Benchmarking Large Language Models for Molecule Prediction Tasks

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.

EvolMPNN: Predicting Mutational Effect on Homologous Proteins by Evolution Encoding

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, 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 EvolMPNNcan 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.

Harnessing Large Language Models as Post-hoc Correctors

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 the challenging molecular predictions show that LlmCorr improves the performance of a number of models by up to 39%.

On the Robustness of Post-hoc GNN Explainers to Label Noise

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.

How Faithful are Self-Explainable GNNs?

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.

Tiny-PPG: A Lightweight Deep Neural Network for Real-Time Detection of Motion Artifacts in Photoplethysmogram Signals on Edge Devices

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 deep 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 87.8% 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.

Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey from Precision to Interpretability

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. A thorough review of related KaGML works, collected following a carefully designed search methodology, are organised 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.

"Double vaccinated, 5G boosted!": Learning Attitudes towards COVID-19 Vaccination from Social Media

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.

Simplifying Node Classification on Heterophilous Graphs with Compatible Label Propagation

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.