Zhiqiang Zhong

Zhiqiang Zhong, Anastasia Barkova, Davide Mottin

The integration of Artificial Intelligence (AI) into the field of drug discovery has been a growing area of interdisciplinary scientific research. However, conventional AI models are heavily limited in handling complex biomedical structures (such as 2D or 3D protein and molecule structures) and providing interpretations for outputs, which hinders their practical application. As of late, Graph Machine Learning (GML) has gained considerable attention for its exceptional ability to model graph-structured biomedical data and investigate their properties and functional relationships. Despite extensive efforts, GML methods still suffer from several deficiencies, such as the limited ability to handle supervision sparsity and provide interpretability in learning and inference processes, and their ineffectiveness in utilising relevant domain knowledge. In response, recent studies have proposed integrating external biomedical knowledge into the GML pipeline to realise more precise and interpretable drug discovery with limited training instances. However, a systematic definition for this burgeoning research direction is yet to be established. This survey presents a comprehensive overview of long-standing drug discovery principles, provides the foundational concepts and cutting-edge techniques for graph-structured data and knowledge databases, and formally summarises Knowledge-augmented Graph Machine Learning (KaGML) for drug discovery. we propose a thorough review of related KaGML works, collected following a carefully designed search methodology, and organise them into four categories following a novel-defined taxonomy. To facilitate research in this promptly emerging field, we also share collected practical resources that are valuable for intelligent drug discovery and provide an in-depth discussion of the potential avenues for future advancements.

Marc Christiansen, Lea Villadsen, Zhiqiang Zhong et al.

Self-explainable deep neural networks are a recent class of models that can output ante-hoc local explanations that are faithful to the model's reasoning, and as such represent a step forward toward filling the gap between expressiveness and interpretability. Self-explainable graph neural networks (GNNs) aim at achieving the same in the context of graph data. This begs the question: do these models fulfill their implicit guarantees in terms of faithfulness? In this extended abstract, we analyze the faithfulness of several self-explainable GNNs using different measures of faithfulness, identify several limitations -- both in the models themselves and in the evaluation metrics -- and outline possible ways forward.

Zhiqiang Zhong, Guadalupe Gonzalez, Daniele Grattarola et al.

Network embedding (NE) approaches have emerged as a predominant technique to represent complex networks and have benefited numerous tasks. However, most NE approaches rely on a homophily assumption to learn embeddings with the guidance of supervisory signals, leaving the unsupervised heterophilous scenario relatively unexplored. This problem becomes especially relevant in fields where a scarcity of labels exists. Here, we formulate the unsupervised NE task as an r-ego network discrimination problem and develop the SELENE framework for learning on networks with homophily and heterophily. Specifically, we design a dual-channel feature embedding pipeline to discriminate r-ego networks using node attributes and structural information separately. We employ heterophily adapted self-supervised learning objective functions to optimise the framework to learn intrinsic node embeddings. We show that SELENE's components improve the quality of node embeddings, facilitating the discrimination of connected heterophilous nodes. Comprehensive empirical evaluations on both synthetic and real-world datasets with varying homophily ratios validate the effectiveness of SELENE in homophilous and heterophilous settings showing an up to 12.52% clustering accuracy gain.

Zhiqiang Zhong, Sergey Ivanov, Jun Pang

Graph Neural Networks (GNNs) have been predominant for graph learning tasks; however, recent studies showed that a well-known graph algorithm, Label Propagation (LP), combined with a shallow neural network can achieve comparable performance to GNNs in semi-supervised node classification on graphs with high homophily. In this paper, we show that this approach falls short on graphs with low homophily, where nodes often connect to the nodes of the opposite classes. To overcome this, we carefully design a combination of a base predictor with LP algorithm that enjoys a closed-form solution as well as convergence guarantees. Our algorithm first learns the class compatibility matrix and then aggregates label predictions using LP algorithm weighted by class compatibilities. On a wide variety of benchmarks, we show that our approach achieves the leading performance on graphs with various levels of homophily. Meanwhile, it has orders of magnitude fewer parameters and requires less execution time. Empirical evaluations demonstrate that simple adaptations of LP can be competitive in semi-supervised node classification in both homophily and heterophily regimes.

