imagine you have a long string of LEGO blocks, but these blocks only come in four colors: red (A), yellow (C), blue (G), and green (U). This string is called RNA.
\nThis string isn't just straight; it likes to fold up and stick to itself in a very special, complicated 3D shape, like a tangled-up, knotted-up toy. The way it folds is super important because it tells the RNA what job to do in our bodies, like a secret code!
\nThe problem is, we only know the order of the colors (the sequence, like \"red-yellow-blue-green-red-red…\"). We don't know what the final, folded-up 3D shape looks like. It's like having the instructions for a LEGO castle but no picture of the finished castle.
\nSo, the game is this:
\nWe give you the color order (the RNA sequence).
\nYou have to guess what the folded-up 3D shape looks like. You have to make five different guesses, because sometimes the RNA can fold in a few slightly different ways.
\nFor each guess, you tell us exactly where each colored block is in 3D space. Imagine putting tiny little coordinates (x, y, z) on each LEGO block in your folded-up shape. You provide those values.
\nWe compare your guesses to the real 3D shape (which we know, but you don't!).
\nWe give you a score. The closer your guess is to the real shape, the better your score. It's like a puzzle – the better you put the pieces together, the higher your score. We measure that using something called the \"TM-score,\" which is just a fancy way of saying \"how close is your guess?\". The score is between 0 (totally wrong) and 1 (perfect!).
\nThe files are like this:
\n[train/validation/test]_sequences.csv: These are like instruction sheets that tell you the color order of the LEGO blocks (A, C, G, U) for different RNA strings. They also have some extra information, like a code name for each RNA string (target_id) and when scientists first figured out that particular color order (temporal_cutoff).
\n[train/validation]_labels.csv: These are like the answer keys for some of the RNA strings. They tell you the real 3D positions (x, y, z coordinates) of each colored block in the folded-up shape. You use these to practice and teach your computer to guess better.
\nsample_submission.csv: This is an example of how you should tell us your guesses. You give us the code name, the color of each block, and your five guesses for the x, y, and z coordinates of each block.
\nMSA: Multiple Sequence Alignments, are like comparing several similar but not completely the same strings of LEGO bricks. It tell you how similar these strings are.
\nSo, you're building a computer program that's really good at guessing the 3D shapes of these folded-up RNA strings, just from knowing the color order. It's a tough puzzle, but solving it helps us understand how our bodies work and even make new medicines! (Used AI for assistance)
", "messages": [ { "id": 3149822, "postDate": "2025-03-14T18:06:29.663Z", "content": "imagine you have a long string of LEGO blocks, but these blocks only come in four colors: red (A), yellow (C), blue (G), and green (U). This string is called RNA.
\nThis string isn't just straight; it likes to fold up and stick to itself in a very special, complicated 3D shape, like a tangled-up, knotted-up toy. The way it folds is super important because it tells the RNA what job to do in our bodies, like a secret code!
\nThe problem is, we only know the order of the colors (the sequence, like \"red-yellow-blue-green-red-red…\"). We don't know what the final, folded-up 3D shape looks like. It's like having the instructions for a LEGO castle but no picture of the finished castle.
\nSo, the game is this:
\nWe give you the color order (the RNA sequence).
\nYou have to guess what the folded-up 3D shape looks like. You have to make five different guesses, because sometimes the RNA can fold in a few slightly different ways.
\nFor each guess, you tell us exactly where each colored block is in 3D space. Imagine putting tiny little coordinates (x, y, z) on each LEGO block in your folded-up shape. You provide those values.
\nWe compare your guesses to the real 3D shape (which we know, but you don't!).
\nWe give you a score. The closer your guess is to the real shape, the better your score. It's like a puzzle – the better you put the pieces together, the higher your score. We measure that using something called the \"TM-score,\" which is just a fancy way of saying \"how close is your guess?\". The score is between 0 (totally wrong) and 1 (perfect!).
