamics, and role specialization patterns arising when autonomous agents operate as decentralized decision-makers in an unconstrained multi-agent environment. Through longitudinal observation of 90,704 active agents over three weeks, we characterize three aspects. First, spontaneous role specialization: network-based clustering reveals six structural roles (silhouette 0.91), though the result primarily reflects core-periphery organization -- 93.5\% of agents occupy a homogeneous peripheral cluster, with meaningful differentiation confined to the active minority. Second, decentralized information dissemination: cascade analysis of 10,323 inter-agent propagation events reveals power-law distributed cascade sizes (α= 2.57 pm 0.02) and saturating adoption dynamics where adoption probability shows diminishing returns with repeated exposures (Cox hazard ratio 0.53, concordance 0.78). Third, distributed cooperative task resolution: 164 multi-agent collaborative events show detectable coordination patterns, but success rates are low (6.7\%, p = 0.057) and cooperative outcomes are significantly worse than a matched single-agent baseline (Cohen's d = -0.88), indicating emergent cooperative behavior is nascent. These findings establish an empirical baseline for coordination dynamics in decentralized autonomous agent systems, with implications for multi-agent system design, agent communication protocol engineering, and AI safety.

  • 2 authors
·
Mar 3

Flag Aggregator: Scalable Distributed Training under Failures and Augmented Losses using Convex Optimization

Modern ML applications increasingly rely on complex deep learning models and large datasets. There has been an exponential growth in the amount of computation needed to train the largest models. Therefore, to scale computation and data, these models are inevitably trained in a distributed manner in clusters of nodes, and their updates are aggregated before being applied to the model. However, a distributed setup is prone to Byzantine failures of individual nodes, components, and software. With data augmentation added to these settings, there is a critical need for robust and efficient aggregation systems. We define the quality of workers as reconstruction ratios in (0,1], and formulate aggregation as a Maximum Likelihood Estimation procedure using Beta densities. We show that the Regularized form of log-likelihood wrt subspace can be approximately solved using iterative least squares solver, and provide convergence guarantees using recent Convex Optimization landscape results. Our empirical findings demonstrate that our approach significantly enhances the robustness of state-of-the-art Byzantine resilient aggregators. We evaluate our method in a distributed setup with a parameter server, and show simultaneous improvements in communication efficiency and accuracy across various tasks. The code is publicly available at https://github.com/hamidralmasi/FlagAggregator

  • 4 authors
·
Feb 12, 2023

Ensembling Diffusion Models via Adaptive Feature Aggregation

The success of the text-guided diffusion model has inspired the development and release of numerous powerful diffusion models within the open-source community. These models are typically fine-tuned on various expert datasets, showcasing diverse denoising capabilities. Leveraging multiple high-quality models to produce stronger generation ability is valuable, but has not been extensively studied. Existing methods primarily adopt parameter merging strategies to produce a new static model. However, they overlook the fact that the divergent denoising capabilities of the models may dynamically change across different states, such as when experiencing different prompts, initial noises, denoising steps, and spatial locations. In this paper, we propose a novel ensembling method, Adaptive Feature Aggregation (AFA), which dynamically adjusts the contributions of multiple models at the feature level according to various states (i.e., prompts, initial noises, denoising steps, and spatial locations), thereby keeping the advantages of multiple diffusion models, while suppressing their disadvantages. Specifically, we design a lightweight Spatial-Aware Block-Wise (SABW) feature aggregator that adaptive aggregates the block-wise intermediate features from multiple U-Net denoisers into a unified one. The core idea lies in dynamically producing an individual attention map for each model's features by comprehensively considering various states. It is worth noting that only SABW is trainable with about 50 million parameters, while other models are frozen. Both the quantitative and qualitative experiments demonstrate the effectiveness of our proposed Adaptive Feature Aggregation method. The code is available at https://github.com/tenvence/afa/.

