arXiv subjects

Jia Li

Publications and source records attributed to Jia Li.

At least 361 records · Page 20Linked to original sources

arXiv2024

Data Imputation from the Perspective of Graph Dirichlet Energy

Data imputation is a crucial task due to the widespread occurrence of missing data. Many methods adopt a two-step approach: initially crafting a preliminary imputation (the "draft") and then refining it to produce the final missing data imputation result, commonly referred to as "draft-then-refine". In our study, we examine this prevalent strategy through the lens of graph Dirichlet energy. We observe that a basic "draft" imputation tends to decrease the Dirichlet energy. Therefore, a subsequent "refine" step is necessary to restore the overall energy balance. Existing refinement techniques, such as the Graph Convolutional Network (GCN), often result in further energy reduction. To address this, we introduce a new framework, the Graph Laplacian Pyramid Network (GLPN). GLPN incorporates a U-shaped autoencoder and residual networks to capture both global and local details effectively. Through extensive experiments on multiple real-world datasets, GLPN consistently outperforms state-of-the-art methods across three different missing data mechanisms. The code is available at https://github.com/liguanlue/GLPN.

cs.LG↗

arXiv2024

M2CVD: Enhancing Vulnerability Semantic through Multi-Model Collaboration for Code Vulnerability Detection

Large Language Models (LLMs) have strong capabilities in code comprehension, but fine-tuning costs and semantic alignment issues limit their project-specific optimization; conversely, code models such CodeBERT are easy to fine-tune, but it is often difficult to learn vulnerability semantics from complex code languages. To address these challenges, this paper introduces the Multi-Model Collaborative Vulnerability Detection approach (M2CVD) that leverages the strong capability of analyzing vulnerability semantics from LLMs to improve the detection accuracy of code models. M2CVD employs a novel collaborative process: first enhancing the quality of vulnerability semantic description produced by LLMs through the understanding of project code by code models, and then using these improved vulnerability semantic description to boost the detection accuracy of code models. We demonstrated M2CVD's effectiveness on two real-world datasets, where M2CVD significantly outperformed the baseline. In addition, we demonstrate that the M2CVD collaborative method can extend to other different LLMs and code models to improve their accuracy in vulnerability detection tasks.

cs.SE↗

arXiv2024

GraphWiz: An Instruction-Following Language Model for Graph Problems

Large language models (LLMs) have achieved impressive success across several fields, but their proficiency in understanding and resolving complex graph problems is less explored. To bridge this gap, we introduce GraphInstruct, a novel and comprehensive instruction-tuning dataset designed to equip language models with the ability to tackle a broad spectrum of graph problems using explicit reasoning paths. Utilizing GraphInstruct, we build GraphWiz, an open-source language model capable of resolving various graph problem types while generating clear reasoning processes. To enhance the model's capability and reliability, we incorporate the Direct Preference Optimization (DPO) framework into the graph problem-solving context. The enhanced model, GraphWiz-DPO, achieves an average accuracy of 65% across nine tasks with different complexity levels, surpassing GPT-4 which has an average accuracy of 43.8%. Moreover, our research delves into the delicate balance between training data volume and model performance, highlighting the potential for overfitting with increased data. We also explore the transferability of the model's reasoning ability across different graph tasks, indicating the model's adaptability and practical application potential. Our investigation offers a new blueprint and valuable insights for developing LLMs specialized in graph reasoning and problem-solving.

cs.CL↗

arXiv2024

Compress to Impress: Unleashing the Potential of Compressive Memory in Real-World Long-Term Conversations

Existing retrieval-based methods have made significant strides in maintaining long-term conversations. However, these approaches face challenges in memory database management and accurate memory retrieval, hindering their efficacy in dynamic, real-world interactions. This study introduces a novel framework, COmpressive Memory-Enhanced Dialogue sYstems (COMEDY), which eschews traditional retrieval modules and memory databases. Instead, COMEDY adopts a "One-for-All" approach, utilizing a single language model to manage memory generation, compression, and response generation. Central to this framework is the concept of compressive memory, which intergrates session-specific summaries, user-bot dynamics, and past events into a concise memory format. To support COMEDY, we curated a large-scale Chinese instruction-tuning dataset, Dolphin, derived from real user-chatbot interactions. Comparative evaluations demonstrate COMEDY's superiority over traditional retrieval-based methods in producing more nuanced and human-like conversational experiences. Our codes are available at https://github.com/nuochenpku/COMEDY.

