{
  "id": 256051,
  "title": "[Introducing] Visualize the entire dataset using W&B Tables",
  "url": "/competitions/rsna-miccai-brain-tumor-radiogenomic-classification/discussion/256051",
  "author_name": "Ayush Thakur",
  "post_date": "2021-07-30T15:14:58.731000",
  "votes": 33,
  "comment_count": 8,
  "views": 0,
  "content": "<p><a href=\"https://wandb.ai/site\" target=\"_blank\">Weights and Biases</a> have been working on a new feature called <a href=\"https://docs.wandb.ai/guides/data-vis\" target=\"_blank\">Tables</a> for a couple of months now. They have recently launched the feature. You can read more about the announcement in this <a href=\"https://wandb.ai/wandb/posts/reports/Announcing-W-B-Tables-Iterate-on-Your-Data--Vmlldzo4NTMxNDU\" target=\"_blank\">W&amp;B report</a>.</p>\n<p>I believe that this feature will be useful for Kagglers. Let's see Tables in the context of this competition. </p>\n<hr>\n<p>In this competition, we are given four different MRI Image Sequences for individual patients. These sequences are - FLAIR, T1w, T1wCE, and T2w. There is a total of 585 patients. The task is to predict the presence of MGMT promoter methylation. </p>\n<p>Given the importance of EDA, especially for a tricky dataset like this, it's useful to visualize as much of the dataset as possible. This is where W&amp;B Tables can be really useful. The GIF shown below is a screengrab of the dataset logged as Tables in action. </p>\n<h4><a href=\"http://wandb.me/brain-tumor-tables\" target=\"_blank\">Check out the logged Tables here ▶️</a></h4>\n<p><img src=\"https://i.imgur.com/QdZZk1U.gif\" alt=\"img\"></p>\n<h4>Some quick insights:</h4>\n<ul>\n<li>There are 585 unique patients. <br></li>\n<li>The MRI sequences have different planes. Check out this excellent <a href=\"https://www.kaggle.com/davidbroberts/determining-mr-image-planes\" target=\"_blank\">kernel</a> by <a href=\"https://www.kaggle.com/davidbroberts\" target=\"_blank\">@davidbroberts</a>. If you are interested, you can log the plane information as well as Tables (I will do so in the next version). <br></li>\n<li>The number of frames in each GIF is different, implying variable sequence length. <br></li>\n<li>There's variation in the contrast of sequences. </li>\n</ul>\n<h4>Find Missing Files:</h4>\n<p>There are multiple patient ids for which either one or multiple MRI sequences are missing. Let's find them. The GIF shown below is a screengrab of the steps required to do the same. </p>\n<ul>\n<li>Patient IDs 00109 and 00709 are missing FLAIR MRI type. <br></li>\n<li>Patient ID 00123 is missing Tw1 and Tw2. <br></li>\n</ul>\n<p>SPEND TIME LOOKING AT THE DATASET AND COME UP WITH INTERESTING IDEAS. :)</p>\n<h3>Reproduce the results:</h3>\n<p>Visit the section \"Visualizing dataset interactively with W&amp;B Tables\" in the Kaggle kernel, titled \"<a href=\"http://wandb.me/brain-tables-kernel\" target=\"_blank\">Brain Tumor EDA and Interactive Viz with W&amp;B</a>\"</p>\n<hr>\n<p>Here's are some other resources that you might feel useful:</p>\n<ul>\n<li><a href=\"https://www.kaggle.com/c/rsna-miccai-brain-tumor-radiogenomic-classification/discussion/new\" target=\"_blank\">Better Data Understanding with W&amp;B Tables</a> <br></li>\n<li><a href=\"https://wandb.ai/stacey/mendeleev/reports/Tables-Tutorial-Visualize-Data-for-Image-Classification--VmlldzozNjE3NjA\" target=\"_blank\">Tables Tutorial: Visualize Data for Image Classification</a> <br></li>\n<li><a href=\"https://docs.wandb.ai/guides/data-vis\" target=\"_blank\">Official Tables doc</a></li>\n</ul>",