  • 9 authors
·
May 27, 2024

Theoretical Foundations of Latent Posterior Factors: Formal Guarantees for Multi-Evidence Reasoning

We present a complete theoretical characterization of Latent Posterior Factors (LPF), a principled framework for aggregating multiple heterogeneous evidence items in probabilistic prediction tasks. Multi-evidence reasoning arises pervasively in high-stakes domains including healthcare diagnosis, financial risk assessment, legal case analysis, and regulatory compliance, yet existing approaches either lack formal guarantees or fail to handle multi-evidence scenarios architecturally. LPF encodes each evidence item into a Gaussian latent posterior via a variational autoencoder, converting posteriors to soft factors through Monte Carlo marginalization, and aggregating factors via exact Sum-Product Network inference (LPF-SPN) or a learned neural aggregator (LPF-Learned). We prove seven formal guarantees spanning the key desiderata for trustworthy AI: Calibration Preservation (ECE <= epsilon + C/sqrt(K_eff)); Monte Carlo Error decaying as O(1/sqrt(M)); a non-vacuous PAC-Bayes bound with train-test gap of 0.0085 at N=4200; operation within 1.12x of the information-theoretic lower bound; graceful degradation as O(epsilon*delta*sqrt(K)) under corruption, maintaining 88% performance with half of evidence adversarially replaced; O(1/sqrt(K)) calibration decay with R^2=0.849; and exact epistemic-aleatoric uncertainty decomposition with error below 0.002%. All theorems are empirically validated on controlled datasets spanning up to 4,200 training examples. Our theoretical framework establishes LPF as a foundation for trustworthy multi-evidence AI in safety-critical applications.

  • 1 authors
·
Mar 13 2

Bridging Academia and Industry: A Comprehensive Benchmark for Attributed Graph Clustering

Attributed Graph Clustering (AGC) is a fundamental unsupervised task that integrates structural topology and node attributes to uncover latent patterns in graph-structured data. Despite its significance in industrial applications such as fraud detection and user segmentation, a significant chasm persists between academic research and real-world deployment. Current evaluation protocols suffer from the small-scale, high-homophily citation datasets, non-scalable full-batch training paradigms, and a reliance on supervised metrics that fail to reflect performance in label-scarce environments. To bridge these gaps, we present PyAGC, a comprehensive, production-ready benchmark and library designed to stress-test AGC methods across diverse scales and structural properties. We unify existing methodologies into a modular Encode-Cluster-Optimize framework and, for the first time, provide memory-efficient, mini-batch implementations for a wide array of state-of-the-art AGC algorithms. Our benchmark curates 12 diverse datasets, ranging from 2.7K to 111M nodes, specifically incorporating industrial graphs with complex tabular features and low homophily. Furthermore, we advocate for a holistic evaluation protocol that mandates unsupervised structural metrics and efficiency profiling alongside traditional supervised metrics. Battle-tested in high-stakes industrial workflows at Ant Group, this benchmark offers the community a robust, reproducible, and scalable platform to advance AGC research towards realistic deployment. The code and resources are publicly available via GitHub (https://github.com/Cloudy1225/PyAGC), PyPI (https://pypi.org/project/pyagc), and Documentation (https://pyagc.readthedocs.io).

antgroup Ant Group
·
Feb 9 2

G-Rank: Unsupervised Continuous Learn-to-Rank for Edge Devices in a P2P Network

Ranking algorithms in traditional search engines are powered by enormous training data sets that are meticulously engineered and curated by a centralized entity. Decentralized peer-to-peer (p2p) networks such as torrenting applications and Web3 protocols deliberately eschew centralized databases and computational architectures when designing services and features. As such, robust search-and-rank algorithms designed for such domains must be engineered specifically for decentralized networks, and must be lightweight enough to operate on consumer-grade personal devices such as a smartphone or laptop computer. We introduce G-Rank, an unsupervised ranking algorithm designed exclusively for decentralized networks. We demonstrate that accurate, relevant ranking results can be achieved in fully decentralized networks without any centralized data aggregation, feature engineering, or model training. Furthermore, we show that such results are obtainable with minimal data preprocessing and computational overhead, and can still return highly relevant results even when a user's device is disconnected from the network. G-Rank is highly modular in design, is not limited to categorical data, and can be implemented in a variety of domains with minimal modification. The results herein show that unsupervised ranking models designed for decentralized p2p networks are not only viable, but worthy of further research.

