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Chemical language models (CLMs) \u2013 which generate molecules in the form of molecular strings \u2013 bear particular promise for this endeavor. Here, we introduce a recent deep learning architecture, termed Structured State-Space Sequence (S4) model, into de novo drug design. In addition to its unprecedented performance in various fields, S4 has a remarkable capability to capture the global properties of long sequences. This aspect is key for chemical language modeling, where complex molecular properties like bioactivity can 'emerge' from distant positions in the molecular strings. This observation gives rise to the following question: Can S4 advance chemical language modeling for de novo design? To provide an answer, we systematically benchmark S4 with state-of-the-art CLMs on an array of drug discovery tasks, such as the identification of bioactive compounds, and the design of drug-like molecules and natural products. S4 showed a superior capacity to learn complex molecular properties, while at the same time exploring diverse scaffolds. Finally, when applied prospectively to kinase inhibition, S4 designed eight of out ten molecules that were predicted as highly active by molecular dynamics simulations. Taken together, these findings advocate for the introduction of S4 into chemical language modeling -- uncovering its untapped potential in the molecular sciences.<\/jats:p>","DOI":"10.26434\/chemrxiv-2023-jwmf3-v2","type":"posted-content","created":{"date-parts":[[2024,1,25]],"date-time":"2024-01-25T04:14:40Z","timestamp":1706156080000},"source":"Crossref","is-referenced-by-count":2,"title":["Chemical Language Modeling with Structured State Spaces"],"prefix":"10.26434","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4052-9721","authenticated-orcid":false,"given":"R\u0131za","family":"\u00d6z\u00e7elik","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02c2kyt77","id-type":"ROR","asserted-by":"publisher"}],"name":"Eindhoven University of Technology","place":["Netherlands"]},{"name":"Centre for Living Technologies, Alliance TU\/e, WUR, UU, UMC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"de Ruiter","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02c2kyt77","id-type":"ROR","asserted-by":"publisher"}],"name":"Eindhoven University of Technology","place":["Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emanuele","family":"Criscuolo","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02c2kyt77","id-type":"ROR","asserted-by":"publisher"}],"name":"Eindhoven University of Technology","place":["Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Grisoni","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02c2kyt77","id-type":"ROR","asserted-by":"publisher"}],"name":"Eindhoven University of Technology","place":["Netherlands"]},{"name":"Centre for Living Technologies, Alliance TU\/e, WUR, UU, UMC"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","link":[{"URL":"https:\/\/chemrxiv.org\/doi\/pdf\/10.26434\/chemrxiv-2023-jwmf3-v2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T10:22:05Z","timestamp":1778754125000},"score":29.057632,"resource":{"primary":{"URL":"https:\/\/chemrxiv.org\/doi\/full\/10.26434\/chemrxiv-2023-jwmf3-v2"}},"issued":{"date-parts":[[2024,1,25]]},"references-count":0,"URL":"https:\/\/doi.org\/10.26434\/chemrxiv-2023-jwmf3-v2","published":{"date-parts":[[2024,1,25]]},"subtype":"preprint"},{"indexed":{"date-parts":[[2026,10,25]],"date-time":"2026-10-25T20:05:05Z","timestamp":1792958705640,"version":"4.5.0"},"reference-count":27,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/ieeexplore.ieee.org\/Xplorehelp\/downloads\/license-information\/IEEE.html"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"}],"funder":[{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["21DZ2203100"],"award-info":[{"award-number":["21DZ2203100"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62006150"],"award-info":[{"award-number":["62006150"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE Signal Process. 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Here we report a novel method\n                  <jats:bold>H<\/jats:bold>\n                  ighly\n                  <jats:bold>E<\/jats:bold>\n                  fficient\n                  <jats:bold>R<\/jats:bold>\n                  epeat\n                  <jats:bold>A<\/jats:bold>\n                  ssembly (HERA), which includes a new concept called a connection graph as well as algorithms for constructing the graph. HERA resolves repeats at high efficiency with single-molecule sequencing data, and enables the assembly of chromosome-scale contigs by further integrating genome maps and Hi-C data. We tested HERA with the genomes of rice R498, maize B73, human HX1 and Tartary buckwheat Pinku1. HERA can correctly assemble most of the tandemly repetitive sequences in rice using single-molecule sequencing data only. Using the same maize and human sequencing data published by Jiao\n                  <jats:italic>et al.<\/jats:italic>\n                  (2017) and Shi\n                  <jats:italic>et al.<\/jats:italic>\n                  (2016), respectively, we dramatically improved on the sequence contiguity compared with the published assemblies, increasing the contig N50 from 1.3 Mb to 61.2 Mb in maize B73 assembly and from 8.3 Mb to 54.4 Mb in human HX1 assembly with HERA. We provided a high-quality maize reference genome with 96.9% of the gaps filled (only 76 gaps left) and several incorrectly positioned sequences fixed compared with the B73 RefGen_v4 assembly. Comparisons between the HERA assembly of HX1 and the human GRCh38 reference genome showed that many gaps in GRCh38 could be filled, and that GRCh38 contained some potential errors that could be fixed. We assembled the Pinku1 genome into 12 scaffolds with a contig N50 size of 27.85 Mb. HERA serves as a new genome assembly\/phasing method to generate high quality sequences for complex genomes and as a curation tool to improve the contiguity and completeness of existing reference genomes, including the correction of assembly errors in repetitive regions.\n                <\/jats:p>","DOI":"10.1101\/345983","type":"posted-content","created":{"date-parts":[[2018,6,13]],"date-time":"2018-06-13T12:25:47Z","timestamp":1528892747000},"source":"Crossref","is-referenced-by-count":3,"title":["Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads"],"prefix":"10.64898","author":[{"given":"Huilong","family":"Du","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengzhi","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2019071913095605000_345983v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3367"},{"key":"2019071913095605000_345983v1.2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1162986"},{"key":"2019071913095605000_345983v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3290"},{"key":"2019071913095605000_345983v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms12065"},{"key":"2019071913095605000_345983v1.5","doi-asserted-by":"crossref","first-page":"15324","DOI":"10.1038\/ncomms15324","article-title":"Sequencing and de novo assembly of a near complete indica rice genome","volume":"8","year":"2017","journal-title":"Nat Commun"},{"key":"2019071913095605000_345983v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/nature22971"},{"key":"2019071913095605000_345983v1.7","doi-asserted-by":"publisher","DOI":"10.1126\/science.1072047"},{"key":"2019071913095605000_345983v1.8","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti1114"},{"key":"2019071913095605000_345983v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4035"},{"key":"2019071913095605000_345983v1.10","doi-asserted-by":"publisher","DOI":"10.1126\/science.287.5461.2196"},{"key":"2019071913095605000_345983v1.11","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.1995.2.275"},{"key":"2019071913095605000_345983v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3238"},{"key":"2019071913095605000_345983v1.13","doi-asserted-by":"publisher","DOI":"10.1101\/gr.215087.116"},{"key":"2019071913095605000_345983v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4432"},{"key":"2019071913095605000_345983v1.15","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2727"},{"key":"2019071913095605000_345983v1.16","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2303"},{"key":"2019071913095605000_345983v1.17","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1016\/j.molp.2017.08.013","article-title":"The Tartary Buckwheat Genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance","volume":"10","year":"2017","journal-title":"Mol. 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