arXiv subjects

Pan Li

Publications and source records attributed to Pan Li.

At least 109 records · Page 6Linked to original sources

arXiv2025

GAD-NR: Graph Anomaly Detection via Neighborhood Reconstruction

Graph Anomaly Detection (GAD) is a technique used to identify abnormal nodes within graphs, finding applications in network security, fraud detection, social media spam detection, and various other domains. A common method for GAD is Graph Auto-Encoders (GAEs), which encode graph data into node representations and identify anomalies by assessing the reconstruction quality of the graphs based on these representations. However, existing GAE models are primarily optimized for direct link reconstruction, resulting in nodes connected in the graph being clustered in the latent space. As a result, they excel at detecting cluster-type structural anomalies but struggle with more complex structural anomalies that do not conform to clusters. To address this limitation, we propose a novel solution called GAD-NR, a new variant of GAE that incorporates neighborhood reconstruction for graph anomaly detection. GAD-NR aims to reconstruct the entire neighborhood of a node, encompassing the local structure, self-attributes, and neighbor attributes, based on the corresponding node representation. By comparing the neighborhood reconstruction loss between anomalous nodes and normal nodes, GAD-NR can effectively detect any anomalies. Extensive experimentation conducted on six real-world datasets validates the effectiveness of GAD-NR, showcasing significant improvements (by up to 30% in AUC) over state-of-the-art competitors. The source code for GAD-NR is openly available. Importantly, the comparative analysis reveals that the existing methods perform well only in detecting one or two types of anomalies out of the three types studied. In contrast, GAD-NR excels at detecting all three types of anomalies across the datasets, demonstrating its comprehensive anomaly detection capabilities.

cs.LG↗

arXiv2025

Notes on the Factorisation of the Hilbert Space for Two-Sided Black Holes in Higher Dimensions

In this paper, we investigate the Hilbert space factorisation problem of two-sided black holes in high dimensions. We demonstrate that the Hilbert space of two-sided black holes can be factorized into the tensor product of two one-sided bulk Hilbert spaces when the effect of non-perturbative replica wormholes is taken into account. We further interpret the one-sided bulk Hilbert space as the Hilbert space of a one-sided black hole. Therefore, since the Hilbert space of a two-sided black hole can be obtained from the tensor product of two single-sided black hole Hilbert spaces, we consider this as an embodiment of the ER=EPR conjecture, and we show when the entanglement between the two single-sided black holes is sufficiently strong, the (Lorentzian) geometry of a two-sided black hole will emerge.

hep-th↗

arXiv2025

Enhancing The Open Network: Definition and Automated Detection of Smart Contract Defects

The Open Network (TON), designed to support Telegram's extensive user base of hundreds of millions, has garnered considerable attention since its launch in 2022. FunC is the most popular programming language for writing smart contracts on TON. It is distinguished by a unique syntax compared to other smart contract languages. Despite growing interest, research on the practical defects of TON smart contracts is still in its early stages. In this paper, we summarize eight smart contract defects identified from TON's official blogs and audit reports, each with detailed definitions and code examples. Furthermore, we propose a static analysis framework called TONScanner to facilitate the detection of these defects. Specifically, TONScanner reuses FunC compiler's frontend code to transform the FunC source code into FunC intermediate representation (IR) in the form of a directed acyclic graph (DAG). Based on this IR, TONScanner constructs a control flow graph (CFG), then transforms it into a static single assignment (SSA) form to simplify further analysis. TONScanner also integrates Data Dependency, Call Graph, Taint Analysis, and Cell Construct, which are specifically tailored for TON blockchain's unique data structures. These components finally facilitate the identification of the eight defects. We evaluate the effectiveness of TONScanner by applying it to 1,640 smart contracts and find a total of 14,995 defects. Through random sampling and manual labeling, we find that TONScanner achieves an overall precision of 97.49%. The results reveal that current TON contracts contain numerous defects, indicating that developers are prone to making errors. TONScanner has proven its ability to accurately identify these defects, thereby aiding in their correction.

