arXiv subjects

Meng Qu

Publications and source records attributed to Meng Qu.

At least 19 recordsLinked to original sources

arXiv2025

AdaCoT: Pareto-Optimal Adaptive Chain-of-Thought Triggering via Reinforcement Learning

Large Language Models (LLMs) have demonstrated remarkable capabilities but often face challenges with tasks requiring sophisticated reasoning. While Chain-of-Thought (CoT) prompting significantly enhances reasoning, it indiscriminately generates lengthy reasoning steps for all queries, leading to substantial computational costs and inefficiency, especially for simpler inputs. To address this critical issue, we introduce AdaCoT (Adaptive Chain-of-Thought), a novel framework enabling LLMs to adaptively decide when to invoke CoT. AdaCoT framed adaptive reasoning as a Pareto optimization problem that seeks to balance model performance with the costs associated with CoT invocation (both frequency and computational overhead). We propose a reinforcement learning (RL) based method, specifically utilizing Proximal Policy Optimization (PPO), to dynamically control the CoT triggering decision boundary by adjusting penalty coefficients, thereby allowing the model to determine CoT necessity based on implicit query complexity. A key technical contribution is Selective Loss Masking (SLM), designed to counteract decision boundary collapse during multi-stage RL training, ensuring robust and stable adaptive triggering. Experimental results demonstrate that AdaCoT successfully navigates the Pareto frontier, achieving substantial reductions in CoT usage for queries not requiring elaborate reasoning. For instance, on our production traffic testset, AdaCoT reduced CoT triggering rates to as low as 3.18\% and decreased average response tokens by 69.06%, while maintaining high performance on complex tasks.

cs.LG↗

arXiv2024

Risks of AI Scientists: Prioritizing Safeguarding Over Autonomy

AI scientists powered by large language models have demonstrated substantial promise in autonomously conducting experiments and facilitating scientific discoveries across various disciplines. While their capabilities are promising, these agents also introduce novel vulnerabilities that require careful consideration for safety. However, there has been limited comprehensive exploration of these vulnerabilities. This perspective examines vulnerabilities in AI scientists, shedding light on potential risks associated with their misuse, and emphasizing the need for safety measures. We begin by providing an overview of the potential risks inherent to AI scientists, taking into account user intent, the specific scientific domain, and their potential impact on the external environment. Then, we explore the underlying causes of these vulnerabilities and provide a scoping review of the limited existing works. Based on our analysis, we propose a triadic framework involving human regulation, agent alignment, and an understanding of environmental feedback (agent regulation) to mitigate these identified risks. Furthermore, we highlight the limitations and challenges associated with safeguarding AI scientists and advocate for the development of improved models, robust benchmarks, and comprehensive regulations.

cs.CY↗

arXiv2023

GraphText: Graph Reasoning in Text Space

Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both humans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.

cs.CL↗

arXiv2023

TGNN: A Joint Semi-supervised Framework for Graph-level Classification

This paper studies semi-supervised graph classification, a crucial task with a wide range of applications in social network analysis and bioinformatics. Recent works typically adopt graph neural networks to learn graph-level representations for classification, failing to explicitly leverage features derived from graph topology (e.g., paths). Moreover, when labeled data is scarce, these methods are far from satisfactory due to their insufficient topology exploration of unlabeled data. We address the challenge by proposing a novel semi-supervised framework called Twin Graph Neural Network (TGNN). To explore graph structural information from complementary views, our TGNN has a message passing module and a graph kernel module. To fully utilize unlabeled data, for each module, we calculate the similarity of each unlabeled graph to other labeled graphs in the memory bank and our consistency loss encourages consistency between two similarity distributions in different embedding spaces. The two twin modules collaborate with each other by exchanging instance similarity knowledge to fully explore the structure information of both labeled and unlabeled data. We evaluate our TGNN on various public datasets and show that it achieves strong performance.

cs.LG↗

arXiv2022

Learning on Large-scale Text-attributed Graphs via Variational Inference

This paper studies learning on text-attributed graphs (TAGs), where each node is associated with a text description. An ideal solution for such a problem would be integrating both the text and graph structure information with large language models and graph neural networks (GNNs). However, the problem becomes very challenging when graphs are large due to the high computational complexity brought by training large language models and GNNs together. In this paper, we propose an efficient and effective solution to learning on large text-attributed graphs by fusing graph structure and language learning with a variational Expectation-Maximization (EM) framework, called GLEM. Instead of simultaneously training large language models and GNNs on big graphs, GLEM proposes to alternatively update the two modules in the E-step and M-step. Such a procedure allows training the two modules separately while simultaneously allowing the two modules to interact and mutually enhance each other. Extensive experiments on multiple data sets demonstrate the efficiency and effectiveness of the proposed approach.

