Training large language models (LLMs) is resource-intensive and expensive, making intellectual property (IP) protection essential. Most existing model fingerprint methods inject fingerprints into LLMs to protect model ownership. These methods create fingerprint pairs with weak semantic correlations, lacking the contextual coherence and semantic relatedness founded in normal question-answer (QA) pairs in LLMs. In this paper, we propose a Generation Revision Intervention (GRI) attack that can effectively exploit this flaw to erase fingerprints, highlighting the need for more secure model fingerprint methods. Thus, we propose a novel injected fingerprint paradigm called Implicit Fingerprints (ImF). ImF constructs fingerprint pairs with strong semantic correlations, disguising them as natural QA pairs within LLMs. This ensures the fingerprints are consistent with normal model behavior, making them indistinguishable and robust against detection and removal. Our experiment on multiple LLMs demonstrates that ImF retains high verification success rates under adversarial conditions, offering a reliable solution for protecting LLM ownership.

Fast screening of drug molecules based on the ligand binding affinity is an important step in the drug discovery pipeline. Graph neural fingerprint is a promising method for developing molecular docking surrogates with high throughput and great fidelity. In this study, we built a COVID-19 drug docking dataset of about 300,000 drug candidates on 23 coronavirus protein targets. With this dataset, we trained graph neural fingerprint docking models for high-throughput virtual COVID-19 drug screening. The graph neural fingerprint models yield high prediction accuracy on docking scores with the mean squared error lower than $0.21$ kcal/mol for most of the docking targets, showing significant improvement over conventional circular fingerprint methods. To make the neural fingerprints transferable for unknown targets, we also propose a transferable graph neural fingerprint method trained on multiple targets. With comparable accuracy to target-specific graph neural fingerprint models, the transferable model exhibits superb training and data efficiency. We highlight that the impact of this study extends beyond COVID-19 dataset, as our approach for fast virtual ligand screening can be easily adapted and integrated into a general machine learning-accelerated pipeline to battle future bio-threats.

Graph neural networks have become very popular for machine learning on molecules due to the expressive power of their learnt representations. However, molecular machine learning is a classically low-data regime and it isn't clear that graph neural networks can avoid overfitting in low-resource settings. In contrast, fingerprint methods are the traditional standard for low-data environments due to their reduced number of parameters and manually engineered features. In this work, we investigate whether graph neural networks are competitive in small data settings compared to the parametrically 'cheaper' alternative of fingerprint methods. When we find that they are not, we explore pretraining and the meta-learning method MAML (and variants FO-MAML and ANIL) for improving graph neural network performance by transfer learning from related tasks. We find that MAML and FO-MAML do enable the graph neural network to outperform models based on fingerprints, providing a path to using graph neural networks even in settings with severely restricted data availability. In contrast to previous work, we find ANIL performs worse that other meta-learning approaches in this molecule setting. Our results suggest two reasons: molecular machine learning tasks may require significant task-specific adaptation, and distribution shifts in test tasks relative to train tasks may contribute to worse ANIL performance.