cs.CL↗

arXiv2024

ZeroG: Investigating Cross-dataset Zero-shot Transferability in Graphs

With the development of foundation models such as large language models, zero-shot transfer learning has become increasingly significant. This is highlighted by the generative capabilities of NLP models like GPT-4, and the retrieval-based approaches of CV models like CLIP, both of which effectively bridge the gap between seen and unseen data. In the realm of graph learning, the continuous emergence of new graphs and the challenges of human labeling also amplify the necessity for zero-shot transfer learning, driving the exploration of approaches that can generalize across diverse graph data without necessitating dataset-specific and label-specific fine-tuning. In this study, we extend such paradigms to zero-shot transferability in graphs by introducing ZeroG, a new framework tailored to enable cross-dataset generalization. Addressing the inherent challenges such as feature misalignment, mismatched label spaces, and negative transfer, we leverage a language model to encode both node attributes and class semantics, ensuring consistent feature dimensions across datasets. We also propose a prompt-based subgraph sampling module that enriches the semantic information and structure information of extracted subgraphs using prompting nodes and neighborhood aggregation, respectively. We further adopt a lightweight fine-tuning strategy that reduces the risk of overfitting and maintains the zero-shot learning efficacy of the language model. The results underscore the effectiveness of our model in achieving significant cross-dataset zero-shot transferability, opening pathways for the development of graph foundation models. Codes and data are available at https://github.com/NineAbyss/ZeroG.

cs.LG↗

arXiv2024

Relaxing Continuous Constraints of Equivariant Graph Neural Networks for Physical Dynamics Learning

Incorporating Euclidean symmetries (e.g. rotation equivariance) as inductive biases into graph neural networks has improved their generalization ability and data efficiency in unbounded physical dynamics modeling. However, in various scientific and engineering applications, the symmetries of dynamics are frequently discrete due to the boundary conditions. Thus, existing GNNs either overlook necessary symmetry, resulting in suboptimal representation ability, or impose excessive equivariance, which fails to generalize to unobserved symmetric dynamics. In this work, we propose a general Discrete Equivariant Graph Neural Network (DEGNN) that guarantees equivariance to a given discrete point group. Specifically, we show that such discrete equivariant message passing could be constructed by transforming geometric features into permutation-invariant embeddings. Through relaxing continuous equivariant constraints, DEGNN can employ more geometric feature combinations to approximate unobserved physical object interaction functions. Two implementation approaches of DEGNN are proposed based on ranking or pooling permutation-invariant functions. We apply DEGNN to various physical dynamics, ranging from particle, molecular, crowd to vehicle dynamics. In twenty scenarios, DEGNN significantly outperforms existing state-of-the-art approaches. Moreover, we show that DEGNN is data efficient, learning with less data, and can generalize across scenarios such as unobserved orientation.

cs.LG↗

arXiv2024

All in One and One for All: A Simple yet Effective Method towards Cross-domain Graph Pretraining

Large Language Models (LLMs) have revolutionized the fields of computer vision (CV) and natural language processing (NLP). One of the most notable advancements of LLMs is that a single model is trained on vast and diverse datasets spanning multiple domains -- a paradigm we term `All in One'. This methodology empowers LLMs with super generalization capabilities, facilitating an encompassing comprehension of varied data distributions. Leveraging these capabilities, a single LLM demonstrates remarkable versatility across a variety of domains -- a paradigm we term `One for All'. However, applying this idea to the graph field remains a formidable challenge, with cross-domain pretraining often resulting in negative transfer. This issue is particularly important in few-shot learning scenarios, where the paucity of training data necessitates the incorporation of external knowledge sources. In response to this challenge, we propose a novel approach called Graph COordinators for PrEtraining (GCOPE), that harnesses the underlying commonalities across diverse graph datasets to enhance few-shot learning. Our novel methodology involves a unification framework that amalgamates disparate graph datasets during the pretraining phase to distill and transfer meaningful knowledge to target tasks. Extensive experiments across multiple graph datasets demonstrate the superior efficacy of our approach. By successfully leveraging the synergistic potential of multiple graph datasets for pretraining, our work stands as a pioneering contribution to the realm of graph foundational model.

