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pathway_prediction_in_batch_mode

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pathway_prediction_in_batch_mode [2025/04/29 09:05] – shankarpathway_prediction_in_batch_mode [2025/05/22 09:53] (current) – shankar
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-  * **Input file**: A .tsv file containing SMILES strings and compound names,** without a header**. A template input file can be downloaded [[https://drive.switch.ch/index.php/s/ZGxStHlMTITB7ys|here]]. There is an upper limit of **250 compounds per file**. If your input file contains more than 250 compounds, please split it into smaller batches before running the predictions.+  * **Input file**: A .tsv file containing SMILES strings and compound names,** without a header**. A **template input file** can be downloaded [[https://drive.switch.ch/index.php/s/ZGxStHlMTITB7ys|here]]. There is an upper limit of **250 compounds per file**. If your input file contains more than 250 compounds, please split it into smaller batches before running the predictions.
   * **Relative Reasoning model**: The relative reasoning model that will be used for the predictions. A default model is pre-selected, but users can     also choose a different model if preferred.   * **Relative Reasoning model**: The relative reasoning model that will be used for the predictions. A default model is pre-selected, but users can     also choose a different model if preferred.
-  * **Number of transformation products (TPs)**: The maximum number of TPs to predict per input compound.The default value is set to 30 TPs per compound, but users can choose any number between 1 and 50.+  * **Number of transformation products (TPs)**: The maximum number of TPs to predict per input compound. The default value is set to 30 TPs per compound, but users can choose any number between 1 and 50.
  
 ==== Algorithm Description ==== ==== Algorithm Description ====
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 The probability of a child node generated during pathway search, also known as the **combined probability**, is determined based on the probability of the parent node and the reaction probability, as illustrated in the below figure. The probability of a child node generated during pathway search, also known as the **combined probability**, is determined based on the probability of the parent node and the reaction probability, as illustrated in the below figure.
  
-{{ :batch_mode_.png?nolink |}}+{{ :batch_mode_edited.png |}}
  
 All transformation products (TPs) resulting from reactions with a probability greater than zero are stored in a priority queue, ordered in descending order based on their combined probability. All transformation products (TPs) resulting from reactions with a probability greater than zero are stored in a priority queue, ordered in descending order based on their combined probability.
pathway_prediction_in_batch_mode.1745917523.txt.gz · Last modified: 2025/04/29 09:05 by shankar