  "messages": [
    {
      "id": 1405194,
      "postDate": "2021-07-30T15:14:58.733Z",
      "content": "<p><a href=\"https://wandb.ai/site\" target=\"_blank\">Weights and Biases</a> have been working on a new feature called <a href=\"https://docs.wandb.ai/guides/data-vis\" target=\"_blank\">Tables</a> for a couple of months now. They have recently launched the feature. You can read more about the announcement in this <a href=\"https://wandb.ai/wandb/posts/reports/Announcing-W-B-Tables-Iterate-on-Your-Data--Vmlldzo4NTMxNDU\" target=\"_blank\">W&amp;B report</a>.</p>\n<p>I believe that this feature will be useful for Kagglers. Let's see Tables in the context of this competition. </p>\n<hr>\n<p>In this competition, we are given four different MRI Image Sequences for individual patients. These sequences are - FLAIR, T1w, T1wCE, and T2w. There is a total of 585 patients. The task is to predict the presence of MGMT promoter methylation. </p>\n<p>Given the importance of EDA, especially for a tricky dataset like this, it's useful to visualize as much of the dataset as possible. This is where W&amp;B Tables can be really useful. The GIF shown below is a screengrab of the dataset logged as Tables in action. </p>\n<h4><a href=\"http://wandb.me/brain-tumor-tables\" target=\"_blank\">Check out the logged Tables here ▶️</a></h4>\n<p><img src=\"https://i.imgur.com/QdZZk1U.gif\" alt=\"img\"></p>\n<h4>Some quick insights:</h4>\n<ul>\n<li>There are 585 unique patients. <br></li>\n<li>The MRI sequences have different planes. Check out this excellent <a href=\"https://www.kaggle.com/davidbroberts/determining-mr-image-planes\" target=\"_blank\">kernel</a> by <a href=\"https://www.kaggle.com/davidbroberts\" target=\"_blank\">@davidbroberts</a>. If you are interested, you can log the plane information as well as Tables (I will do so in the next version). <br></li>\n<li>The number of frames in each GIF is different, implying variable sequence length. <br></li>\n<li>There's variation in the contrast of sequences. </li>\n</ul>\n<h4>Find Missing Files:</h4>\n<p>There are multiple patient ids for which either one or multiple MRI sequences are missing. Let's find them. The GIF shown below is a screengrab of the steps required to do the same. </p>\n<ul>\n<li>Patient IDs 00109 and 00709 are missing FLAIR MRI type. <br></li>\n<li>Patient ID 00123 is missing Tw1 and Tw2. <br></li>\n</ul>\n<p>SPEND TIME LOOKING AT THE DATASET AND COME UP WITH INTERESTING IDEAS. :)</p>\n<h3>Reproduce the results:</h3>\n<p>Visit the section \"Visualizing dataset interactively with W&amp;B Tables\" in the Kaggle kernel, titled \"<a href=\"http://wandb.me/brain-tables-kernel\" target=\"_blank\">Brain Tumor EDA and Interactive Viz with W&amp;B</a>\"</p>\n<hr>\n<p>Here's are some other resources that you might feel useful:</p>\n<ul>\n<li><a href=\"https://www.kaggle.com/c/rsna-miccai-brain-tumor-radiogenomic-classification/discussion/new\" target=\"_blank\">Better Data Understanding with W&amp;B Tables</a> <br></li>\n<li><a href=\"https://wandb.ai/stacey/mendeleev/reports/Tables-Tutorial-Visualize-Data-for-Image-Classification--VmlldzozNjE3NjA\" target=\"_blank\">Tables Tutorial: Visualize Data for Image Classification</a> <br></li>\n<li><a href=\"https://docs.wandb.ai/guides/data-vis\" target=\"_blank\">Official Tables doc</a></li>\n</ul>",