cs.SE↗

arXiv2024

Security and Privacy of Digital Twins for Advanced Manufacturing: A Survey

In Industry 4.0, the digital twin is one of the emerging technologies, offering simulation abilities to predict, refine, and interpret conditions and operations, where it is crucial to emphasize a heightened concentration on the associated security and privacy risks. To be more specific, the adoption of digital twins in the manufacturing industry relies on integrating technologies like cyber-physical systems, the Industrial Internet of Things, virtualization, and advanced manufacturing. The interactions of these technologies give rise to numerous security and privacy vulnerabilities that remain inadequately explored. Towards that end, this paper analyzes the cybersecurity threats of digital twins for advanced manufacturing in the context of data collection, data sharing, machine learning and deep learning, and system-level security and privacy. We also provide several solutions to the threats in those four categories that can help establish more trust in digital twins.

eess.SY↗

arXiv2024

xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

q-bio.QM↗

arXiv2024

Scalable and Efficient Temporal Graph Representation Learning via Forward Recent Sampling

Temporal graph representation learning (TGRL) is essential for modeling dynamic systems in real-world networks. However, traditional TGRL methods, despite their effectiveness, often face significant computational challenges and inference delays due to the inefficient sampling of temporal neighbors. Conventional sampling methods typically involve backtracking through the interaction history of each node. In this paper, we propose a novel TGRL framework, No-Looking-Back (NLB), which overcomes these challenges by introducing a forward recent sampling strategy. This strategy eliminates the need to backtrack through historical interactions by utilizing a GPU-executable, size-constrained hash table for each node. The hash table records a down-sampled set of recent interactions, enabling rapid query responses with minimal inference latency. The maintenance of this hash table is highly efficient, operating with $O(1)$ complexity. Fully compatible with GPU processing, NLB maximizes programmability, parallelism, and power efficiency. Empirical evaluations demonstrate that NLB not only matches or surpasses state-of-the-art methods in accuracy for tasks like link prediction and node classification across six real-world datasets but also achieves 1.32-4.40x faster training, 1.2-7.94x greater energy efficiency, and 1.63-12.95x lower inference latency compared to competitive baselines. The link to the code: https://github.com/Graph-COM/NLB.

cs.LG↗

arXiv2024

Dynamic Self-Distillation via Previous Mini-batches for Fine-tuning Small Language Models

Knowledge distillation (KD) has become a widely adopted approach for compressing large language models (LLMs) to reduce computational costs and memory footprints. However, the availability of complex teacher models is a prerequisite for running most KD pipelines. Thus, the traditional KD procedure can be unachievable or budget-unfriendly, particularly when relying on commercial LLMs like GPT4. In this regard, Self-distillation (SelfD) emerges as an advisable alternative, enabling student models to learn without teachers' guidance. Nonetheless, existing SelfD approaches for LMs often involve architectural modifications, assuming the models are open-source, which may not always be practical. In this work, we introduce a model-agnostic and task-agnostic method named dynamic SelfD from the previous minibatch (DynSDPB), which realizes current iterations' distillation from the last ones' generated logits. Additionally, to address prediction inaccuracies during the early iterations, we dynamically adjust the distillation influence and temperature values to enhance the adaptability of fine-tuning. Furthermore, DynSDPB is a novel fine-tuning policy that facilitates the seamless integration of existing self-correction and self-training techniques for small language models (SLMs) because they all require updating SLMs' parameters. We demonstrate the superior performance of DynSDPB on both encoder-only LMs (e.g., BERT model families) and decoder-only LMs (e.g., LLaMA model families), validating its effectiveness across natural language understanding (NLU) and natural language generation (NLG) benchmarks.

cs.CL↗

arXiv2024

GeSS: Benchmarking Geometric Deep Learning under Scientific Applications with Distribution Shifts

