Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular structures presents significant challenges. Two primary obstacles emerge: (1) the difficulty in designing a 3D line notation that ensures SE(3)-invariant atomic coordinates, and (2) the non-trivial task of tokenizing continuous coordinates for use in LMs, which inherently require discrete inputs. To address these challenges, we propose Mol-StrucTok, a novel method for tokenizing 3D molecular structures. Our approach comprises two key innovations: (1) We design a line notation for 3D molecules by extracting local atomic coordinates in a spherical coordinate system. This notation builds upon existing 2D line notations and remains agnostic to their specific forms, ensuring compatibility with various molecular representation schemes. (2) We employ a Vector Quantized Variational Autoencoder (VQ-VAE) to tokenize these coordinates, treating them as generation descriptors. To further enhance the representation, we incorporate neighborhood bond lengths and bond angles as understanding descriptors. Leveraging this tokenization framework, we train a GPT-2 style model for 3D molecular generation tasks. Results demonstrate strong performance with significantly faster generation speeds and competitive chemical stability compared to previous methods. Further, by integrating our learned discrete representations into Graphormer model for property prediction on QM9 dataset, Mol-StrucTok reveals consistent improvements across various molecular properties, underscoring the versatility and robustness of our approach.

Towards Generalist Prompting for Large Language Models by Mental Models

Large language models (LLMs) have demonstrated impressive performance on many tasks. However, to achieve optimal performance, specially designed prompting methods are still needed. These methods either rely on task-specific few-shot examples that require a certain level of domain knowledge, or are designed to be simple but only perform well on a few types of tasks. In this work, we attempt to introduce the concept of generalist prompting, which operates on the design principle of achieving optimal or near-optimal performance on a wide range of tasks while eliminating the need for manual selection and customization of prompts tailored to specific problems. Furthermore, we propose MeMo (Mental Models), an innovative prompting method that is simple-designed yet effectively fulfills the criteria of generalist prompting. MeMo distills the cores of various prompting methods into individual mental models and allows LLMs to autonomously select the most suitable mental models for the problem, achieving or being near to the state-of-the-art results on diverse tasks such as STEM, logical reasoning, and commonsense reasoning in zero-shot settings. We hope that the insights presented herein will stimulate further exploration of generalist prompting methods for LLMs.