cs.LG↗

arXiv2022

KGNN: Harnessing Kernel-based Networks for Semi-supervised Graph Classification

This paper studies semi-supervised graph classification, which is an important problem with various applications in social network analysis and bioinformatics. This problem is typically solved by using graph neural networks (GNNs), which yet rely on a large number of labeled graphs for training and are unable to leverage unlabeled graphs. We address the limitations by proposing the Kernel-based Graph Neural Network (KGNN). A KGNN consists of a GNN-based network as well as a kernel-based network parameterized by a memory network. The GNN-based network performs classification through learning graph representations to implicitly capture the similarity between query graphs and labeled graphs, while the kernel-based network uses graph kernels to explicitly compare each query graph with all the labeled graphs stored in a memory for prediction. The two networks are motivated from complementary perspectives, and thus combing them allows KGNN to use labeled graphs more effectively. We jointly train the two networks by maximizing their agreement on unlabeled graphs via posterior regularization, so that the unlabeled graphs serve as a bridge to let both networks mutually enhance each other. Experiments on a range of well-known benchmark datasets demonstrate that KGNN achieves impressive performance over competitive baselines.

cs.LG↗

arXiv2022

Neural Structured Prediction for Inductive Node Classification

This paper studies node classification in the inductive setting, i.e., aiming to learn a model on labeled training graphs and generalize it to infer node labels on unlabeled test graphs. This problem has been extensively studied with graph neural networks (GNNs) by learning effective node representations, as well as traditional structured prediction methods for modeling the structured output of node labels, e.g., conditional random fields (CRFs). In this paper, we present a new approach called the Structured Proxy Network (SPN), which combines the advantages of both worlds. SPN defines flexible potential functions of CRFs with GNNs. However, learning such a model is nontrivial as it involves optimizing a maximin game with high-cost inference. Inspired by the underlying connection between joint and marginal distributions defined by Markov networks, we propose to solve an approximate version of the optimization problem as a proxy, which yields a near-optimal solution, making learning more efficient. Extensive experiments on two settings show that our approach outperforms many competitive baselines.

cs.LG↗

arXiv2022

Structured Multi-task Learning for Molecular Property Prediction

Multi-task learning for molecular property prediction is becoming increasingly important in drug discovery. However, in contrast to other domains, the performance of multi-task learning in drug discovery is still not satisfying as the number of labeled data for each task is too limited, which calls for additional data to complement the data scarcity. In this paper, we study multi-task learning for molecular property prediction in a novel setting, where a relation graph between tasks is available. We first construct a dataset (ChEMBL-STRING) including around 400 tasks as well as a task relation graph. Then to better utilize such relation graph, we propose a method called SGNN-EBM to systematically investigate the structured task modeling from two perspectives. (1) In the \emph{latent} space, we model the task representations by applying a state graph neural network (SGNN) on the relation graph. (2) In the \emph{output} space, we employ structured prediction with the energy-based model (EBM), which can be efficiently trained through noise-contrastive estimation (NCE) approach. Empirical results justify the effectiveness of SGNN-EBM. Code is available on https://github.com/chao1224/SGNN-EBM.

q-bio.BM↗

arXiv2022

TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery

Machine learning has huge potential to revolutionize the field of drug discovery and is attracting increasing attention in recent years. However, lacking domain knowledge (e.g., which tasks to work on), standard benchmarks and data preprocessing pipelines are the main obstacles for machine learning researchers to work in this domain. To facilitate the progress of machine learning for drug discovery, we develop TorchDrug, a powerful and flexible machine learning platform for drug discovery built on top of PyTorch. TorchDrug benchmarks a variety of important tasks in drug discovery, including molecular property prediction, pretrained molecular representations, de novo molecular design and optimization, retrosynthsis prediction, and biomedical knowledge graph reasoning. State-of-the-art techniques based on geometric deep learning (or graph machine learning), deep generative models, reinforcement learning and knowledge graph reasoning are implemented for these tasks. TorchDrug features a hierarchical interface that facilitates customization from both novices and experts in this domain. Tutorials, benchmark results and documentation are available at https://torchdrug.ai. Code is released under Apache License 2.0.

cs.LG↗

arXiv2020

COVI-AgentSim: an Agent-based Model for Evaluating Methods of Digital Contact Tracing