Geometric deep learning (GDL) has gained significant attention in scientific fields, for its proficiency in modeling data with intricate geometric structures. However, very few works have delved into its capability of tackling the distribution shift problem, a prevalent challenge in many applications. To bridge this gap, we propose GeSS, a comprehensive benchmark designed for evaluating the performance of GDL models in scientific scenarios with distribution shifts. Our evaluation datasets cover diverse scientific domains from particle physics, materials science to biochemistry, and encapsulate a broad spectrum of distribution shifts including conditional, covariate, and concept shifts. Furthermore, we study three levels of information access from the out-of-distribution (OOD) test data, including no OOD information, only unlabeled OOD data, and OOD data with a few labels. Overall, our benchmark results in 30 different experiment settings, and evaluates 3 GDL backbones and 11 learning algorithms in each setting. A thorough analysis of the evaluation results is provided, poised to illuminate insights for GDL researchers and domain practitioners who are to use GDL in their applications.

cs.LG↗

arXiv2024

Holographic images of a charged black hole in Lorentz symmetry breaking massive gravity

Using the AdS/CFT correspondence, this paper investigates the holographic images of a charged black hole within the context of Lorentz symmetry breaking massive gravity. The photon rings, luminosity-deformed rings, or light points from various observational perspectives are obtained. We also study the influences of both the chemical potential and temperature on the Einstein ring. Unlike the previous work, which primarily examines the effect of chemical potential on ring radius at high temperatures and find no change in the radius with varying chemical potential, we also investigate the effect of chemical potential on the ring radius at low temperature besides at high temperature. Our findings indicate that at low temperatures, the photon ring radius decreases with increasing of chemical potential, while at high temperatures, the results are consistent with previous studies. Additionally, we explore the impact of the model parameter λ on the Einstein ring radius and find the the ring radius increases as the model parameter λ increases. More interestingly, for the large chemical potential, u = 1, the temperature dependence of the photon ring radius is reversed for λ = 2 and λ = 4. Conversely, for a small chemical potential u = 0.1, the temperature dependence of the Einstein ring stays the same as λ = 2 and λ = 4.

gr-qc↗

arXiv2024

Training Compute-Optimal Protein Language Models

We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains plateau, focusing primarily on increasing model sizes rather than optimizing the efficient compute frontier that balances performance and compute budgets. Our investigation is grounded in a massive dataset consisting of 939 million protein sequences. We trained over 300 models ranging from 3.5 million to 10.7 billion parameters on 5 to 200 billion unique tokens, to investigate the relations between model sizes, training token numbers, and objectives. First, we observed the effect of diminishing returns for the Causal Language Model (CLM) and that of overfitting for the Masked Language Model~(MLM) when repeating the commonly used Uniref database. To address this, we included metagenomic protein sequences in the training set to increase the diversity and avoid the plateau or overfitting effects. Second, we obtained the scaling laws of CLM and MLM on Transformer, tailored to the specific characteristics of protein sequence data. Third, we observe a transfer scaling phenomenon from CLM to MLM, further demonstrating the effectiveness of transfer through scaling behaviors based on estimated Effectively Transferred Tokens. Finally, to validate our scaling laws, we compare the large-scale versions of ESM-2 and PROGEN2 on downstream tasks, encompassing evaluations of protein generation as well as structure- and function-related tasks, all within less or equivalent pre-training compute budgets.

cs.LG↗

arXiv2024

MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

q-bio.BM↗

arXiv2024

GraphMaker: Can Diffusion Models Generate Large Attributed Graphs?

Large-scale graphs with node attributes are increasingly common in various real-world applications. Creating synthetic, attribute-rich graphs that mirror real-world examples is crucial, especially for sharing graph data for analysis and developing learning models when original data is restricted to be shared. Traditional graph generation methods are limited in their capacity to handle these complex structures. Recent advances in diffusion models have shown potential in generating graph structures without attributes and smaller molecular graphs. However, these models face challenges in generating large attributed graphs due to the complex attribute-structure correlations and the large size of these graphs. This paper introduces a novel diffusion model, GraphMaker, specifically designed for generating large attributed graphs. We explore various combinations of node attribute and graph structure generation processes, finding that an asynchronous approach more effectively captures the intricate attribute-structure correlations. We also address scalability issues through edge mini-batching generation. To demonstrate the practicality of our approach in graph data dissemination, we introduce a new evaluation pipeline. The evaluation demonstrates that synthetic graphs generated by GraphMaker can be used to develop competitive graph machine learning models for the tasks defined over the original graphs without actually accessing these graphs, while many leading graph generation methods fall short in this evaluation.

