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Empirical Evidence for the Fragment level Understanding on Drug Molecular Structure of LLMs
Jan 15, 2024
AI for drug discovery has been a research hotspot in recent years, and SMILES-based language models has been increasingly applied in drug molecular design. However, no work has explored whether and how language models understand the chemical spatial structure from 1D sequences. In this work, we pre-train a transformer model on chemical language and fine-tune it toward drug design objectives, and investigate the correspondence between high-frequency SMILES substrings and molecular fragments. The results indicate that language models can understand chemical structures from the perspective of molecular fragments, and the structural knowledge learned through fine-tuning is reflected in the high-frequency SMILES substrings generated by the model.
De novo Drug Design using Reinforcement Learning with Multiple GPT Agents
Dec 21, 2023De novo drug design is a pivotal issue in pharmacology and a new area of focus in AI for science research. A central challenge in this field is to generate molecules with specific properties while also producing a wide range of diverse candidates. Although advanced technologies such as transformer models and reinforcement learning have been applied in drug design, their potential has not been fully realized. Therefore, we propose MolRL-MGPT, a reinforcement learning algorithm with multiple GPT agents for drug molecular generation. To promote molecular diversity, we encourage the agents to collaborate in searching for desirable molecules in diverse directions. Our algorithm has shown promising results on the GuacaMol benchmark and exhibits efficacy in designing inhibitors against SARS-CoV-2 protein targets. The codes are available at: https://github.com/HXYfighter/MolRL-MGPT.
SS-SAM : Stochastic Scheduled Sharpness-Aware Minimization for Efficiently Training Deep Neural Networks
Mar 18, 2022
By driving optimizers to converge to flat minima, sharpness-aware minimization (SAM) has shown the power to improve the model generalization. However, SAM requires to perform two forward-backward propagations for one parameter update, which largely burdens the practical computation. In this paper, we propose a novel and efficient training scheme, called Stochastic Scheduled SAM (SS-SAM). Specifically, in SS-SAM, the optimizer is arranged by a predefined scheduling function to perform a random trial at each update step, which would randomly select to perform the SGD optimization or the SAM optimization. In this way, the overall count of propagation pair could be largely reduced. Then, we empirically investigate four typical types of scheduling functions, and demonstrates the computational efficiency and their impact on model performance respectively. We show that with proper scheduling functions, models could be trained to achieve comparable or even better performance with much lower computation cost compared to models trained with only SAM training scheme.
Penalizing Gradient Norm for Efficiently Improving Generalization in Deep Learning
Feb 08, 2022
How to train deep neural networks (DNNs) to generalize well is a central concern in deep learning, especially for severely overparameterized networks nowadays. In this paper, we propose an effective method to improve the model generalization by additionally penalizing the gradient norm of loss function during optimization. We demonstrate that confining the gradient norm of loss function could help lead the optimizers towards finding flat minima. We leverage the first-order approximation to efficiently implement the corresponding gradient to fit well in the gradient descent framework. In our experiments, we confirm that when using our methods, generalization performance of various models could be improved on different datasets. Also, we show that the recent sharpness-aware minimization method \cite{DBLP:conf/iclr/ForetKMN21} is a special, but not the best, case of our method, where the best case of our method could give new state-of-art performance on these tasks.