The rapid global spread of COVID-19 has led to an unprecedented demand for effective methods to mitigate the spread of the disease, and various digital contact tracing (DCT) methods have emerged as a component of the solution. In order to make informed public health choices, there is a need for tools which allow evaluation and comparison of DCT methods. We introduce an agent-based compartmental simulator we call COVI-AgentSim, integrating detailed consideration of virology, disease progression, social contact networks, and mobility patterns, based on parameters derived from empirical research. We verify by comparing to real data that COVI-AgentSim is able to reproduce realistic COVID-19 spread dynamics, and perform a sensitivity analysis to verify that the relative performance of contact tracing methods are consistent across a range of settings. We use COVI-AgentSim to perform cost-benefit analyses comparing no DCT to: 1) standard binary contact tracing (BCT) that assigns binary recommendations based on binary test results; and 2) a rule-based method for feature-based contact tracing (FCT) that assigns a graded level of recommendation based on diverse individual features. We find all DCT methods consistently reduce the spread of the disease, and that the advantage of FCT over BCT is maintained over a wide range of adoption rates. Feature-based methods of contact tracing avert more disability-adjusted life years (DALYs) per socioeconomic cost (measured by productive hours lost). Our results suggest any DCT method can help save lives, support re-opening of economies, and prevent second-wave outbreaks, and that FCT methods are a promising direction for enriching BCT using self-reported symptoms, yielding earlier warning signals and a significantly reduced spread of the virus per socioeconomic cost.

cs.CY↗

arXiv2020

Predicting Infectiousness for Proactive Contact Tracing

The COVID-19 pandemic has spread rapidly worldwide, overwhelming manual contact tracing in many countries and resulting in widespread lockdowns for emergency containment. Large-scale digital contact tracing (DCT) has emerged as a potential solution to resume economic and social activity while minimizing spread of the virus. Various DCT methods have been proposed, each making trade-offs between privacy, mobility restrictions, and public health. The most common approach, binary contact tracing (BCT), models infection as a binary event, informed only by an individual's test results, with corresponding binary recommendations that either all or none of the individual's contacts quarantine. BCT ignores the inherent uncertainty in contacts and the infection process, which could be used to tailor messaging to high-risk individuals, and prompt proactive testing or earlier warnings. It also does not make use of observations such as symptoms or pre-existing medical conditions, which could be used to make more accurate infectiousness predictions. In this paper, we use a recently-proposed COVID-19 epidemiological simulator to develop and test methods that can be deployed to a smartphone to locally and proactively predict an individual's infectiousness (risk of infecting others) based on their contact history and other information, while respecting strong privacy constraints. Predictions are used to provide personalized recommendations to the individual via an app, as well as to send anonymized messages to the individual's contacts, who use this information to better predict their own infectiousness, an approach we call proactive contact tracing (PCT). We find a deep-learning based PCT method which improves over BCT for equivalent average mobility, suggesting PCT could help in safe re-opening and second-wave prevention.

cs.LG↗

arXiv2020

RNNLogic: Learning Logic Rules for Reasoning on Knowledge Graphs

This paper studies learning logic rules for reasoning on knowledge graphs. Logic rules provide interpretable explanations when used for prediction as well as being able to generalize to other tasks, and hence are critical to learn. Existing methods either suffer from the problem of searching in a large search space (e.g., neural logic programming) or ineffective optimization due to sparse rewards (e.g., techniques based on reinforcement learning). To address these limitations, this paper proposes a probabilistic model called RNNLogic. RNNLogic treats logic rules as a latent variable, and simultaneously trains a rule generator as well as a reasoning predictor with logic rules. We develop an EM-based algorithm for optimization. In each iteration, the reasoning predictor is first updated to explore some generated logic rules for reasoning. Then in the E-step, we select a set of high-quality rules from all generated rules with both the rule generator and reasoning predictor via posterior inference; and in the M-step, the rule generator is updated with the rules selected in the E-step. Experiments on four datasets prove the effectiveness of RNNLogic.

cs.AI↗

arXiv2020

Few-shot Relation Extraction via Bayesian Meta-learning on Relation Graphs

This paper studies few-shot relation extraction, which aims at predicting the relation for a pair of entities in a sentence by training with a few labeled examples in each relation. To more effectively generalize to new relations, in this paper we study the relationships between different relations and propose to leverage a global relation graph. We propose a novel Bayesian meta-learning approach to effectively learn the posterior distribution of the prototype vectors of relations, where the initial prior of the prototype vectors is parameterized with a graph neural network on the global relation graph. Moreover, to effectively optimize the posterior distribution of the prototype vectors, we propose to use the stochastic gradient Langevin dynamics, which is related to the MAML algorithm but is able to handle the uncertainty of the prototype vectors. The whole framework can be effectively and efficiently optimized in an end-to-end fashion. Experiments on two benchmark datasets prove the effectiveness of our proposed approach against competitive baselines in both the few-shot and zero-shot settings.

cs.LG↗

arXiv2020

Graph Policy Network for Transferable Active Learning on Graphs

Graph neural networks (GNNs) have been attracting increasing popularity due to their simplicity and effectiveness in a variety of fields. However, a large number of labeled data is generally required to train these networks, which could be very expensive to obtain in some domains. In this paper, we study active learning for GNNs, i.e., how to efficiently label the nodes on a graph to reduce the annotation cost of training GNNs. We formulate the problem as a sequential decision process on graphs and train a GNN-based policy network with reinforcement learning to learn the optimal query strategy. By jointly training on several source graphs with full labels, we learn a transferable active learning policy which can directly generalize to unlabeled target graphs. Experimental results on multiple datasets from different domains prove the effectiveness of the learned policy in promoting active learning performance in both settings of transferring between graphs in the same domain and across different domains.