Zhiqiang Zhong, Kuangyu Zhou, Davide Mottin

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

Ninghan Chen, Xihui Chen, Zhiqiang Zhong et al.

To address the vaccine hesitancy which impairs the efforts of the COVID-19 vaccination campaign, it is imperative to understand public vaccination attitudes and timely grasp their changes. In spite of reliability and trustworthiness, conventional attitude collection based on surveys is time-consuming and expensive, and cannot follow the fast evolution of vaccination attitudes. We leverage the textual posts on social media to extract and track users' vaccination stances in near real time by proposing a deep learning framework. To address the impact of linguistic features such as sarcasm and irony commonly used in vaccine-related discourses, we integrate into the framework the recent posts of a user's social network neighbours to help detect the user's genuine attitude. Based on our annotated dataset from Twitter, the models instantiated from our framework can increase the performance of attitude extraction by up to 23% compared to state-of-the-art text-only models. Using this framework, we successfully validate the feasibility of using social media to track the evolution of vaccination attitudes in real life. We further show one practical use of our framework by validating the possibility to forecast a user's vaccine hesitancy changes with information perceived from social media.

Zhiqiang Zhong, Davide Mottin

Predicting protein properties is paramount for biological and medical advancements. Current protein engineering mutates on a typical protein, called the wild-type, to construct a family of homologous proteins and study their properties. Yet, existing methods easily neglect subtle mutations, failing to capture the effect on the protein properties. To this end, we propose EvolMPNN, Evolution-aware Message Passing Neural Network, an efficient model to learn evolution-aware protein embeddings. EvolMPNN samples sets of anchor proteins, computes evolutionary information by means of residues and employs a differentiable evolution-aware aggregation scheme over these sampled anchors. This way, EvolMPNN can efficiently utilise a novel message-passing method to capture the mutation effect on proteins with respect to the anchor proteins. Afterwards, the aggregated evolution-aware embeddings are integrated with sequence embeddings to generate final comprehensive protein embeddings. Our model shows up to 6.4% better than state-of-the-art methods and attains 36X inference speedup in comparison with large pre-trained models. Code and models are available at https://github.com/zhiqiangzhongddu/EvolMPNN.

Zhiqiang Zhong, Yangqianzi Jiang, Davide Mottin

Proposed as a solution to the inherent black-box limitations of graph neural networks (GNNs), post-hoc GNN explainers aim to provide precise and insightful explanations of the behaviours exhibited by trained GNNs. Despite their recent notable advancements in academic and industrial contexts, the robustness of post-hoc GNN explainers remains unexplored when confronted with label noise. To bridge this gap, we conduct a systematic empirical investigation to evaluate the efficacy of diverse post-hoc GNN explainers under varying degrees of label noise. Our results reveal several key insights: Firstly, post-hoc GNN explainers are susceptible to label perturbations. Secondly, even minor levels of label noise, inconsequential to GNN performance, harm the quality of generated explanations substantially. Lastly, we engage in a discourse regarding the progressive recovery of explanation effectiveness with escalating noise levels.

Zhiqiang Zhong, Davide Mottin

Large Language Models (LLMs) have shown remarkable capabilities in processing various data structures, including graphs. While previous research has focused on developing textual encoding methods for graph representation, the emergence of multimodal LLMs presents a new frontier for graph comprehension. These advanced models, capable of processing both text and images, offer potential improvements in graph understanding by incorporating visual representations alongside traditional textual data. This study investigates the impact of graph visualisations on LLM performance across a range of benchmark tasks at node, edge, and graph levels. Our experiments compare the effectiveness of multimodal approaches against purely textual graph representations. The results provide valuable insights into both the potential and limitations of leveraging visual graph modalities to enhance LLMs' graph structure comprehension abilities.