cs.LG↗

arXiv2024

ProG: A Graph Prompt Learning Benchmark

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional 'Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

cs.LG↗

arXiv2024

SynthTree: Co-supervised Local Model Synthesis for Explainable Prediction

Explainable machine learning (XML) has emerged as a major challenge in artificial intelligence (AI). Although black-box models such as Deep Neural Networks and Gradient Boosting often exhibit exceptional predictive accuracy, their lack of interpretability is a notable drawback, particularly in domains requiring transparency and trust. This paper tackles this core AI problem by proposing a novel method to enhance explainability with minimal accuracy loss, using a Mixture of Linear Models (MLM) estimated under the co-supervision of black-box models. We have developed novel methods for estimating MLM by leveraging AI techniques. Specifically, we explore two approaches for partitioning the input space: agglomerative clustering and decision trees. The agglomerative clustering approach provides greater flexibility in model construction, while the decision tree approach further enhances explainability, yielding a decision tree model with linear or logistic regression models at its leaf nodes. Comparative analyses with widely-used and state-of-the-art predictive models demonstrate the effectiveness of our proposed methods. Experimental results show that statistical models can significantly enhance the explainability of AI, thereby broadening their potential for real-world applications. Our findings highlight the critical role that statistical methodologies can play in advancing explainable AI.

stat.ME↗

arXiv2024

A Lean Simulation Framework for Stress Testing IoT Cloud Systems

The Internet of Things connects a plethora of smart devices globally across various applications like smart cities, autonomous vehicles and health monitoring. Simulation plays a key role in the testing of IoT systems, noting that field testing of a complete IoT product may be infeasible or prohibitively expensive. This paper addresses a specific yet important need in simulation-based testing for IoT: Stress testing of cloud systems. Existing stress testing solutions for IoT demand significant computational resources, making them ill-suited and costly. We propose a lean simulation framework designed for IoT cloud stress testing which enables efficient simulation of a large array of IoT and edge devices that communicate with the cloud. To facilitate simulation construction for practitioners, we develop a domain-specific language (DSL), named IoTECS, for generating simulators from model-based specifications. We provide the syntax and semantics of IoTECS and implement IoTECS using Xtext and Xtend. We assess simulators generated from IoTECS specifications for stress testing two real-world systems: a cloud-based IoT monitoring system and an IoT-connected vehicle system. Our empirical results indicate that simulators created using IoTECS: (1)achieve best performance when configured with Docker containerization; (2)effectively assess the service capacity of our case-study systems, and (3)outperform industrial stress-testing baseline tools, JMeter and Locust, by a factor of 3.5 in terms of the number of IoT and edge devices they can simulate using identical hardware resources. To gain initial insights about the usefulness of IoTECS in practice, we interviewed two engineers from our industry partner who have firsthand experience with IoTECS. Feedback from these interviews suggests that IoTECS is effective in stress testing IoT cloud systems, saving significant time and effort.

cs.SE↗

arXiv2024

Towards Imbalanced Motion: Part-Decoupling Network for Video Portrait Segmentation

Video portrait segmentation (VPS), aiming at segmenting prominent foreground portraits from video frames, has received much attention in recent years. However, simplicity of existing VPS datasets leads to a limitation on extensive research of the task. In this work, we propose a new intricate large-scale Multi-scene Video Portrait Segmentation dataset MVPS consisting of 101 video clips in 7 scenario categories, in which 10,843 sampled frames are finely annotated at pixel level. The dataset has diverse scenes and complicated background environments, which is the most complex dataset in VPS to our best knowledge. Through the observation of a large number of videos with portraits during dataset construction, we find that due to the joint structure of human body, motion of portraits is part-associated, which leads that different parts are relatively independent in motion. That is, motion of different parts of the portraits is imbalanced. Towards this imbalance, an intuitive and reasonable idea is that different motion states in portraits can be better exploited by decoupling the portraits into parts. To achieve this, we propose a Part-Decoupling Network (PDNet) for video portrait segmentation. Specifically, an Inter-frame Part-Discriminated Attention (IPDA) module is proposed which unsupervisedly segments portrait into parts and utilizes different attentiveness on discriminative features specified to each different part. In this way, appropriate attention can be imposed to portrait parts with imbalanced motion to extract part-discriminated correlations, so that the portraits can be segmented more accurately. Experimental results demonstrate that our method achieves leading performance with the comparison to state-of-the-art methods.

