Jianguo Lu

Shaghayegh Sadeghi, Alan Bui, Ali Forooghi et al.

Purpose: Large Language Models (LLMs) like GPT (Generative Pre-trained Transformer) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI are increasingly recognized for their potential in the field of cheminformatics, particularly in understanding Simplified Molecular Input Line Entry System (SMILES), a standard method for representing chemical structures. These LLMs also have the ability to decode SMILES strings into vector representations. Method: We investigate the performance of GPT and LLaMA compared to pre-trained models on SMILES in embedding SMILES strings on downstream tasks, focusing on two key applications: molecular property prediction and drug-drug interaction prediction. Results: We find that SMILES embeddings generated using LLaMA outperform those from GPT in both molecular property and DDI prediction tasks. Notably, LLaMA-based SMILES embeddings show results comparable to pre-trained models on SMILES in molecular prediction tasks and outperform the pre-trained models for the DDI prediction tasks. Conclusion: The performance of LLMs in generating SMILES embeddings shows great potential for further investigation of these models for molecular embedding. We hope our study bridges the gap between LLMs and molecular embedding, motivating additional research into the potential of LLMs in the molecular representation field. GitHub: https://github.com/sshaghayeghs/LLaMA-VS-GPT

Ali Forooghi, Shaghayegh Sadeghi, Jianguo Lu

Sentence embedding is a cornerstone in NLP. Whitening has been claimed to be an effective operation to improve embedding quality obtained from Large Language Models (LLMs). However, we find that the efficacy of whitening is model-dependent and task-dependent. In particular, whitening degenerates embeddings for classification tasks. The conclusion is supported by extensive experiments. We also explored a variety of whitening operations, including PCA, ZCA, PCA-Cor, ZCA-Cor and Cholesky whitenings. A by-product of our research is embedding evaluation platform for LLMs called SentEval+.

Haichao Cao, Hong Liu, Enmin Song et al.

An accurate segmentation of lung nodules in computed tomography (CT) images is critical to lung cancer analysis and diagnosis. However, due to the variety of lung nodules and the similarity of visual characteristics between nodules and their surroundings, a robust segmentation of nodules becomes a challenging problem. In this study, we propose the Dual-branch Residual Network (DB-ResNet) which is a data-driven model. Our approach integrates two new schemes to improve the generalization capability of the model: 1) the proposed model can simultaneously capture multi-view and multi-scale features of different nodules in CT images; 2) we combine the features of the intensity and the convolution neural networks (CNN). We propose a pooling method, called the central intensity-pooling layer (CIP), to extract the intensity features of the center voxel of the block, and then use the CNN to obtain the convolutional features of the center voxel of the block. In addition, we designed a weighted sampling strategy based on the boundary of nodules for the selection of those voxels using the weighting score, to increase the accuracy of the model. The proposed method has been extensively evaluated on the LIDC dataset containing 986 nodules. Experimental results show that the DB-ResNet achieves superior segmentation performance with an average dice score of 82.74% on the dataset. Moreover, we compared our results with those of four radiologists on the same dataset. The comparison showed that our average dice score was 0.49% higher than that of human experts. This proves that our proposed method is as good as the experienced radiologist.