      "rawMarkdown": "[Weights and Biases](https://wandb.ai/site) have been working on a new feature called [Tables](https://docs.wandb.ai/guides/data-vis) for a couple of months now. They have recently launched the feature. You can read more about the announcement in this [W&B report](https://wandb.ai/wandb/posts/reports/Announcing-W-B-Tables-Iterate-on-Your-Data--Vmlldzo4NTMxNDU).\n\nI believe that this feature will be useful for Kagglers. Let's see Tables in the context of this competition. \n\n---\n\nIn this competition, we are given four different MRI Image Sequences for individual patients. These sequences are - FLAIR, T1w, T1wCE, and T2w. There is a total of 585 patients. The task is to predict the presence of MGMT promoter methylation. \n\nGiven the importance of EDA, especially for a tricky dataset like this, it's useful to visualize as much of the dataset as possible. This is where W&B Tables can be really useful. The GIF shown below is a screengrab of the dataset logged as Tables in action. \n\n#### [Check out the logged Tables here ▶️](http://wandb.me/brain-tumor-tables)\n\n![img](https://i.imgur.com/QdZZk1U.gif)\n\n#### Some quick insights:\n\n* There are 585 unique patients. <br>\n* The MRI sequences have different planes. Check out this excellent [kernel](https://www.kaggle.com/davidbroberts/determining-mr-image-planes) by @davidbroberts. If you are interested, you can log the plane information as well as Tables (I will do so in the next version). <br>\n* The number of frames in each GIF is different, implying variable sequence length. <br>\n* There's variation in the contrast of sequences. \n\n#### Find Missing Files:\n\nThere are multiple patient ids for which either one or multiple MRI sequences are missing. Let's find them. The GIF shown below is a screengrab of the steps required to do the same. \n\n* Patient IDs 00109 and 00709 are missing FLAIR MRI type. <br>\n* Patient ID 00123 is missing Tw1 and Tw2. <br>\n\n\nSPEND TIME LOOKING AT THE DATASET AND COME UP WITH INTERESTING IDEAS. :)\n\n### Reproduce the results:\n\nVisit the section \"Visualizing dataset interactively with W&B Tables\" in the Kaggle kernel, titled \"[Brain Tumor EDA and Interactive Viz with W&B](http://wandb.me/brain-tables-kernel)\"\n\n---\n\nHere's are some other resources that you might feel useful:\n* [Better Data Understanding with W&B Tables](https://www.kaggle.com/c/rsna-miccai-brain-tumor-radiogenomic-classification/discussion/new) <br>\n* [Tables Tutorial: Visualize Data for Image Classification](https://wandb.ai/stacey/mendeleev/reports/Tables-Tutorial-Visualize-Data-for-Image-Classification--VmlldzozNjE3NjA) <br>\n* [Official Tables doc](https://docs.wandb.ai/guides/data-vis)",
      "votes": 33
    },
    {
      "id": 1470811,
      "postDate": "2021-08-13T18:15:16.110Z",
      "content": "<p>After reading your notebook, I wanna use W &amp; B. Good advertise 😄<br>\nHow about your progress? Does your network become stable? I tried 2d model but it doesn't work for this problem. I am going to try 3D CNN or LSTM in the next step. </p>",
      "rawMarkdown": "After reading your notebook, I wanna use W & B. Good advertise 😄\nHow about your progress? Does your network become stable? I tried 2d model but it doesn't work for this problem. I am going to try 3D CNN or LSTM in the next step. ",
      "replies": [
        {
          "id": 1471980,
          "postDate": "2021-08-14T15:21:29.700Z",
          "content": "<p>Hey glad you liked it. I will be working on stabilizing the network tomorrow. :D</p>\n<p>3D CNN is a viable option.</p>",
          "rawMarkdown": "Hey glad you liked it. I will be working on stabilizing the network tomorrow. :D\n\n3D CNN is a viable option."
