{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/tsis-a-supplementary-algorithm-to-t-smiles","title":"Hierarchical Structure Enhances the Convergence and Generalizability of Linear Molecular Representation","arxiv_id":"2402.02164","date":"2024-02-03","proceeding":null,"authors":["Juan-Ni Wu","Tong Wang","Li-Juan Tang","Hai-Long Wu","Ru-Qin Yu"],"abstract":"Language models demonstrate fundamental abilities in syntax, semantics, and reasoning, though their performance often depends significantly on the inputs they process. This study introduces TSIS (Simplified TSID) and its variants:TSISD (TSIS with Depth-First Search), TSISO (TSIS in Order), and TSISR (TSIS in Random), as integral components of the t-SMILES framework. These additions complete the framework's design, providing diverse approaches to molecular representation. Through comprehensive analysis and experiments employing deep generative models, including GPT, diffusion models, and reinforcement learning, the findings reveal that the hierarchical structure of t-SMILES is more straightforward to parse than initially anticipated. Furthermore, t-SMILES consistently outperforms other linear representations such as SMILES, SELFIES, and SAFE, demonstrating superior convergence speed and enhanced generalization capabilities.","url_abs":"https://arxiv.org/abs/2402.02164v4","url_pdf":"https://arxiv.org/pdf/2402.02164v4.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"tsis-a-supplementary-algorithm-to-t-smiles","repo_url":"https://github.com/juanniwu/t-smiles","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"molecular-representation","task_name":"molecular representation"}],"methods":[{"method_slug":"absolute-position-encodings","method_name":"Absolute Position Encodings"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"attention-dropout","method_name":"Attention Dropout"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"cosine-annealing","method_name":"Cosine Annealing"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"diffusion","method_name":"Diffusion"},{"method_slug":"discriminative-fine-tuning","method_name":"Discriminative Fine-Tuning"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"gpt","method_name":"GPT"},{"method_slug":"lstm","method_name":"LSTM"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"linear-warmup-with-cosine-annealing","method_name":"Linear Warmup With Cosine Annealing"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"position-wise-feed-forward-layer","method_name":"Position-Wise Feed-Forward Layer"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"speed","method_name":"SPEED"},{"method_slug":"sigmoid-activation","method_name":"Sigmoid Activation"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"tanh-activation","method_name":"Tanh Activation"},{"method_slug":"transformer","method_name":"Transformer"},{"method_slug":"weight-decay","method_name":"Weight Decay"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}