PascalNotin commited on
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e750e94
1 Parent(s): ed68b5c

Fixed layout references

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  1. app.py +4 -4
app.py CHANGED
@@ -108,10 +108,10 @@ def score_and_create_matrix_all_singles(sequence,mutation_range_start=None,mutat
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  #######################################################################################################################################
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  title = "Interactive in silico directed evolution with Tranception"
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- description = "Perform in silico directed evolution with Tranception to iteratively improve the fitness of a starting protein sequence one mutation at a time. At each step, the Tranception model computes the log likelihood ratios of all possible single amino acid substitution Vs the starting sequence, and outputs a fitness heatmap and recommandations to guide the selection of the mutation to apply. Note: The current version does not currently leverage homologs retrieval at inference time to boost fitness prediction performance."
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- article = "<p style='text-align: left'>**Tranception: Protein Fitness Prediction with Autoregressive Transformers and Inference-time Retrieval**</p>"
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- article += "<br><p style='text-align: left'> Pascal Notin, Mafalda Dias, Jonathan Frazer, Javier Marchena-Hurtado, Aidan N. Gomez, Debora S. Marks<sup>*</sup>, Yarin Gal<sup>*</sup>"
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- article += "<br><p style='text-align: left'> <a href='https://proceedings.mlr.press/v162/notin22a.html' target='_blank'>Paper</a> *** <a href='https://github.com/OATML-Markslab/Tranception' target='_blank'>Code</a> </p>"
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  examples=[
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  ['ADRB2_HUMAN --> MGQPGNGSAFLLAPNGSHAPDHDVTQERDEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYANETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRSSLKAYGNGYSSNGNTGEQSGYHVEQEKENKLLCEDLPGTEDFVGHQGTVPSDNIDSQGRNCSTNDSLL', 1, 10, "Small", True],
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  ['IF1_ECOLI --> MAKEDNIEMQGTVLETLPNTMFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRSR', 1, None, "Medium", False],
 
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  #######################################################################################################################################
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  title = "Interactive in silico directed evolution with Tranception"
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+ description = "Perform in silico directed evolution with Tranception to iteratively improve the fitness of a starting protein sequence, one mutation at a time. At each step, the Tranception model computes the log likelihood ratios of all possible single amino acid substitution Vs the starting sequence, and outputs a fitness heatmap and recommandations to guide the selection of the mutation to apply. Note: The current version does not leverage retrieval of homologs at inference time to increase fitness prediction performance."
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+ article = "<p style='text-align: left'><b>Tranception: Protein Fitness Prediction with Autoregressive Transformers and Inference-time Retrieval</b></p>"
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+ article += "<p style='text-align: left'> Pascal Notin, Mafalda Dias, Jonathan Frazer, Javier Marchena-Hurtado, Aidan N. Gomez, Debora S. Marks<sup>*</sup>, Yarin Gal<sup>*</sup>"
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+ article += "<p style='text-align: left'> <a href='https://proceedings.mlr.press/v162/notin22a.html' target='_blank'>Paper</a> - <a href='https://github.com/OATML-Markslab/Tranception' target='_blank'>Code</a> </p>"
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  examples=[
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  ['ADRB2_HUMAN --> MGQPGNGSAFLLAPNGSHAPDHDVTQERDEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYANETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRSSLKAYGNGYSSNGNTGEQSGYHVEQEKENKLLCEDLPGTEDFVGHQGTVPSDNIDSQGRNCSTNDSLL', 1, 10, "Small", True],
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  ['IF1_ECOLI --> MAKEDNIEMQGTVLETLPNTMFRVELENGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRSR', 1, None, "Medium", False],