Zhiqiang Zhong, Kuangyu Zhou, Davide Mottin

As Machine Learning (ML) models grow in size and demand higher-quality training data, the expenses associated with re-training and fine-tuning these models are escalating rapidly. Inspired by recent impressive achievements of Large Language Models (LLMs) in different fields, this paper delves into the question: can LLMs efficiently improve an ML's performance at a minimal cost? We show that, through our proposed training-free framework LlmCorr, an LLM can work as a post-hoc corrector to propose corrections for the predictions of an arbitrary ML model. In particular, we form a contextual knowledge database by incorporating the dataset's label information and the ML model's predictions on the validation dataset. Leveraging the in-context learning capability of LLMs, we ask the LLM to summarise the instances in which the ML model makes mistakes and the correlation between primary predictions and true labels. Following this, the LLM can transfer its acquired knowledge to suggest corrections for the ML model's predictions. Our experimental results on text analysis and the challenging molecular predictions show that \model improves the performance of a number of models by up to 39%.

Benjamin Kiefer, Lojze Žust, Jon Muhovič et al.

The 3rd Workshop on Maritime Computer Vision (MaCVi) 2025 addresses maritime computer vision for Unmanned Surface Vehicles (USV) and underwater. This report offers a comprehensive overview of the findings from the challenges. We provide both statistical and qualitative analyses, evaluating trends from over 700 submissions. All datasets, evaluation code, and the leaderboard are available to the public at https://macvi.org/workshop/macvi25.

Zahra Hashemi, Zhiqiang Zhong, Jun Pang et al.

The rapid evolution of large language models (LLMs) has fuelled enthusiasm about their role in advancing scientific discovery, with studies exploring LLMs that autonomously generate and evaluate novel research ideas. However, little attention has been given to the possibility that such models could be exploited to produce harmful research by repurposing open science artefacts for malicious ends. We fill the gap by introducing an end-to-end pipeline that first bypasses LLM safeguards through persuasion-based jailbreaking, then reinterprets NLP papers to identify and repurpose their artefacts (datasets, methods, and tools) by exploiting their vulnerabilities, and finally assesses the safety of these proposals using our evaluation framework across three dimensions: harmfulness, feasibility of misuse, and soundness of technicality. Overall, our findings demonstrate that LLMs can generate harmful proposals by repurposing ethically designed open artefacts; however, we find that LLMs acting as evaluators strongly disagree with one another on evaluation outcomes: GPT-4.1 assigns higher scores (indicating greater potential harms, higher soundness and feasibility of misuse), Gemini-2.5-pro is markedly stricter, and Grok-3 falls between these extremes. This indicates that LLMs cannot yet serve as reliable judges in a malicious evaluation setup, making human evaluation essential for credible dual-use risk assessment.

Zhiqiang Zhong, Simon Sataa-Yu Larsen, Haoyu Guo et al.

Recent advancements in AI for biological research focus on integrating molecular data with natural language to accelerate drug discovery. However, the scarcity of high-quality annotations limits progress in this area. This paper introduces LA$^3$, a Language-based Automatic Annotation Augmentation framework that leverages large language models to augment existing datasets, thereby improving AI training. We demonstrate the effectiveness of LA$^3$ by creating an enhanced dataset, LaChEBI-20, where we systematically rewrite the annotations of molecules from an established dataset. These rewritten annotations preserve essential molecular information while providing more varied sentence structures and vocabulary. Using LaChEBI-20, we train LaMolT5 based on a benchmark architecture to learn the mapping between molecular representations and augmented annotations. Experimental results on text-based *de novo* molecule generation and molecule captioning demonstrate that LaMolT5 outperforms state-of-the-art models. Notably, incorporating LA$^3$ leads to improvements of up to 301% over the benchmark architecture. Furthermore, we validate the effectiveness of LA$^3$ notable applications in *image*, *text* and *graph* tasks, affirming its versatility and utility.