        }
      ]
    },
    {
      "id": 1405996,
      "postDate": "2021-07-31T12:04:10.507Z",
      "content": "<p>Very nice! I checked out your notebook, has a lot of detail! Thanks!</p>",
      "rawMarkdown": "Very nice! I checked out your notebook, has a lot of detail! Thanks!",
      "replies": [
        {
          "id": 1407643,
          "postDate": "2021-08-02T04:23:35.770Z",
          "content": "<p>Awesome thanks ElenaEB :)</p>",
          "rawMarkdown": "Awesome thanks ElenaEB :)"
        }
      ]
    },
    {
      "id": 1405312,
      "postDate": "2021-07-30T17:35:22.990Z",
      "content": "<p>Very cool <a href=\"https://www.kaggle.com/ayuraj\" target=\"_blank\">@ayuraj</a> .. I'm just getting into WandB myself. I haven't looked at the tables feature yet though. I think you forgot to paste in the planes kernel link.</p>",
      "rawMarkdown": "Very cool @ayuraj .. I'm just getting into WandB myself. I haven't looked at the tables feature yet though. I think you forgot to paste in the planes kernel link.",
      "replies": [
        {
          "id": 1405612,
          "postDate": "2021-07-31T05:07:50.640Z",
          "content": "<p>Hey <a href=\"https://www.kaggle.com/davidbroberts\" target=\"_blank\">@davidbroberts</a> thanks for pointing that out. My bad. :)</p>\n<p>W&amp;B will be useful. :)</p>",
          "rawMarkdown": "Hey @davidbroberts thanks for pointing that out. My bad. :)\n\nW&B will be useful. :)"
        }
      ]
    },
    {
      "id": 1405410,
      "postDate": "2021-07-30T19:54:59.667Z",
      "rawMarkdown": "",
      "isDeleted": true,
      "replies": [
        {
          "id": 1405614,
          "postDate": "2021-07-31T05:08:31.677Z",
          "content": "<p>Thanks <a href=\"https://www.kaggle.com/weka511\" target=\"_blank\">@weka511</a>. Yeah, exploding brain will kill tumors and humans alike. :P</p>",
          "rawMarkdown": "Thanks @weka511. Yeah, exploding brain will kill tumors and humans alike. :P"
        }
      ]
    }
  ],
  "comments": [
    {
      "id": 1470811,
      "author_name": "Shanshan Yu",
      "author_url": "",
      "post_date": "2021-08-13T18:15:16.110000",
      "content": "<p>After reading your notebook, I wanna use W &amp; B. Good advertise 😄<br>\nHow about your progress? Does your network become stable? I tried 2d model but it doesn't work for this problem. I am going to try 3D CNN or LSTM in the next step. </p>",
      "votes": 0,
      "replies": [
        {
          "id": 1471980,
          "author_name": "Ayush Thakur",
          "author_url": "",
          "post_date": "2021-08-14T15:21:29.700000",
          "content": "<p>Hey glad you liked it. I will be working on stabilizing the network tomorrow. :D</p>\n<p>3D CNN is a viable option.</p>",
          "votes": 0,
          "replies": []
        }
      ]
    },
    {
      "id": 1405996,
      "author_name": "ElenaEB",
      "author_url": "",
      "post_date": "2021-07-31T12:04:10.507000",
      "content": "<p>Very nice! I checked out your notebook, has a lot of detail! Thanks!</p>",
      "votes": 0,
      "replies": [
        {
          "id": 1407643,
          "author_name": "Ayush Thakur",
          "author_url": "",
          "post_date": "2021-08-02T04:23:35.770000",
          "content": "<p>Awesome thanks ElenaEB :)</p>",
          "votes": 0,
          "replies": []
        }
      ]
    },
    {
      "id": 1405312,
      "author_name": "David Roberts",
      "author_url": "",
      "post_date": "2021-07-30T17:35:22.990000",
      "content": "<p>Very cool <a href=\"https://www.kaggle.com/ayuraj\" target=\"_blank\">@ayuraj</a> .. I'm just getting into WandB myself. I haven't looked at the tables feature yet though. I think you forgot to paste in the planes kernel link.</p>",
      "votes": 0,
      "replies": [
        {
          "id": 1405612,
          "author_name": "Ayush Thakur",
          "author_url": "",
          "post_date": "2021-07-31T05:07:50.640000",
