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.

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.

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.

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.

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.

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.

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.

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.

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.

Graph Neural Networks (GNNs) have been increasingly deployed in a multitude of different applications that involve node-wise and graph-level tasks. The existing literature usually studies these questions independently while they are inherently correlated. We propose in this work a unified model, Adaptive Multi-grained GNN (AdamGNN), to learn node and graph level representation interactively. Compared with the existing GNN models and pooling methods, AdamGNN enhances node representation with multi-grained semantics and avoids node feature and graph structure information loss during pooling. More specifically, a differentiable pooling operator in AdamGNN is used to obtain a multi-grained structure that involves node-wise and meso/macro level semantic information. The unpooling and flyback aggregators in AdamGNN is to leverage the multi-grained semantics to enhance node representation. The updated node representation can further enrich the generated graph representation in the next iteration. Experimental results on twelve real-world graphs demonstrate the effectiveness of AdamGNN on multiple tasks, compared with several competing methods. In addition, the ablation and empirical studies confirm the effectiveness of different components in AdamGNN.