Xinger Li, Zhiqiang Zhong, Bo Huang et al.

This paper is the first-place solution for ICASSP MEIJU@2025 Track I, which focuses on low-resource multimodal emotion and intention recognition. How to effectively utilize a large amount of unlabeled data, while ensuring the mutual promotion of different difficulty levels tasks in the interaction stage, these two points become the key to the competition. In this paper, pseudo-label labeling is carried out on the model trained with labeled data, and samples with high confidence and their labels are selected to alleviate the problem of low resources. At the same time, the characteristic of easy represented ability of intention recognition found in the experiment is used to make mutually promote with emotion recognition under different attention heads, and higher performance of intention recognition is achieved through fusion. Finally, under the refined processing data, we achieve the score of 0.5532 in the Test set, and win the championship of the track.

Zhiqiang Zhong, Yang Yang, Fengqiang Wan et al.

This report presents our method for Single Object Tracking (SOT), which aims to track a specified object throughout a video sequence. We employ the LoRAT method. The essence of the work lies in adapting LoRA, a technique that fine-tunes a small subset of model parameters without adding inference latency, to the domain of visual tracking. We train our model using the extensive LaSOT and GOT-10k datasets, which provide a solid foundation for robust performance. Additionally, we implement the alpha-refine technique for post-processing the bounding box outputs. Although the alpha-refine method does not yield the anticipated results, our overall approach achieves a score of 0.813, securing first place in the competition.

Yali Zheng, Chen Wu, Peizheng Cai et al.

Photoplethysmogram (PPG) signals are easily contaminated by motion artifacts in real-world settings, despite their widespread use in Internet-of-Things (IoT) based wearable and smart health devices for cardiovascular health monitoring. This study proposed a lightweight deep neural network, called Tiny-PPG, for accurate and real-time PPG artifact segmentation on IoT edge devices. The model was trained and tested on a public dataset, PPG DaLiA, which featured complex artifacts with diverse lengths and morphologies during various daily activities of 15 subjects using a watch-type device (Empatica E4). The model structure, training method and loss function were specifically designed to balance detection accuracy and speed for real-time PPG artifact detection in resource-constrained embedded devices. To optimize the model size and capability in multi-scale feature representation, the model employed depth-wise separable convolution and atrous spatial pyramid pooling modules, respectively. Additionally, the contrastive loss was also utilized to further optimize the feature embeddings. With additional model pruning, Tiny-PPG achieved state-of-the-art detection accuracy of 87.4% while only having 19,726 model parameters (0.15 megabytes), and was successfully deployed on an STM32 embedded system for real-time PPG artifact detection. Therefore, this study provides an effective solution for resource-constraint IoT smart health devices in PPG artifact detection.

Zhiqiang Zhong, Cheng-Te Li, Jun Pang

Recently, increasing attention has been paid to heterogeneous graph representation learning (HGRL), which aims to embed rich structural and semantic information in heterogeneous information networks (HINs) into low-dimensional node representations. To date, most HGRL models rely on hand-crafted meta-paths. However, the dependency on manually-defined meta-paths requires domain knowledge, which is difficult to obtain for complex HINs. More importantly, the pre-defined or generated meta-paths of all existing HGRL methods attached to each node type or node pair cannot be personalised to each individual node. To fully unleash the power of HGRL, we present a novel framework, Personalised Meta-path based Heterogeneous Graph Neural Networks (PM-HGNN), to jointly generate meta-paths that are personalised for each individual node in a HIN and learn node representations for the target downstream task like node classification. Precisely, PM-HGNN treats the meta-path generation as a Markov Decision Process and utilises a policy network to adaptively generate a meta-path for each individual node and simultaneously learn effective node representations. The policy network is trained with deep reinforcement learning by exploiting the performance improvement on a downstream task. We further propose an extension, PM-HGNN++, to better encode relational structure and accelerate the training during the meta-path generation. Experimental results reveal that both PM-HGNN and PM-HGNN++ can significantly and consistently outperform 16 competing baselines and state-of-the-art methods in various settings of node classification. Qualitative analysis also shows that PM-HGNN++ can identify meaningful meta-paths overlooked by human knowledge.