  • 2 authors
·
Jan 29, 2023

A Heat Diffusion Perspective on Geodesic Preserving Dimensionality Reduction

Diffusion-based manifold learning methods have proven useful in representation learning and dimensionality reduction of modern high dimensional, high throughput, noisy datasets. Such datasets are especially present in fields like biology and physics. While it is thought that these methods preserve underlying manifold structure of data by learning a proxy for geodesic distances, no specific theoretical links have been established. Here, we establish such a link via results in Riemannian geometry explicitly connecting heat diffusion to manifold distances. In this process, we also formulate a more general heat kernel based manifold embedding method that we call heat geodesic embeddings. This novel perspective makes clearer the choices available in manifold learning and denoising. Results show that our method outperforms existing state of the art in preserving ground truth manifold distances, and preserving cluster structure in toy datasets. We also showcase our method on single cell RNA-sequencing datasets with both continuum and cluster structure, where our method enables interpolation of withheld timepoints of data. Finally, we show that parameters of our more general method can be configured to give results similar to PHATE (a state-of-the-art diffusion based manifold learning method) as well as SNE (an attraction/repulsion neighborhood based method that forms the basis of t-SNE).

  • 7 authors
·
May 30, 2023

Understanding Graph Databases: A Comprehensive Tutorial and Survey

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

  • 3 authors
·
Nov 15, 2024

Learned Low Precision Graph Neural Networks

Deep Graph Neural Networks (GNNs) show promising performance on a range of graph tasks, yet at present are costly to run and lack many of the optimisations applied to DNNs. We show, for the first time, how to systematically quantise GNNs with minimal or no loss in performance using Network Architecture Search (NAS). We define the possible quantisation search space of GNNs. The proposed novel NAS mechanism, named Low Precision Graph NAS (LPGNAS), constrains both architecture and quantisation choices to be differentiable. LPGNAS learns the optimal architecture coupled with the best quantisation strategy for different components in the GNN automatically using back-propagation in a single search round. On eight different datasets, solving the task of classifying unseen nodes in a graph, LPGNAS generates quantised models with significant reductions in both model and buffer sizes but with similar accuracy to manually designed networks and other NAS results. In particular, on the Pubmed dataset, LPGNAS shows a better size-accuracy Pareto frontier compared to seven other manual and searched baselines, offering a 2.3 times reduction in model size but a 0.4% increase in accuracy when compared to the best NAS competitor. Finally, from our collected quantisation statistics on a wide range of datasets, we suggest a W4A8 (4-bit weights, 8-bit activations) quantisation strategy might be the bottleneck for naive GNN quantisations.

  • 6 authors
·
Sep 19, 2020

Computer Use at the Edge of the Statistical Precipice

Evaluating Computer Use Agents (CUAs) on interactive environments is fraught with methodological pitfalls that the field has yet to systematically address. We show that a 1MB replay script that blindly executes a recorded action sequence without ever observing the screen outperforms frontier models on prominent static benchmarks, and prove that its expected success rate is exactly equal to the source agent's pass@k in deterministic environments. We trace this and other failures to two root causes: non-principled environment design (static, unsandboxed, or unreliably verified environments) and non-principled evaluation methodology (naive aggregation and misuse of pass@k for stateful UI interactions). To address the first, we propose PRISM, five design principles for CUA environments (privileged verification, realistic environments, integrity-checked configurations, sandboxed execution, and multifactorial variability) and instantiate them in DigiWorld, a benchmark of 15 realistic sandboxed mobile applications able to evaluate agents in over 3.2 million verified unique configurations. To address the second, we develop an aggregation framework pairing Wilson score intervals with hierarchical bootstrap, producing confidence intervals that correctly account for the nested structure of CUA benchmarks, as we empirically demonstrate. All together, we show that principled environment design and rigorous evaluation methodology are not optional refinements but prerequisites for meaningful CUA research.