\nThe files are like this:
\n[train/validation/test]_sequences.csv: These are like instruction sheets that tell you the color order of the LEGO blocks (A, C, G, U) for different RNA strings. They also have some extra information, like a code name for each RNA string (target_id) and when scientists first figured out that particular color order (temporal_cutoff).
\n[train/validation]_labels.csv: These are like the answer keys for some of the RNA strings. They tell you the real 3D positions (x, y, z coordinates) of each colored block in the folded-up shape. You use these to practice and teach your computer to guess better.
\nsample_submission.csv: This is an example of how you should tell us your guesses. You give us the code name, the color of each block, and your five guesses for the x, y, and z coordinates of each block.
\nMSA: Multiple Sequence Alignments, are like comparing several similar but not completely the same strings of LEGO bricks. It tell you how similar these strings are.
\nSo, you're building a computer program that's really good at guessing the 3D shapes of these folded-up RNA strings, just from knowing the color order. It's a tough puzzle, but solving it helps us understand how our bodies work and even make new medicines! (Used AI for assistance)
", "rawMarkdown": "imagine you have a long string of LEGO blocks, but these blocks only come in four colors: red (A), yellow (C), blue (G), and green (U). This string is called RNA.\n\nThis string isn't just straight; it likes to fold up and stick to itself in a very special, complicated 3D shape, like a tangled-up, knotted-up toy. The way it folds is super important because it tells the RNA what job to do in our bodies, like a secret code!\n\nThe problem is, we only know the order of the colors (the sequence, like \"red-yellow-blue-green-red-red...\"). We don't know what the final, folded-up 3D shape looks like. It's like having the instructions for a LEGO castle but no picture of the finished castle.\n\nSo, the game is this:\n\nWe give you the color order (the RNA sequence).\n\nYou have to guess what the folded-up 3D shape looks like. You have to make five different guesses, because sometimes the RNA can fold in a few slightly different ways.\n\nFor each guess, you tell us exactly where each colored block is in 3D space. Imagine putting tiny little coordinates (x, y, z) on each LEGO block in your folded-up shape. You provide those values.\n\nWe compare your guesses to the real 3D shape (which we know, but you don't!).\n\nWe give you a score. The closer your guess is to the real shape, the better your score. It's like a puzzle – the better you put the pieces together, the higher your score. We measure that using something called the \"TM-score,\" which is just a fancy way of saying \"how close is your guess?\". The score is between 0 (totally wrong) and 1 (perfect!).\n\nThe files are like this:\n\n[train/validation/test]_sequences.csv: These are like instruction sheets that tell you the color order of the LEGO blocks (A, C, G, U) for different RNA strings. They also have some extra information, like a code name for each RNA string (target_id) and when scientists first figured out that particular color order (temporal_cutoff).\n\n[train/validation]_labels.csv: These are like the answer keys for some of the RNA strings. They tell you the real 3D positions (x, y, z coordinates) of each colored block in the folded-up shape. You use these to practice and teach your computer to guess better.\n\nsample_submission.csv: This is an example of how you should tell us your guesses. You give us the code name, the color of each block, and your five guesses for the x, y, and z coordinates of each block.\n\nMSA: Multiple Sequence Alignments, are like comparing several similar but not completely the same strings of LEGO bricks. It tell you how similar these strings are.\n\nSo, you're building a computer program that's really good at guessing the 3D shapes of these folded-up RNA strings, just from knowing the color order. It's a tough puzzle, but solving it helps us understand how our bodies work and even make new medicines! (Used AI for assistance)", "votes": 23 }, { "id": 3149971, "postDate": "2025-03-14T22:39:44.253Z", "content": "Good introduction. However, a major piece of information is missing. Whenever RNA nucleotides pair with each other, in a vast majority of cases it is A with U (and vice versa) or G with C. Sometimes G pairs with U, but much less frequently than the other two rules. This piece of information makes a big difference in how an RNA molecule is structured.
