Theoretical and Empirical Insights into the Origins of Degree Bias in Graph Neural Networks

Graph Neural Networks (GNNs) often perform better for high-degree nodes than low-degree nodes on node classification tasks. This degree bias can reinforce social marginalization by, e.g., sidelining authors of lowly-cited papers when predicting paper topics in citation networks. While researchers have proposed numerous hypotheses for why GNN degree bias occurs, we find via a survey of 38 degree bias papers that these hypotheses are often not rigorously validated, and can even be contradictory. Thus, we provide an analysis of the origins of degree bias in message-passing GNNs with different graph filters. We prove that high-degree test nodes tend to have a lower probability of misclassification regardless of how GNNs are trained. Moreover, we show that degree bias arises from a variety of factors that are associated with a node's degree (e.g., homophily of neighbors, diversity of neighbors). Furthermore, we show that during training, some GNNs may adjust their loss on low-degree nodes more slowly than on high-degree nodes; however, with sufficiently many epochs of training, message-passing GNNs can achieve their maximum possible training accuracy, which is not significantly limited by their expressive power. Throughout our analysis, we connect our findings to previously-proposed hypotheses for the origins of degree bias, supporting and unifying some while drawing doubt to others. We validate our theoretical findings on 8 common real-world networks, and based on our theoretical and empirical insights, describe a roadmap to alleviate degree bias.

Fast Inference of Removal-Based Node Influence

Graph neural networks (GNNs) are widely utilized to capture the information spreading patterns in graphs. While remarkable performance has been achieved, there is a new trending topic of evaluating node influence. We propose a new method of evaluating node influence, which measures the prediction change of a trained GNN model caused by removing a node. A real-world application is, "In the task of predicting Twitter accounts' polarity, had a particular account been removed, how would others' polarity change?". We use the GNN as a surrogate model whose prediction could simulate the change of nodes or edges caused by node removal. Our target is to obtain the influence score for every node, and a straightforward way is to alternately remove every node and apply the trained GNN on the modified graph to generate new predictions. It is reliable but time-consuming, so we need an efficient method. The related lines of work, such as graph adversarial attack and counterfactual explanation, cannot directly satisfy our needs, since their problem settings are different. We propose an efficient, intuitive, and effective method, NOde-Removal-based fAst GNN inference (NORA), which uses the gradient information to approximate the node-removal influence. It only costs one forward propagation and one backpropagation to approximate the influence score for all nodes. Extensive experiments on six datasets and six GNN models verify the effectiveness of NORA. Our code is available at https://github.com/weikai-li/NORA.git.

Causal Graph ODE: Continuous Treatment Effect Modeling in Multi-agent Dynamical Systems

Real-world multi-agent systems are often dynamic and continuous, where the agents co-evolve and undergo changes in their trajectories and interactions over time. For example, the COVID-19 transmission in the U.S. can be viewed as a multi-agent system, where states act as agents and daily population movements between them are interactions. Estimating the counterfactual outcomes in such systems enables accurate future predictions and effective decision-making, such as formulating COVID-19 policies. However, existing methods fail to model the continuous dynamic effects of treatments on the outcome, especially when multiple treatments (e.g., "stay-at-home" and "get-vaccine" policies) are applied simultaneously. To tackle this challenge, we propose Causal Graph Ordinary Differential Equations (CAG-ODE), a novel model that captures the continuous interaction among agents using a Graph Neural Network (GNN) as the ODE function. The key innovation of our model is to learn time-dependent representations of treatments and incorporate them into the ODE function, enabling precise predictions of potential outcomes. To mitigate confounding bias, we further propose two domain adversarial learning-based objectives, which enable our model to learn balanced continuous representations that are not affected by treatments or interference. Experiments on two datasets (i.e., COVID-19 and tumor growth) demonstrate the superior performance of our proposed model.

An Evaluation of Large Language Models in Bioinformatics Research

Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem solving. However, the potential and efficacy of these models in bioinformatics remain incompletely explored. In this work, we study the performance LLMs on a wide spectrum of crucial bioinformatics tasks. These tasks include the identification of potential coding regions, extraction of named entities for genes and proteins, detection of antimicrobial and anti-cancer peptides, molecular optimization, and resolution of educational bioinformatics problems. Our findings indicate that, given appropriate prompts, LLMs like GPT variants can successfully handle most of these tasks. In addition, we provide a thorough analysis of their limitations in the context of complicated bioinformatics tasks. In conclusion, we believe that this work can provide new perspectives and motivate future research in the field of LLMs applications, AI for Science and bioinformatics.

Structure Guided Prompt: Instructing Large Language Model in Multi-Step Reasoning by Exploring Graph Structure of the Text

Although Large Language Models (LLMs) excel at addressing straightforward reasoning tasks, they frequently struggle with difficulties when confronted by more complex multi-step reasoning due to a range of factors. Firstly, natural language often encompasses complex relationships among entities, making it challenging to maintain a clear reasoning chain over longer spans. Secondly, the abundance of linguistic diversity means that the same entities and relationships can be expressed using different terminologies and structures, complicating the task of identifying and establishing connections between multiple pieces of information. Graphs provide an effective solution to represent data rich in relational information and capture long-term dependencies among entities. To harness the potential of graphs, our paper introduces Structure Guided Prompt, an innovative three-stage task-agnostic prompting framework designed to improve the multi-step reasoning capabilities of LLMs in a zero-shot setting. This framework explicitly converts unstructured text into a graph via LLMs and instructs them to navigate this graph using task-specific strategies to formulate responses. By effectively organizing information and guiding navigation, it enables LLMs to provide more accurate and context-aware responses. Our experiments show that this framework significantly enhances the reasoning capabilities of LLMs, enabling them to excel in a broader spectrum of natural language scenarios.