Zhiqiang Zhong, Cheng-Te Li, Jun Pang

Graph Neural Networks (GNNs) are powerful techniques in representation learning for graphs and have been increasingly deployed in a multitude of different applications that involve node- and graph-wise tasks. Most existing studies solve either the node-wise task or the graph-wise task independently while they are inherently correlated. This work proposes a unified model, AdamGNN, to interactively learn node and graph representations in a mutual-optimisation manner. Compared with existing GNN models and graph pooling methods, AdamGNN enhances the node representation with the learned multi-grained semantics and avoids losing node features and graph structure information during pooling. Specifically, a differentiable pooling operator is proposed to adaptively generate a multi-grained structure that involves meso- and macro-level semantic information in the graph. We also devise the unpooling operator and the flyback aggregator in AdamGNN to better leverage the multi-grained semantics to enhance node representations. The updated node representations can further adjust the graph representation in the next iteration. Experiments on 14 real-world graph datasets show that AdamGNN can significantly outperform 17 competing models on both node- and graph-wise tasks. The ablation studies confirm the effectiveness of AdamGNN's components, and the last empirical analysis further reveals the ingenious ability of AdamGNN in capturing long-range interactions.

Zhiqiang Zhong, Cheng-Te Li, Jun Pang

Graph Neural Networks (GNNs) have become a prominent approach to machine learning with graphs and have been increasingly applied in a multitude of domains. Nevertheless, since most existing GNN models are based on flat message-passing mechanisms, two limitations need to be tackled: (i) they are costly in encoding long-range information spanning the graph structure; (ii) they are failing to encode features in the high-order neighbourhood in the graphs as they only perform information aggregation across the observed edges in the original graph. To deal with these two issues, we propose a novel Hierarchical Message-passing Graph Neural Networks framework. The key idea is generating a hierarchical structure that re-organises all nodes in a flat graph into multi-level super graphs, along with innovative intra- and inter-level propagation manners. The derived hierarchy creates shortcuts connecting far-away nodes so that informative long-range interactions can be efficiently accessed via message passing and incorporates meso- and macro-level semantics into the learned node representations. We present the first model to implement this framework, termed Hierarchical Community-aware Graph Neural Network (HC-GNN), with the assistance of a hierarchical community detection algorithm. The theoretical analysis illustrates HC-GNN's remarkable capacity in capturing long-range information without introducing heavy additional computation complexity. Empirical experiments conducted on 9 datasets under transductive, inductive, and few-shot settings exhibit that HC-GNN can outperform state-of-the-art GNN models in network analysis tasks, including node classification, link prediction, and community detection. Moreover, the model analysis further demonstrates HC-GNN's robustness facing graph sparsity and the flexibility in incorporating different GNN encoders.

Ninghan Chen, Zhiqiang Zhong, Jun Pang

The outbreak of the COVID-19 leads to a burst of information in major online social networks (OSNs). Facing this constantly changing situation, OSNs have become an essential platform for people expressing opinions and seeking up-to-the-minute information. Thus, discussions on OSNs may become a reflection of reality. This paper aims to figure out the distinctive characteristics of the Greater Region (GR) through conducting a data-driven exploratory study of Twitter COVID-19 information in the GR and related countries using machine learning and representation learning methods. We find that tweets volume and COVID-19 cases in GR and related countries are correlated, but this correlation only exists in a particular period of the pandemic. Moreover, we plot the changing of topics in each country and region from 2020-01-22 to 2020-06-05, figuring out the main differences between GR and related countries.