cs.CV↗

arXiv2024

Text Guided Image Editing with Automatic Concept Locating and Forgetting

With the advancement of image-to-image diffusion models guided by text, significant progress has been made in image editing. However, a persistent challenge remains in seamlessly incorporating objects into images based on textual instructions, without relying on extra user-provided guidance. Text and images are inherently distinct modalities, bringing out difficulties in fully capturing the semantic intent conveyed through language and accurately translating that into the desired visual modifications. Therefore, text-guided image editing models often produce generations with residual object attributes that do not fully align with human expectations. To address this challenge, the models should comprehend the image content effectively away from a disconnect between the provided textual editing prompts and the actual modifications made to the image. In our paper, we propose a novel method called Locate and Forget (LaF), which effectively locates potential target concepts in the image for modification by comparing the syntactic trees of the target prompt and scene descriptions in the input image, intending to forget their existence clues in the generated image. Compared to the baselines, our method demonstrates its superiority in text-guided image editing tasks both qualitatively and quantitatively.

cs.CV↗

arXiv2024

DevEval: A Manually-Annotated Code Generation Benchmark Aligned with Real-World Code Repositories

How to evaluate the coding abilities of Large Language Models (LLMs) remains an open question. We find that existing benchmarks are poorly aligned with real-world code repositories and are insufficient to evaluate the coding abilities of LLMs. To address the knowledge gap, we propose a new benchmark named DevEval, which has three advances. (1) DevEval aligns with real-world repositories in multiple dimensions, e.g., code distributions and dependency distributions. (2) DevEval is annotated by 13 developers and contains comprehensive annotations (e.g., requirements, original repositories, reference code, and reference dependencies). (3) DevEval comprises 1,874 testing samples from 117 repositories, covering 10 popular domains (e.g., Internet, Database). Based on DevEval, we propose repository-level code generation and evaluate 8 popular LLMs on DevEval (e.g., gpt-4, gpt-3.5, StarCoder 2, DeepSeek Coder, CodeLLaMa). Our experiments reveal these LLMs' coding abilities in real-world code repositories. For example, in our experiments, the highest Pass@1 of gpt-4-turbo is only 53.04%. We also analyze LLMs' failed cases and summarize their shortcomings. We hope DevEval can facilitate the development of LLMs in real code repositories. DevEval, prompts, and LLMs' predictions have been released.

cs.CL↗

arXiv2024

One QuantLLM for ALL: Fine-tuning Quantized LLMs Once for Efficient Deployments

Large Language Models (LLMs) have advanced rapidly but face significant memory demands. While quantization has shown promise for LLMs, current methods typically require lengthy training to alleviate the performance degradation from quantization loss. However, deploying LLMs across diverse scenarios with different resource constraints, e.g., servers and personal computers, requires repeated training per application, which amplifies the lengthy training problem. Given that, it is advantageous to train a once-for-all (OFA) supernet capable of yielding diverse optimal subnets for downstream applications through one-shot training. Nonetheless, the scale of current language models impedes efficiency and amplifies interference from weight sharing between subnets. We make an initial attempt to extend the once-for-all framework to large language models. Specifically, we decouple shared weights to eliminate the interference and incorporate Low-Rank adapters for training efficiency. Furthermore, we observe the imbalance allocation of training resources from the traditional uniform sampling. A non-parametric scheduler is introduced to adjust the sampling rate for each quantization configuration, achieving a more balanced allocation among subnets with varying demands. We validate the approach on LLaMA2 families, and downstream evaluation confirms our ability to maintain high performance while significantly reducing deployment time faced with multiple scenarios.

cs.AI↗

arXiv2024

Data-driven Nucleus Subclassification on Colon H&E using Style-transferred Digital Pathology

Understanding the way cells communicate, co-locate, and interrelate is essential to furthering our understanding of how the body functions. H&E is widely available, however, cell subtyping often requires expert knowledge and the use of specialized stains. To reduce the annotation burden, AI has been proposed for the classification of cells on H&E. For example, the recent Colon Nucleus Identification and Classification (CoNIC) Challenge focused on labeling 6 cell types on H&E of the colon. However, the CoNIC Challenge was unable to classify epithelial subtypes (progenitor, enteroendocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), and connective subtypes (fibroblasts). We use inter-modality learning to label previously un-labelable cell types on H&E. We take advantage of multiplexed immunofluorescence (MxIF) histology to label 14 cell subclasses. We performed style transfer on the same MxIF tissues to synthesize realistic virtual H&E which we paired with the MxIF-derived cell subclassification labels. We evaluated the efficacy of using a supervised learning scheme where the input was realistic-quality virtual H&E and the labels were MxIF-derived cell subclasses. We assessed our model on private virtual H&E and public real H&E. On virtual H&E, we were able to classify helper T cells and epithelial progenitors with positive predictive values of $0.34 \pm 0.15$ (prevalence $0.03 \pm 0.01$) and $0.47 \pm 0.1$ (prevalence $0.07 \pm 0.02$) respectively, when using ground truth centroid information. On real H&E we could classify helper T cells and epithelial progenitors with upper bound positive predictive values of $0.43 \pm 0.03$ (parent class prevalence 0.21) and $0.94 \pm 0.02$ (parent class prevalence 0.49) when using ground truth centroid information. This is the first work to provide cell type classification for helper T and epithelial progenitor nuclei on H&E.