Graph ODE with Factorized Prototypes for Modeling Complicated Interacting Dynamics

This paper studies the problem of modeling interacting dynamical systems, which is critical for understanding physical dynamics and biological processes. Recent research predominantly uses geometric graphs to represent these interactions, which are then captured by powerful graph neural networks (GNNs). However, predicting interacting dynamics in challenging scenarios such as out-of-distribution shift and complicated underlying rules remains unsolved. In this paper, we propose a new approach named Graph ODE with factorized prototypes (GOAT) to address the problem. The core of GOAT is to incorporate factorized prototypes from contextual knowledge into a continuous graph ODE framework. Specifically, GOAT employs representation disentanglement and system parameters to extract both object-level and system-level contexts from historical trajectories, which allows us to explicitly model their independent influence and thus enhances the generalization capability under system changes. Then, we integrate these disentangled latent representations into a graph ODE model, which determines a combination of various interacting prototypes for enhanced model expressivity. The entire model is optimized using an end-to-end variational inference framework to maximize the likelihood. Extensive experiments in both in-distribution and out-of-distribution settings validate the superiority of GOAT.

TANGO: Time-Reversal Latent GraphODE for Multi-Agent Dynamical Systems

Learning complex multi-agent system dynamics from data is crucial across many domains, such as in physical simulations and material modeling. Extended from purely data-driven approaches, existing physics-informed approaches such as Hamiltonian Neural Network strictly follow energy conservation law to introduce inductive bias, making their learning more sample efficiently. However, many real-world systems do not strictly conserve energy, such as spring systems with frictions. Recognizing this, we turn our attention to a broader physical principle: Time-Reversal Symmetry, which depicts that the dynamics of a system shall remain invariant when traversed back over time. It still helps to preserve energies for conservative systems and in the meanwhile, serves as a strong inductive bias for non-conservative, reversible systems. To inject such inductive bias, in this paper, we propose a simple-yet-effective self-supervised regularization term as a soft constraint that aligns the forward and backward trajectories predicted by a continuous graph neural network-based ordinary differential equation (GraphODE). It effectively imposes time-reversal symmetry to enable more accurate model predictions across a wider range of dynamical systems under classical mechanics. In addition, we further provide theoretical analysis to show that our regularization essentially minimizes higher-order Taylor expansion terms during the ODE integration steps, which enables our model to be more noise-tolerant and even applicable to irreversible systems. Experimental results on a variety of physical systems demonstrate the effectiveness of our proposed method. Particularly, it achieves an MSE improvement of 11.5 % on a challenging chaotic triple-pendulum systems.

Resprompt: Residual Connection Prompting Advances Multi-Step Reasoning in Large Language Models

Chain-of-thought (CoT) prompting, which offers step-by-step problem-solving rationales, has impressively unlocked the reasoning potential of large language models (LLMs). Yet, the standard CoT is less effective in problems demanding multiple reasoning steps. This limitation arises from the complex reasoning process in multi-step problems: later stages often depend on the results of several steps earlier, not just the results of the immediately preceding step. Such complexities suggest the reasoning process is naturally represented as a graph. The almost linear and straightforward structure of CoT prompting, however, struggles to capture this complex reasoning graph. To address this challenge, we propose Residual Connection Prompting (RESPROMPT), a new prompting strategy that advances multi-step reasoning in LLMs. Our key idea is to reconstruct the reasoning graph within prompts. We achieve this by integrating necessary connections-links present in the reasoning graph but missing in the linear CoT flow-into the prompts. Termed "residual connections", these links are pivotal in morphing the linear CoT structure into a graph representation, effectively capturing the complex reasoning graphs inherent in multi-step problems. We evaluate RESPROMPT on six benchmarks across three diverse domains: math, sequential, and commonsense reasoning. For the open-sourced LLaMA family of models, RESPROMPT yields a significant average reasoning accuracy improvement of 12.5% on LLaMA-65B and 6.8% on LLaMA2-70B. Breakdown analysis further highlights RESPROMPT particularly excels in complex multi-step reasoning: for questions demanding at least five reasoning steps, RESPROMPT outperforms the best CoT based benchmarks by a remarkable average improvement of 21.1% on LLaMA-65B and 14.3% on LLaMA2-70B. Through extensive ablation studies and analyses, we pinpoint how to most effectively build residual connections.

Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often overlook the flexible nature of molecules, which continuously interconvert across conformations via chemical bond rotations and minor vibrational perturbations. To better account for molecular flexibility, some recent works formulate MRL as an ensemble learning problem, focusing on explicitly learning from a set of conformer structures. However, most of these studies have limited datasets, tasks, and models. In this work, we introduce the first MoleculAR Conformer Ensemble Learning (MARCEL) benchmark to thoroughly evaluate the potential of learning on conformer ensembles and suggest promising research directions. MARCEL includes four datasets covering diverse molecule- and reaction-level properties of chemically diverse molecules including organocatalysts and transition-metal catalysts, extending beyond the scope of common GNN benchmarks that are confined to drug-like molecules. In addition, we conduct a comprehensive empirical study, which benchmarks representative 1D, 2D, and 3D molecular representation learning models, along with two strategies that explicitly incorporate conformer ensembles into 3D MRL models. Our findings reveal that direct learning from an accessible conformer space can improve performance on a variety of tasks and models.