  • 9 authors
·
May 6

Breaking the Entanglement of Homophily and Heterophily in Semi-supervised Node Classification

Recently, graph neural networks (GNNs) have shown prominent performance in semi-supervised node classification by leveraging knowledge from the graph database. However, most existing GNNs follow the homophily assumption, where connected nodes are more likely to exhibit similar feature distributions and the same labels, and such an assumption has proven to be vulnerable in a growing number of practical applications. As a supplement, heterophily reflects dissimilarity in connected nodes, which has gained significant attention in graph learning. To this end, data engineers aim to develop a powerful GNN model that can ensure performance under both homophily and heterophily. Despite numerous attempts, most existing GNNs struggle to achieve optimal node representations due to the constraints of undirected graphs. The neglect of directed edges results in sub-optimal graph representations, thereby hindering the capacity of GNNs. To address this issue, we introduce AMUD, which quantifies the relationship between node profiles and topology from a statistical perspective, offering valuable insights for Adaptively Modeling the natural directed graphs as the Undirected or Directed graph to maximize the benefits from subsequent graph learning. Furthermore, we propose Adaptive Directed Pattern Aggregation (ADPA) as a new directed graph learning paradigm for AMUD. Empirical studies have demonstrated that AMUD guides efficient graph learning. Meanwhile, extensive experiments on 14 benchmark datasets substantiate the impressive performance of ADPA, outperforming baselines by significant margins of 3.96\%.

  • 6 authors
·
Dec 7, 2023

Measuring Primitive Accumulation: An Information-Theoretic Approach to Capitalist Enclosure in PIK2, Indonesia

Large-scale land enclosure for speculative mega-development constitutes a non-equilibrium spatial process whose velocity, topology, and irreversibility remain poorly quantified. We study the Pantai Indah Kapuk 2 (PIK2) coastal mega-development north of Jakarta, Indonesia, using eight years (2017--2024) of Sentinel-2 land-use/land-cover (LULC) data at 10-meter resolution. The landscape is projected onto a Marxian probability simplex partitioning terrestrial pixels into Commons, Agrarian, and Capital fractions. Fisher-Rao (FR) geodesic distances on this simplex identify a transformation pulse of 0.405~rad/yr during 2019--2020, coinciding with major construction activity. Absorbing Markov chain analysis yields expected absorption times into the built environment of 46.0~years for cropland and 38.1~years for tree cover, with a pooled built-area self-retention rate of 96.4%. Percolation analysis reveals that a giant connected component containing 89--95% of all built pixels persists at occupation probabilities p in [0.096, 0.162], far below the random percolation threshold p_c approx 0.593, indicating planned rather than stochastic spatial growth. The box-counting fractal dimension of the urban boundary increases from d_f = 1.316 to 1.397, consistent with increasingly irregular frontier expansion. These results suggest that information-geometric and statistical-mechanical tools can characterize the kinematic and topological signatures of capitalist spatial accumulation with quantitative precision.

Neighborhood-aware Scalable Temporal Network Representation Learning

Temporal networks have been widely used to model real-world complex systems such as financial systems and e-commerce systems. In a temporal network, the joint neighborhood of a set of nodes often provides crucial structural information useful for predicting whether they may interact at a certain time. However, recent representation learning methods for temporal networks often fail to extract such information or depend on online construction of structural features, which is time-consuming. To address the issue, this work proposes Neighborhood-Aware Temporal network model (NAT). For each node in the network, NAT abandons the commonly-used one-single-vector-based representation while adopting a novel dictionary-type neighborhood representation. Such a dictionary representation records a downsampled set of the neighboring nodes as keys, and allows fast construction of structural features for a joint neighborhood of multiple nodes. We also design a dedicated data structure termed N-cache to support parallel access and update of those dictionary representations on GPUs. NAT gets evaluated over seven real-world large-scale temporal networks. NAT not only outperforms all cutting-edge baselines by averaged 1.2% and 4.2% in transductive and inductive link prediction accuracy, respectively, but also keeps scalable by achieving a speed-up of 4.1-76.7x against the baselines that adopt joint structural features and achieves a speed-up of 1.6-4.0x against the baselines that cannot adopt those features. The link to the code: https: //github.com/Graph-COM/Neighborhood-Aware-Temporal-Network.

