AdaMR: Adaptable Molecular Representation for Unified Pre-training Strategy

• URL: http://arxiv.org/abs/2401.06166v2
• Date: Sat, 27 Apr 2024 13:28:02 GMT
• Title: AdaMR: Adaptable Molecular Representation for Unified Pre-training Strategy
• Authors: Yan Ding, Hao Cheng, Ziliang Ye, Ruyi Feng, Wei Tian, Peng Xie, Juan Zhang, Zhongze Gu,
• Abstract summary: We propose a new large-scale uniform pre-training strategy for small-molecule drugs, called Molecular Adjustable Representation (AdaMR) AdaMR utilizes a granularity-adjustable molecular encoding strategy, which is accomplished through a pre-training job termed molecular canonicalization. We fine-tuned our proposed pre-trained model on six molecular property prediction tasks and two generative tasks, achieving state-of-the-art (SOTA) results on five out of eight tasks.
• Score: 11.710702202071573
• License: http://creativecommons.org/licenses/by-sa/4.0/
• Abstract: We propose Adjustable Molecular Representation (AdaMR), a new large-scale uniform pre-training strategy for small-molecule drugs, as a novel unified pre-training strategy. AdaMR utilizes a granularity-adjustable molecular encoding strategy, which is accomplished through a pre-training job termed molecular canonicalization, setting it apart from recent large-scale molecular models. This adaptability in granularity enriches the model's learning capability at multiple levels and improves its performance in multi-task scenarios. Specifically, the substructure-level molecular representation preserves information about specific atom groups or arrangements, influencing chemical properties and functionalities. This proves advantageous for tasks such as property prediction. Simultaneously, the atomic-level representation, combined with generative molecular canonicalization pre-training tasks, enhances validity, novelty, and uniqueness in generative tasks. All of these features work together to give AdaMR outstanding performance on a range of downstream tasks. We fine-tuned our proposed pre-trained model on six molecular property prediction tasks (MoleculeNet datasets) and two generative tasks (ZINC250K datasets), achieving state-of-the-art (SOTA) results on five out of eight tasks.

Related papers

• Pre-trained Molecular Language Models with Random Functional Group Masking [54.900360309677794]
  We propose a SMILES-based underlineem Molecular underlineem Language underlineem Model, which randomly masking SMILES subsequences corresponding to specific molecular atoms. This technique aims to compel the model to better infer molecular structures and properties, thus enhancing its predictive capabilities.
  arXiv  Detail & Related papers  (2024-11-03T01:56:15Z)
• MultiModal-Learning for Predicting Molecular Properties: A Framework Based on Image and Graph Structures [2.5563339057415218]
  MolIG is a novel MultiModaL molecular pre-training framework for predicting molecular properties based on Image and Graph structures. It amalgamates the strengths of both molecular representation forms. It exhibits enhanced performance in downstream tasks pertaining to molecular property prediction within benchmark groups.
  arXiv  Detail & Related papers  (2023-11-28T10:28:35Z)
• Improving Molecular Properties Prediction Through Latent Space Fusion [9.912768918657354]
  We present a multi-view approach that combines latent spaces derived from state-of-the-art chemical models. Our approach relies on two pivotal elements: the embeddings derived from MHG-GNN, which represent molecular structures as graphs, and MoLFormer embeddings rooted in chemical language. We demonstrate the superior performance of our proposed multi-view approach compared to existing state-of-the-art methods.
  arXiv  Detail & Related papers  (2023-10-20T20:29:32Z)
• Atomic and Subgraph-aware Bilateral Aggregation for Molecular Representation Learning [57.670845619155195]
  We introduce a new model for molecular representation learning called the Atomic and Subgraph-aware Bilateral Aggregation (ASBA) ASBA addresses the limitations of previous atom-wise and subgraph-wise models by incorporating both types of information. Our method offers a more comprehensive way to learn representations for molecular property prediction and has broad potential in drug and material discovery applications.
  arXiv  Detail & Related papers  (2023-05-22T00:56:00Z)
• Implicit Geometry and Interaction Embeddings Improve Few-Shot Molecular Property Prediction [53.06671763877109]
  We develop molecular embeddings that encode complex molecular characteristics to improve the performance of few-shot molecular property prediction. Our approach leverages large amounts of synthetic data, namely the results of molecular docking calculations. On multiple molecular property prediction benchmarks, training from the embedding space substantially improves Multi-Task, MAML, and Prototypical Network few-shot learning performance.
  arXiv  Detail & Related papers  (2023-02-04T01:32:40Z)
• Supervised Pretraining for Molecular Force Fields and Properties Prediction [16.86839767858162]
  We propose to pretrain neural networks on a dataset of 86 millions of molecules with atom charges and 3D geometries as inputs and molecular energies as labels. Experiments show that, compared to training from scratch, fine-tuning the pretrained model can significantly improve the performance for seven molecular property prediction tasks and two force field tasks.
  arXiv  Detail & Related papers  (2022-11-23T08:36:50Z)
• Improving Molecular Pretraining with Complementary Featurizations [20.86159731100242]
  Molecular pretraining is a paradigm to solve a variety of tasks in computational chemistry and drug discovery. We show that different featurization techniques convey chemical information differently. We propose a simple and effective MOlecular pretraining framework with COmplementary featurizations (MOCO)
  arXiv  Detail & Related papers  (2022-09-29T21:11:09Z)
• Retrieval-based Controllable Molecule Generation [63.44583084888342]
  We propose a new retrieval-based framework for controllable molecule generation. We use a small set of molecules to steer the pre-trained generative model towards synthesizing molecules that satisfy the given design criteria. Our approach is agnostic to the choice of generative models and requires no task-specific fine-tuning.
  arXiv  Detail & Related papers  (2022-08-23T17:01:16Z)
• Molecular Attributes Transfer from Non-Parallel Data [57.010952598634944]
  We formulate molecular optimization as a style transfer problem and present a novel generative model that could automatically learn internal differences between two groups of non-parallel data. Experiments on two molecular optimization tasks, toxicity modification and synthesizability improvement, demonstrate that our model significantly outperforms several state-of-the-art methods.
  arXiv  Detail & Related papers  (2021-11-30T06:10:22Z)
• Few-Shot Graph Learning for Molecular Property Prediction [46.60746023179724]
  We propose Meta-MGNN, a novel model for few-shot molecular property prediction. To exploit unlabeled molecular information, Meta-MGNN further incorporates molecular structure, attribute based self-supervised modules and self-attentive task weights. Extensive experiments on two public multi-property datasets demonstrate that Meta-MGNN outperforms a variety of state-of-the-art methods.
  arXiv  Detail & Related papers  (2021-02-16T01:55:34Z)

This list is automatically generated from the titles and abstracts of the papers in this site.

This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.