", "rawMarkdown": "Good introduction. However, a major piece of information is missing. Whenever RNA nucleotides pair with each other, in a vast majority of cases it is A with U (and *vice versa*) or G with C. Sometimes G pairs with U, but much less frequently than the other two rules. This piece of information makes a big difference in how an RNA molecule is structured.", "votes": 4, "replies": [ { "id": 3150086, "postDate": "2025-03-15T04:02:39.400Z", "content": "Thanks for highlighting this!!
", "rawMarkdown": "Thanks for highlighting this!!\n", "replies": [ { "id": 3154838, "postDate": "2025-03-20T12:46:33.783Z", "content": "anyone looking for what the missing part is in this post highlighted by @tilii7 feel free to refer: https://www.kaggle.com/competitions/stanford-rna-3d-folding/discussion/568445 discussion by @tilii7 himself, very nicely explained and saved me a ton of researching time! Although i found part 2 little difficult : (
", "rawMarkdown": "anyone looking for what the missing part is in this post highlighted by @tilii7 feel free to refer: https://www.kaggle.com/competitions/stanford-rna-3d-folding/discussion/568445 discussion by @tilii7 himself, very nicely explained and saved me a ton of researching time! Although i found part 2 little difficult : (" } ] } ] }, { "id": 3163548, "postDate": "2025-03-30T23:17:15.867Z", "content": "Thank you for sharing your insights. All this while, I was wondering why should the submission file have five different set of co-ordinates and your discussion post clarified my doubt.
", "rawMarkdown": "Thank you for sharing your insights. All this while, I was wondering why should the submission file have five different set of co-ordinates and your discussion post clarified my doubt.", "votes": 1 }, { "id": 3154142, "postDate": "2025-03-19T15:18:05.663Z", "content": "@lordpatil Well Done! Good job for that easy explanation! Thank you for sharing.
\nIf you want you can check out my approach, https://www.kaggle.com/code/dantheshark/rna-3d-folding-understand-data
\nbest, dan
@dantheshark , just had a look at it. This is great and will save some of time. I will be building upon your notebook
", "rawMarkdown": "@dantheshark , just had a look at it. This is great and will save some of time. I will be building upon your notebook", "votes": 1 } ] }, { "id": 3150139, "postDate": "2025-03-15T05:30:35.103Z", "content": "i have a doubt.. how do we handle cases where the RNA can fold in multiple valid ways? (also is this possible?) and is there a way to know which folding is most likely?
", "rawMarkdown": "i have a doubt.. how do we handle cases where the RNA can fold in multiple valid ways? (also is this possible?) and is there a way to know which folding is most likely?", "votes": 2, "replies": [ { "id": 3151402, "postDate": "2025-03-16T16:41:50.030Z", "content": "i will get back to you on this!
", "rawMarkdown": "i will get back to you on this!", "replies": [ { "id": 3153465, "postDate": "2025-03-18T21:06:45.397Z", "content": "I don’t know what is most likely unless the model tells me but here’s what I can say the competition allows you to submit up to 5 predicted structures for each RNA sequence. This explicitly acknowledges the possibility of multiple valid foldings. You can try to predict some of the most likely conformations. The scoring considers the best-of-5 TM-scores, meaning that if one of your predicted structures is close to a valid conformation, you'll get a good score.
", "rawMarkdown": "I don’t know what is most likely unless the model tells me but here’s what I can say the competition allows you to submit up to 5 predicted structures for each RNA sequence. This explicitly acknowledges the possibility of multiple valid foldings. You can try to predict some of the most likely conformations. The scoring considers the best-of-5 TM-scores, meaning that if one of your predicted structures is close to a valid conformation, you'll get a good score." } ] } ] }, { "id": 3150104, "postDate": "2025-03-15T04:33:21.457Z", "content": "Great explanation! As a beginner, do I need to understand biology to work on this, or can I approach it purely from a machine learning perspective?
", "rawMarkdown": "Great explanation! As a beginner, do I need to understand biology to work on this, or can I approach it purely from a machine learning perspective?", "votes": 2, "replies": [ { "id": 3150199, "postDate": "2025-03-15T06:41:14.677Z", "content": "Same question
", "rawMarkdown": "Same question\n", "votes": 1, "replies": [ { "id": 3151401, "postDate": "2025-03-16T16:41:04.953Z", "content": "well, am new to this problem too. however here how i am going approach this.