  • 2 authors
·
Sep 2, 2022

UMMAN: Unsupervised Multi-graph Merge Adversarial Network for Disease Prediction Based on Intestinal Flora

The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit connection among gut microbes poses a significant challenge for disease prediction using abundance information from OTU data. Recently, several methods have shown potential in predicting corresponding diseases. However, these methods fail to learn the inner association among gut microbes from different hosts, leading to unsatisfactory performance. In this paper, we present a novel architecture, Unsupervised Multi-graph Merge Adversarial Network (UMMAN). UMMAN can obtain the embeddings of nodes in the Multi-Graph in an unsupervised scenario, so that it helps learn the multiplex association. Our method is the first to combine Graph Neural Network with the task of intestinal flora disease prediction. We employ complex relation-types to construct the Original-Graph and disrupt the relationships among nodes to generate corresponding Shuffled-Graph. We introduce the Node Feature Global Integration (NFGI) module to represent the global features of the graph. Furthermore, we design a joint loss comprising adversarial loss and hybrid attention loss to ensure that the real graph embedding aligns closely with the Original-Graph and diverges from the Shuffled-Graph. Comprehensive experiments on five classical OTU gut microbiome datasets demonstrate the effectiveness and stability of our method. (We will release our code soon.)

  • 5 authors
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Jul 31, 2024

Earth Embeddings Reveal Diverse Urban Signals from Space

Conventional urban indicators derived from censuses, surveys, and administrative records are often costly, spatially inconsistent, and slow to update. Recent geospatial foundation models enable Earth embeddings, compact satellite image representations transferable across downstream tasks, but their utility for neighborhood-scale urban monitoring remains unclear. Here, we benchmark three Earth embedding families, AlphaEarth, Prithvi, and Clay, for urban signal prediction across six U.S. metropolitan areas from 2020 to 2023. Using a unified supervised-learning framework, we predict 14 neighborhood-level indicators spanning crime, income, health, and travel behavior, and evaluate performance under four settings: global, city-wise, year-wise, and city-year. Results show that Earth embeddings capture substantial urban variation, with the highest predictive skill for outcomes more directly tied to built-environment structure, including chronic health burdens and dominant commuting modes. By contrast, indicators shaped more strongly by fine-scale behavior and local policy, such as cycling, remain difficult to infer. Predictive performance varies markedly across cities but remains comparatively stable across years, indicating strong spatial heterogeneity alongside temporal robustness. Exploratory analysis suggests that cross-city variation in predictive performance is associated with urban form in task-specific ways. Controlled dimensionality experiments show that representation efficiency is critical: compact 64-dimensional AlphaEarth embeddings remain more informative than 64-dimensional reductions of Prithvi and Clay. This study establishes a benchmark for evaluating Earth embeddings in urban remote sensing and demonstrates their potential as scalable, low-cost features for SDG-aligned neighborhood-scale urban monitoring.

  • 9 authors
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Apr 2

p-adic Bi-Filtrations for Topological Machine Learning on Genomic Sequences

We introduce pVR, a topological machine learning framework for alignment-free genomic sequence classification that combines p-adic numbers with topological data analysis. Each DNA sequence is encoded along two complementary axes: a p-adic distance on k-mer prefixes, which captures hierarchical positional structure, and a compositional L_1 distance on k-mer frequencies, which captures local sequence content. The two distances jointly parameterise a bi-filtered Vietoris--Rips complex, and per-sequence topological summaries from this bi-filtration serve as features for standard machine learning classifiers. We establish theoretical guarantees for the construction: stability under metric perturbations and invariance to the choice of prime, alongside a result that explains why a single p-adic axis is topologically uninformative and why the bi-filtration recovers nontrivial homology. On twelve genomic benchmarks (28 to 500 sequences, 3 to 7 classes), pVR outperforms four established alignment-free baselines on three of six low-sample datasets, with gains of up to 21 percentage points; it underperforms only on a SARS-CoV-2 variant benchmark whose point-mutation divergence violates the hierarchical assumption, and all methods saturate in the large-sample regime. pVR also outperforms zero-shot frozen embeddings from the 500M-parameter Nucleotide Transformer v2 by 6.7 to 11.4 percentage points on three low-sample benchmarks. The pVR codebase is publicly available at https://github.com/MAHI-Group/pVR.