eess.IV↗

arXiv2024

Exploring and Unleashing the Power of Large Language Models in Automated Code Translation

Code translation tools (transpilers) are developed for automatic source-to-source translation. Although learning-based transpilers have shown impressive enhancement against rule-based counterparts, owing to their task-specific pre-training on extensive monolingual corpora. Their current performance still remains unsatisfactory for practical deployment, and the associated training resources are also prohibitively expensive. LLMs pre-trained on huge amounts of human-written code/text have shown remarkable performance in many code intelligence tasks due to their powerful generality, even without task-specific training. Thus, LLMs can potentially circumvent the above limitations, but they have not been exhaustively explored yet. This paper investigates diverse LLMs and learning-based transpilers for automated code translation tasks, finding that: although certain LLMs have outperformed current transpilers, they still have some accuracy issues, where most of the failures are induced by a lack of comprehension of source programs, missing clear instructions on I/O types in translation, and ignoring discrepancies between source and target programs. Enlightened by the above findings, we further propose UniTrans, a Unified code Translation framework, applicable to various LLMs, for unleashing their power in this field. Specifically, UniTrans first crafts a series of test cases for target programs with the assistance of source programs. Next, it harnesses the above auto-generated test cases to augment the code translation and then evaluate their correctness via execution. Afterward, UniTrans further (iteratively) repairs incorrectly translated programs prompted by test case execution results. Extensive experiments are conducted on six settings of translation datasets between Python, Java, and C++. Three recent LLMs of diverse sizes are tested with UniTrans, and all achieve substantial improvements.

cs.SE↗

arXiv2024

Deep Reinforcement Learning for Modelling Protein Complexes

AlphaFold can be used for both single-chain and multi-chain protein structure prediction, while the latter becomes extremely challenging as the number of chains increases. In this work, by taking each chain as a node and assembly actions as edges, we show that an acyclic undirected connected graph can be used to predict the structure of multi-chain protein complexes (a.k.a., protein complex modelling, PCM). However, there are still two challenges: 1) The huge combinatorial optimization space of $N^{N-2}$ ($N$ is the number of chains) for the PCM problem can easily lead to high computational cost. 2) The scales of protein complexes exhibit distribution shift due to variance in chain numbers, which calls for the generalization in modelling complexes of various scales. To address these challenges, we propose GAPN, a Generative Adversarial Policy Network powered by domain-specific rewards and adversarial loss through policy gradient for automatic PCM prediction. Specifically, GAPN learns to efficiently search through the immense assembly space and optimize the direct docking reward through policy gradient. Importantly, we design an adversarial reward function to enhance the receptive field of our model. In this way, GAPN will simultaneously focus on a specific batch of complexes and the global assembly rules learned from complexes with varied chain numbers. Empirically, we have achieved both significant accuracy (measured by RMSD and TM-Score) and efficiency improvements compared to leading PCM softwares.

cs.CE↗

arXiv2024

Parameter-Efficient Fine-Tuning with Discrete Fourier Transform

Low-rank adaptation~(LoRA) has recently gained much interest in fine-tuning foundation models. It effectively reduces the number of trainable parameters by incorporating low-rank matrices $A$ and $B$ to represent the weight change, i.e., $ΔW=BA$. Despite LoRA's progress, it faces storage challenges when handling extensive customization adaptations or larger base models. In this work, we aim to further compress trainable parameters by enjoying the powerful expressiveness of the Fourier transform. Specifically, we introduce FourierFT, which treats $ΔW$ as a matrix in the spatial domain and learns only a small fraction of its spectral coefficients. With the trained spectral coefficients, we implement the inverse discrete Fourier transform to recover $ΔW$. Empirically, our FourierFT method shows comparable or better performance with fewer parameters than LoRA on various tasks, including natural language understanding, natural language generation, instruction tuning, and image classification. For example, when performing instruction tuning on the LLaMA2-7B model, FourierFT surpasses LoRA with only 0.064M trainable parameters, compared to LoRA's 33.5M. Our code is released at \url{https://github.com/Chaos96/fourierft}.

cs.LG↗