相关论文: Pretraining Graph Transformers with Atom-in-a-Mole…

Computational screening in heterogeneous catalysis relies increasingly on machine learning models for predicting key input parameters due to the high cost of computing these directly using first-principles methods. This becomes especially…

Image-based profiling techniques have become increasingly popular over the past decade for their applications in target identification, mechanism-of-action inference, and assay development. These techniques have generated large datasets of…

Foundation models leverage large-scale pretraining to capture extensive knowledge, demonstrating generalization in a wide range of language tasks. By comparison, vision foundation models (VFMs) often exhibit uneven improvements across…

Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework…

Discovering gene-disease associations is crucial for understanding disease mechanisms, yet identifying these associations remains challenging due to the time and cost of biological experiments. Computational methods are increasingly vital…

Transformer-based models have improved predictive modeling on longitudinal electronic health records through large-scale self-supervised pretraining. However, most EHR transformer architectures treat each clinical encounter as an unordered…

Fine-tuning pre-trained transformers is a powerful technique for enhancing the performance of base models on specific tasks. From early applications in models like BERT to fine-tuning Large Language Models (LLMs), this approach has been…

We conduct a systematic study of the approximation properties of Transformer for sequence modeling with long, sparse and complicated memory. We investigate the mechanisms through which different components of Transformer, such as the…

Self-supervised learning has emerged as a powerful approach for leveraging large-scale unlabeled data to improve model performance in various domains. In this paper, we explore masked self-supervised pre-training for text recognition…

Pretraining on a large number of unlabeled 3D molecules has showcased superiority in various scientific applications. However, prior efforts typically focus on pretraining models in a specific domain, either proteins or small molecules,…

Molecular representation learning is fundamental for many drug related applications. Most existing molecular pre-training models are limited in using single molecular modality, either SMILES or graph representation. To effectively leverage…

Self-supervised pretraining attempts to enhance model performance by obtaining effective features from unlabeled data, and has demonstrated its effectiveness in the field of histopathology images. Despite its success, few works concentrate…

In this paper, we study how the intrinsic nature of pre-training data contributes to the fine-tuned downstream performance. To this end, we pre-train different transformer-based masked language models on several corpora with certain…

Molecular representation learning is crucial for the problem of molecular property prediction, where graph neural networks (GNNs) serve as an effective solution due to their structure modeling capabilities. Since labeled data is often…

Molecular property prediction is essential in chemistry, especially for drug discovery applications. However, available molecular property data is often limited, encouraging the transfer of information from related data. Transfer learning…

Quantum machine learning methods often rely on fixed, hand-crafted quantum encodings that may not capture optimal features for downstream tasks. In this work, we study the power of quantum autoencoders in learning data-driven quantum…

Foundation models have achieved remarkable success across diverse machine-learning domains through large-scale pretraining on large, diverse datasets. However, pretraining on such datasets introduces significant challenges due to…

Transformers are increasingly employed for graph data, demonstrating competitive performance in diverse tasks. To incorporate graph information into these models, it is essential to enhance node and edge features with positional encodings.…

Molecular representation learning has become a central approach in AI-driven drug discovery, yet existing molecular tokenizations such as SMILES remain largely syntactic and do not naturally align with chemically meaningful substructures.…

Pre-trained machine learning (ML) models have shown great performance for a wide range of applications, in particular in natural language processing (NLP) and computer vision (CV). Here, we study how pre-training could be used for…