cs.LG↗

arXiv2024

A Benchmark on Directed Graph Representation Learning in Hardware Designs

To keep pace with the rapid advancements in design complexity within modern computing systems, directed graph representation learning (DGRL) has become crucial, particularly for encoding circuit netlists, computational graphs, and developing surrogate models for hardware performance prediction. However, DGRL remains relatively unexplored, especially in the hardware domain, mainly due to the lack of comprehensive and user-friendly benchmarks. This study presents a novel benchmark comprising five hardware design datasets and 13 prediction tasks spanning various levels of circuit abstraction. We evaluate 21 DGRL models, employing diverse graph neural networks and graph transformers (GTs) as backbones, enhanced by positional encodings (PEs) tailored for directed graphs. Our results highlight that bidirected (BI) message passing neural networks (MPNNs) and robust PEs significantly enhance model performance. Notably, the top-performing models include PE-enhanced GTs interleaved with BI-MPNN layers and BI-Graph Isomorphism Network, both surpassing baselines across the 13 tasks. Additionally, our investigation into out-of-distribution (OOD) performance emphasizes the urgent need to improve OOD generalization in DGRL models. This benchmark, implemented with a modular codebase, streamlines the evaluation of DGRL models for both hardware and ML practitioners

cs.LG↗

arXiv2024

What Can We Learn from State Space Models for Machine Learning on Graphs?

Machine learning on graphs has recently found extensive applications across domains. However, the commonly used Message Passing Neural Networks (MPNNs) suffer from limited expressive power and struggle to capture long-range dependencies. Graph transformers offer a strong alternative due to their global attention mechanism, but they come with great computational overheads, especially for large graphs. In recent years, State Space Models (SSMs) have emerged as a compelling approach to replace full attention in transformers to model sequential data. It blends the strengths of RNNs and CNNs, offering a) efficient computation, b) the ability to capture long-range dependencies, and c) good generalization across sequences of various lengths. However, extending SSMs to graph-structured data presents unique challenges due to the lack of canonical node ordering in graphs. In this work, we propose Graph State Space Convolution (GSSC) as a principled extension of SSMs to graph-structured data. By leveraging global permutation-equivariant set aggregation and factorizable graph kernels that rely on relative node distances as the convolution kernels, GSSC preserves all three advantages of SSMs. We demonstrate the provably stronger expressiveness of GSSC than MPNNs in counting graph substructures and show its effectiveness across 11 real-world, widely used benchmark datasets. GSSC achieves the best results on 6 out of 11 datasets with all significant improvements compared to the state-of-the-art baselines and second-best results on the other 5 datasets. Our findings highlight the potential of GSSC as a powerful and scalable model for graph machine learning. Our code is available at https://github.com/Graph-COM/GSSC.

cs.LG↗

arXiv2024

Leveraging Inter-Chunk Interactions for Enhanced Retrieval in Large Language Model-Based Question Answering

Retrieving external knowledge and prompting large language models with relevant information is an effective paradigm to enhance the performance of question-answering tasks. Previous research typically handles paragraphs from external documents in isolation, resulting in a lack of context and ambiguous references, particularly in multi-document and complex tasks. To overcome these challenges, we propose a new retrieval framework IIER, that leverages Inter-chunk Interactions to Enhance Retrieval. This framework captures the internal connections between document chunks by considering three types of interactions: structural, keyword, and semantic. We then construct a unified Chunk-Interaction Graph to represent all external documents comprehensively. Additionally, we design a graph-based evidence chain retriever that utilizes previous paths and chunk interactions to guide the retrieval process. It identifies multiple seed nodes based on the target question and iteratively searches for relevant chunks to gather supporting evidence. This retrieval process refines the context and reasoning chain, aiding the large language model in reasoning and answer generation. Extensive experiments demonstrate that IIER outperforms strong baselines across four datasets, highlighting its effectiveness in improving retrieval and reasoning capabilities.