  • 2 authors
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Jun 4

PowerWalk: Scalable Personalized PageRank via Random Walks with Vertex-Centric Decomposition

Most methods for Personalized PageRank (PPR) precompute and store all accurate PPR vectors, and at query time, return the ones of interest directly. However, the storage and computation of all accurate PPR vectors can be prohibitive for large graphs, especially in caching them in memory for real-time online querying. In this paper, we propose a distributed framework that strikes a better balance between offline indexing and online querying. The offline indexing attains a fingerprint of the PPR vector of each vertex by performing billions of "short" random walks in parallel across a cluster of machines. We prove that our indexing method has an exponential convergence, achieving the same precision with previous methods using a much smaller number of random walks. At query time, the new PPR vector is composed by a linear combination of related fingerprints, in a highly efficient vertex-centric decomposition manner. Interestingly, the resulting PPR vector is much more accurate than its offline counterpart because it actually uses more random walks in its estimation. More importantly, we show that such decomposition for a batch of queries can be very efficiently processed using a shared decomposition. Our implementation, PowerWalk, takes advantage of advanced distributed graph engines and it outperforms the state-of-the-art algorithms by orders of magnitude. Particularly, it responses to tens of thousands of queries on graphs with billions of edges in just a few seconds.

  • 4 authors
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Aug 22, 2016

Rethinking Counting and Localization in Crowds:A Purely Point-Based Framework

Localizing individuals in crowds is more in accordance with the practical demands of subsequent high-level crowd analysis tasks than simply counting. However, existing localization based methods relying on intermediate representations (i.e., density maps or pseudo boxes) serving as learning targets are counter-intuitive and error-prone. In this paper, we propose a purely point-based framework for joint crowd counting and individual localization. For this framework, instead of merely reporting the absolute counting error at image level, we propose a new metric, called density Normalized Average Precision (nAP), to provide more comprehensive and more precise performance evaluation. Moreover, we design an intuitive solution under this framework, which is called Point to Point Network (P2PNet). P2PNet discards superfluous steps and directly predicts a set of point proposals to represent heads in an image, being consistent with the human annotation results. By thorough analysis, we reveal the key step towards implementing such a novel idea is to assign optimal learning targets for these proposals. Therefore, we propose to conduct this crucial association in an one-to-one matching manner using the Hungarian algorithm. The P2PNet not only significantly surpasses state-of-the-art methods on popular counting benchmarks, but also achieves promising localization accuracy. The codes will be available at: https://github.com/TencentYoutuResearch/CrowdCounting-P2PNet.

  • 9 authors
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Aug 6, 2021

When Does Bottom-up Beat Top-down in Hierarchical Community Detection?

Hierarchical clustering of networks consists in finding a tree of communities, such that lower levels of the hierarchy reveal finer-grained community structures. There are two main classes of algorithms tackling this problem. Divisive (top-down) algorithms recursively partition the nodes into two communities, until a stopping rule indicates that no further split is needed. In contrast, agglomerative (bottom-up) algorithms first identify the smallest community structure and then repeatedly merge the communities using a linkage method. In this article, we establish theoretical guarantees for the recovery of the hierarchical tree and community structure of a Hierarchical Stochastic Block Model by a bottom-up algorithm. We also establish that this bottom-up algorithm attains the information-theoretic threshold for exact recovery at intermediate levels of the hierarchy. Notably, these recovery conditions are less restrictive compared to those existing for top-down algorithms. This shows that bottom-up algorithms extend the feasible region for achieving exact recovery at intermediate levels. Numerical experiments on both synthetic and real data sets confirm the superiority of bottom-up algorithms over top-down algorithms. We also observe that top-down algorithms can produce dendrograms with inversions. These findings contribute to a better understanding of hierarchical clustering techniques and their applications in network analysis.

  • 4 authors
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Jun 1, 2023