\nokay, biology isn’t actually required much. focus on data science core
", "rawMarkdown": "okay, biology isn’t actually required much. focus on data science core" } ] } ] }, { "id": 3150105, "postDate": "2025-03-15T04:35:26.690Z", "rawMarkdown": "", "isDeleted": true } ], "comments": [ { "id": 3149971, "author_name": "Tilii", "author_url": "", "post_date": "2025-03-14T22:39:44.253000", "content": "Good introduction. However, a major piece of information is missing. Whenever RNA nucleotides pair with each other, in a vast majority of cases it is A with U (and vice versa) or G with C. Sometimes G pairs with U, but much less frequently than the other two rules. This piece of information makes a big difference in how an RNA molecule is structured.
", "votes": 4, "replies": [ { "id": 3150086, "author_name": "Chirag Patil", "author_url": "", "post_date": "2025-03-15T04:02:39.400000", "content": "Thanks for highlighting this!!
", "votes": 0, "replies": [ { "id": 3154838, "author_name": "Chirag Patil", "author_url": "", "post_date": "2025-03-20T12:46:33.783000", "content": "anyone looking for what the missing part is in this post highlighted by @tilii7 feel free to refer: https://www.kaggle.com/competitions/stanford-rna-3d-folding/discussion/568445 discussion by @tilii7 himself, very nicely explained and saved me a ton of researching time! Although i found part 2 little difficult : (
", "votes": 0, "replies": [] } ] } ] }, { "id": 3163548, "author_name": "Apoorva Ajay", "author_url": "", "post_date": "2025-03-30T23:17:15.867000", "content": "Thank you for sharing your insights. All this while, I was wondering why should the submission file have five different set of co-ordinates and your discussion post clarified my doubt.
", "votes": 1, "replies": [] }, { "id": 3154142, "author_name": "dan", "author_url": "", "post_date": "2025-03-19T15:18:05.663000", "content": "@lordpatil Well Done! Good job for that easy explanation! Thank you for sharing.
\nIf you want you can check out my approach, https://www.kaggle.com/code/dantheshark/rna-3d-folding-understand-data
\nbest, dan
@dantheshark , just had a look at it. This is great and will save some of time. I will be building upon your notebook
", "votes": 1, "replies": [] } ] }, { "id": 3150139, "author_name": "Ananya Verma", "author_url": "", "post_date": "2025-03-15T05:30:35.103000", "content": "i have a doubt.. how do we handle cases where the RNA can fold in multiple valid ways? (also is this possible?) and is there a way to know which folding is most likely?
", "votes": 2, "replies": [ { "id": 3151402, "author_name": "Chirag Patil", "author_url": "", "post_date": "2025-03-16T16:41:50.030000", "content": "i will get back to you on this!
", "votes": 0, "replies": [ { "id": 3153465, "author_name": "Chirag Patil", "author_url": "", "post_date": "2025-03-18T21:06:45.397000", "content": "I don’t know what is most likely unless the model tells me but here’s what I can say the competition allows you to submit up to 5 predicted structures for each RNA sequence. This explicitly acknowledges the possibility of multiple valid foldings. You can try to predict some of the most likely conformations. The scoring considers the best-of-5 TM-scores, meaning that if one of your predicted structures is close to a valid conformation, you'll get a good score.
", "votes": 0, "replies": [] } ] } ] }, { "id": 3150104, "author_name": "ManavKhambhayata", "author_url": "", "post_date": "2025-03-15T04:33:21.457000", "content": "Great explanation! As a beginner, do I need to understand biology to work on this, or can I approach it purely from a machine learning perspective?