          "content": "<p>Hey <a href=\"https://www.kaggle.com/davidbroberts\" target=\"_blank\">@davidbroberts</a> thanks for pointing that out. My bad. :)</p>\n<p>W&amp;B will be useful. :)</p>",
          "votes": 0,
          "replies": []
        }
      ]
    },
    {
      "id": 1405410,
      "author_name": "",
      "author_url": "",
      "post_date": "2021-07-30T19:54:59.667000",
      "content": "",
      "votes": 0,
      "replies": [
        {
          "id": 1405614,
          "author_name": "Ayush Thakur",
          "author_url": "",
          "post_date": "2021-07-31T05:08:31.677000",
          "content": "<p>Thanks <a href=\"https://www.kaggle.com/weka511\" target=\"_blank\">@weka511</a>. Yeah, exploding brain will kill tumors and humans alike. :P</p>",
          "votes": 0,
          "replies": []
        }
      ]
    }
  ],
  "raw_markdown_by_id": {
    "1405194": "[Weights and Biases](https://wandb.ai/site) have been working on a new feature called [Tables](https://docs.wandb.ai/guides/data-vis) for a couple of months now. They have recently launched the feature. You can read more about the announcement in this [W&B report](https://wandb.ai/wandb/posts/reports/Announcing-W-B-Tables-Iterate-on-Your-Data--Vmlldzo4NTMxNDU).\n\nI believe that this feature will be useful for Kagglers. Let's see Tables in the context of this competition. \n\n---\n\nIn this competition, we are given four different MRI Image Sequences for individual patients. These sequences are - FLAIR, T1w, T1wCE, and T2w. There is a total of 585 patients. The task is to predict the presence of MGMT promoter methylation. \n\nGiven the importance of EDA, especially for a tricky dataset like this, it's useful to visualize as much of the dataset as possible. This is where W&B Tables can be really useful. The GIF shown below is a screengrab of the dataset logged as Tables in action. \n\n#### [Check out the logged Tables here ▶️](http://wandb.me/brain-tumor-tables)\n\n![img](https://i.imgur.com/QdZZk1U.gif)\n\n#### Some quick insights:\n\n* There are 585 unique patients. <br>\n* The MRI sequences have different planes. Check out this excellent [kernel](https://www.kaggle.com/davidbroberts/determining-mr-image-planes) by @davidbroberts. If you are interested, you can log the plane information as well as Tables (I will do so in the next version). <br>\n* The number of frames in each GIF is different, implying variable sequence length. <br>\n* There's variation in the contrast of sequences. \n\n#### Find Missing Files:\n\nThere are multiple patient ids for which either one or multiple MRI sequences are missing. Let's find them. The GIF shown below is a screengrab of the steps required to do the same. \n\n* Patient IDs 00109 and 00709 are missing FLAIR MRI type. <br>\n* Patient ID 00123 is missing Tw1 and Tw2. <br>\n\n\nSPEND TIME LOOKING AT THE DATASET AND COME UP WITH INTERESTING IDEAS. :)\n\n### Reproduce the results:\n\nVisit the section \"Visualizing dataset interactively with W&B Tables\" in the Kaggle kernel, titled \"[Brain Tumor EDA and Interactive Viz with W&B](http://wandb.me/brain-tables-kernel)\"\n\n---\n\nHere's are some other resources that you might feel useful:\n* [Better Data Understanding with W&B Tables](https://www.kaggle.com/c/rsna-miccai-brain-tumor-radiogenomic-classification/discussion/new) <br>\n* [Tables Tutorial: Visualize Data for Image Classification](https://wandb.ai/stacey/mendeleev/reports/Tables-Tutorial-Visualize-Data-for-Image-Classification--VmlldzozNjE3NjA) <br>\n* [Official Tables doc](https://docs.wandb.ai/guides/data-vis)",
    "1470811": "After reading your notebook, I wanna use W & B. Good advertise 😄\nHow about your progress? Does your network become stable? I tried 2d model but it doesn't work for this problem. I am going to try 3D CNN or LSTM in the next step. ",
    "1405996": "Very nice! I checked out your notebook, has a lot of detail! Thanks!",
    "1405312": "Very cool @ayuraj .. I'm just getting into WandB myself. I haven't looked at the tables feature yet though. I think you forgot to paste in the planes kernel link.",
    "1405410": ""
  }
}