cs.CL↗

arXiv2024

High efficient 120W 1018nm single-frequency narrow linewidth amplification based on wide-tunable DBR fiber seed source

This paper reports the achievement of 120W single-frequency narrow linewidth 1018nm laser based on wide-tunable DBR fiber seed source. The DBR structure seed source uses 8mm long doped optical fibers with a line width of 3.25k. The wavelength tuning range of this seed source exceeds 1.5 nm with the temperature range from 1°C to 95°C. The tuning wavelength and temperature show extremely high linearity, and there is no mode hopping during the tuning process. By adopting a multi-level fiber amplification structure, selecting appropriate doped fibers and optimizing their length, an output power exceeding 120W of 1018nm laser has been achieved. Measurement results indicate that the slope efficiency of the main amplification 77.3%, with an amplified spontaneous emission (ASE) suppression ratio greater than 60 dB. he output linewidth is 10.3 kHz, and the beam quality factor M2 is less than 1.3.

physics.optics↗

arXiv2024

Towards Understanding Sensitive and Decisive Patterns in Explainable AI: A Case Study of Model Interpretation in Geometric Deep Learning

The interpretability of machine learning models has gained increasing attention, particularly in scientific domains where high precision and accountability are crucial. This research focuses on distinguishing between two critical data patterns -- sensitive patterns (model-related) and decisive patterns (task-related) -- which are commonly used as model interpretations but often lead to confusion. Specifically, this study compares the effectiveness of two main streams of interpretation methods: post-hoc methods and self-interpretable methods, in detecting these patterns. Recently, geometric deep learning (GDL) has shown superior predictive performance in various scientific applications, creating an urgent need for principled interpretation methods. Therefore, we conduct our study using several representative GDL applications as case studies. We evaluate thirteen interpretation methods applied to three major GDL backbone models, using four scientific datasets to assess how well these methods identify sensitive and decisive patterns. Our findings indicate that post-hoc methods tend to provide interpretations better aligned with sensitive patterns, whereas certain self-interpretable methods exhibit strong and stable performance in detecting decisive patterns. Additionally, our study offers valuable insights into improving the reliability of these interpretation methods. For example, ensembling post-hoc interpretations from multiple models trained on the same task can effectively uncover the task's decisive patterns.

cs.LG↗

arXiv2024

On the Stability of Expressive Positional Encodings for Graphs

Designing effective positional encodings for graphs is key to building powerful graph transformers and enhancing message-passing graph neural networks. Although widespread, using Laplacian eigenvectors as positional encodings faces two fundamental challenges: (1) \emph{Non-uniqueness}: there are many different eigendecompositions of the same Laplacian, and (2) \emph{Instability}: small perturbations to the Laplacian could result in completely different eigenspaces, leading to unpredictable changes in positional encoding. Despite many attempts to address non-uniqueness, most methods overlook stability, leading to poor generalization on unseen graph structures. We identify the cause of instability to be a ``hard partition'' of eigenspaces. Hence, we introduce Stable and Expressive Positional Encodings (SPE), an architecture for processing eigenvectors that uses eigenvalues to ``softly partition'' eigenspaces. SPE is the first architecture that is (1) provably stable, and (2) universally expressive for basis invariant functions whilst respecting all symmetries of eigenvectors. Besides guaranteed stability, we prove that SPE is at least as expressive as existing methods, and highly capable of counting graph structures. Finally, we evaluate the effectiveness of our method on molecular property prediction, and out-of-distribution generalization tasks, finding improved generalization compared to existing positional encoding methods. Our code is available at \url{https://github.com/Graph-COM/SPE}.

cs.LG↗