Differences

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--- pathway_prediction_in_batch_mode [2025/04/28 14:13] – shankar
+++ pathway_prediction_in_batch_mode [2025/05/22 09:53] (current) – shankar
@@ Line 8: / Line 8: @@
-  * 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 ====
@@ Line 22: / Line 22: @@
 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.