", "votes": 2, "replies": [ { "id": 3150199, "author_name": "Saed Bhati", "author_url": "", "post_date": "2025-03-15T06:41:14.677000", "content": "Same question
", "votes": 1, "replies": [ { "id": 3151401, "author_name": "Chirag Patil", "author_url": "", "post_date": "2025-03-16T16:41:04.953000", "content": "well, am new to this problem too. however here how i am going approach this.
\nokay, biology isn’t actually required much. focus on data science core
", "votes": 0, "replies": [] } ] } ] }, { "id": 3150105, "author_name": "", "author_url": "", "post_date": "2025-03-15T04:35:26.690000", "content": "", "votes": 0, "replies": [] } ], "raw_markdown_by_id": { "3149822": "imagine you have a long string of LEGO blocks, but these blocks only come in four colors: red (A), yellow (C), blue (G), and green (U). This string is called RNA.\n\nThis string isn't just straight; it likes to fold up and stick to itself in a very special, complicated 3D shape, like a tangled-up, knotted-up toy. The way it folds is super important because it tells the RNA what job to do in our bodies, like a secret code!\n\nThe problem is, we only know the order of the colors (the sequence, like \"red-yellow-blue-green-red-red...\"). We don't know what the final, folded-up 3D shape looks like. It's like having the instructions for a LEGO castle but no picture of the finished castle.\n\nSo, the game is this:\n\nWe give you the color order (the RNA sequence).\n\nYou have to guess what the folded-up 3D shape looks like. You have to make five different guesses, because sometimes the RNA can fold in a few slightly different ways.\n\nFor each guess, you tell us exactly where each colored block is in 3D space. Imagine putting tiny little coordinates (x, y, z) on each LEGO block in your folded-up shape. You provide those values.\n\nWe compare your guesses to the real 3D shape (which we know, but you don't!).\n\nWe give you a score. The closer your guess is to the real shape, the better your score. It's like a puzzle – the better you put the pieces together, the higher your score. We measure that using something called the \"TM-score,\" which is just a fancy way of saying \"how close is your guess?\". The score is between 0 (totally wrong) and 1 (perfect!).\n\nThe files are like this:\n\n[train/validation/test]_sequences.csv: These are like instruction sheets that tell you the color order of the LEGO blocks (A, C, G, U) for different RNA strings. They also have some extra information, like a code name for each RNA string (target_id) and when scientists first figured out that particular color order (temporal_cutoff).\n\n[train/validation]_labels.csv: These are like the answer keys for some of the RNA strings. They tell you the real 3D positions (x, y, z coordinates) of each colored block in the folded-up shape. You use these to practice and teach your computer to guess better.\n\nsample_submission.csv: This is an example of how you should tell us your guesses. You give us the code name, the color of each block, and your five guesses for the x, y, and z coordinates of each block.\n\nMSA: Multiple Sequence Alignments, are like comparing several similar but not completely the same strings of LEGO bricks. It tell you how similar these strings are.\n\nSo, you're building a computer program that's really good at guessing the 3D shapes of these folded-up RNA strings, just from knowing the color order. It's a tough puzzle, but solving it helps us understand how our bodies work and even make new medicines! (Used AI for assistance)", "3149971": "Good introduction. However, a major piece of information is missing. Whenever RNA nucleotides pair with each other, in a vast majority of cases it is A with U (and *vice versa*) or G with C. Sometimes G pairs with U, but much less frequently than the other two rules. This piece of information makes a big difference in how an RNA molecule is structured.", "3163548": "Thank you for sharing your insights. All this while, I was wondering why should the submission file have five different set of co-ordinates and your discussion post clarified my doubt.", "3154142": "@lordpatil Well Done! Good job for that easy explanation! Thank you for sharing. \nIf you want you can check out my approach, https://www.kaggle.com/code/dantheshark/rna-3d-folding-understand-data\nbest, dan", "3150139": "i have a doubt.. how do we handle cases where the RNA can fold in multiple valid ways? (also is this possible?) and is there a way to know which folding is most likely?", "3150104": "Great explanation! As a beginner, do I need to understand biology to work on this, or can I approach it purely from a machine learning perspective?", "3150105": "" } }