cs.LG↗

arXiv2020

COVI White Paper

The SARS-CoV-2 (Covid-19) pandemic has caused significant strain on public health institutions around the world. Contact tracing is an essential tool to change the course of the Covid-19 pandemic. Manual contact tracing of Covid-19 cases has significant challenges that limit the ability of public health authorities to minimize community infections. Personalized peer-to-peer contact tracing through the use of mobile apps has the potential to shift the paradigm. Some countries have deployed centralized tracking systems, but more privacy-protecting decentralized systems offer much of the same benefit without concentrating data in the hands of a state authority or for-profit corporations. Machine learning methods can circumvent some of the limitations of standard digital tracing by incorporating many clues and their uncertainty into a more graded and precise estimation of infection risk. The estimated risk can provide early risk awareness, personalized recommendations and relevant information to the user. Finally, non-identifying risk data can inform epidemiological models trained jointly with the machine learning predictor. These models can provide statistical evidence for the importance of factors involved in disease transmission. They can also be used to monitor, evaluate and optimize health policy and (de)confinement scenarios according to medical and economic productivity indicators. However, such a strategy based on mobile apps and machine learning should proactively mitigate potential ethical and privacy risks, which could have substantial impacts on society (not only impacts on health but also impacts such as stigmatization and abuse of personal data). Here, we present an overview of the rationale, design, ethical considerations and privacy strategy of `COVI,' a Covid-19 public peer-to-peer contact tracing and risk awareness mobile application developed in Canada.

cs.CR↗

arXiv2019

Continuous Graph Neural Networks

This paper builds on the connection between graph neural networks and traditional dynamical systems. We propose continuous graph neural networks (CGNN), which generalise existing graph neural networks with discrete dynamics in that they can be viewed as a specific discretisation scheme. The key idea is how to characterise the continuous dynamics of node representations, i.e. the derivatives of node representations, w.r.t. time. Inspired by existing diffusion-based methods on graphs (e.g. PageRank and epidemic models on social networks), we define the derivatives as a combination of the current node representations, the representations of neighbors, and the initial values of the nodes. We propose and analyse two possible dynamics on graphs---including each dimension of node representations (a.k.a. the feature channel) change independently or interact with each other---both with theoretical justification. The proposed continuous graph neural networks are robust to over-smoothing and hence allow us to build deeper networks, which in turn are able to capture the long-range dependencies between nodes. Experimental results on the task of node classification demonstrate the effectiveness of our proposed approach over competitive baselines.

cs.LG↗

arXiv2019

GraphMix: Improved Training of GNNs for Semi-Supervised Learning

We present GraphMix, a regularization method for Graph Neural Network based semi-supervised object classification, whereby we propose to train a fully-connected network jointly with the graph neural network via parameter sharing and interpolation-based regularization. Further, we provide a theoretical analysis of how GraphMix improves the generalization bounds of the underlying graph neural network, without making any assumptions about the "aggregation" layer or the depth of the graph neural networks. We experimentally validate this analysis by applying GraphMix to various architectures such as Graph Convolutional Networks, Graph Attention Networks and Graph-U-Net. Despite its simplicity, we demonstrate that GraphMix can consistently improve or closely match state-of-the-art performance using even simpler architectures such as Graph Convolutional Networks, across three established graph benchmarks: Cora, Citeseer and Pubmed citation network datasets, as well as three newly proposed datasets: Cora-Full, Co-author-CS and Co-author-Physics.

cs.LG↗

arXiv2019

Collaborative Policy Learning for Open Knowledge Graph Reasoning

In recent years, there has been a surge of interests in interpretable graph reasoning methods. However, these models often suffer from limited performance when working on sparse and incomplete graphs, due to the lack of evidential paths that can reach target entities. Here we study open knowledge graph reasoning---a task that aims to reason for missing facts over a graph augmented by a background text corpus. A key challenge of the task is to filter out "irrelevant" facts extracted from corpus, in order to maintain an effective search space during path inference. We propose a novel reinforcement learning framework to train two collaborative agents jointly, i.e., a multi-hop graph reasoner and a fact extractor. The fact extraction agent generates fact triples from corpora to enrich the graph on the fly; while the reasoning agent provides feedback to the fact extractor and guides it towards promoting facts that are helpful for the interpretable reasoning. Experiments on two public datasets demonstrate the effectiveness of the proposed approach. Source code and datasets used in this paper can be downloaded at https://github.com/shanzhenren/CPL

cs.AI↗