Update course book

NeuromatchAcademy · Jun 13, 2024 · a617b32 · a617b32
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diff --git a/_sources/prereqs/DeepLearning.md b/_sources/prereqs/DeepLearning.md
@@ -1,6 +1,6 @@
 # Prerequisites and preparatory materials for NMA Deep Learning
 
-Welcome to the [Neuromatch Academy](https://academy.neuromatch.io/)! We're really excited to bring deep learning to such a wide and varied audience. We're preparing an amazing set of lectures and tutorials for you!
+Welcome to the [Neuromatch Academy](https://neuromatch.io/deep-learning-course/)! We're really excited to bring deep learning to such a wide and varied audience. We're preparing an amazing set of lectures and tutorials for you!
 
 ## Preparing yourself for the course
 

diff --git a/_sources/projects/docs/project_guidance.md b/_sources/projects/docs/project_guidance.md
@@ -28,15 +28,11 @@ Project TAs are your friendly topic experts to consult with on all issues relate
 
 Sometimes the project TAs might need to schedule meetings slightly earlier or later. Please try to be flexible, they are doing a lot of "virtual footwork" to make sure all the groups have enough support during projects. We also encourage you to reach out to them for extra meetings whenever you need them, and to post questions on discord in the #topic channels. 
 
-## Project Mentors
-
-Project mentors are more senior figures in the field, typically senior postdocs, professors, or industry researchers. Each project group will have a mentor to help them refine their hypotheses and navigate the scientific process. They won't be around as often as the TAs, but they are another source of guidance and perspective.
-
 ## Week 1: Getting started
 
 Depending on your time slot, you may or may not have project time on the first day of the course. Regardless of whether your first project meeting is day 1 or day 2, spend your first session doing the following:
 
-* Split into groups alphabetically. First sort yourselves by the first letter of your name. The first half of the students are in group 1, the second in group 2. If the split is not well-balanced, move one or two people around.
+* Split into groups. We recommend intentionally creating groups with diverse skill sets. Groups should have students who are very confident in Python and those who are just learning. Through the project, students can work together to strengthen each other's skills. We want to make sure that all members of each group get a chance to do all parts of the project. We ask that folks who are good with Python share what they know and hand off tasks to peers who are learning so they can improve their skills.
 * Introductions (30 min = 2 min/student): say a few things about yourself, then about your research area or research interests. What are you really curious about, that you might explore in your NMA project?
 * Listen carefully as others talk about their interests.
 * Individual reading time (30 min): browse the projects booklet which includes this guide (skim the entire thing) + 16 project templates with slides and code + docs with further ideas and datasets
@@ -51,8 +47,6 @@ In your next sessions, watch the [Modeling Steps 1-2 tutorials](https://deeplear
 * If you are using a project template, your goal is to translate the information from the slide and colab notebook into the 10-steps format. Some information might not be readily available in the slide or notebook, and you might have to find it in your literature review later this day.
 * Try to write down a few sentences for each of the two steps applied to your project. Putting thoughts into well-defined sentences and paragraphs helps at all stages of a project.
 
-*Stay tuned for your mentor assignments. Once you receive them, reach out to your mentor to set up a first meeting this week. Also try to arrange a meeting for W2D1, ideally the second half of the day, when their feedback on your abstract could be useful.*
-
 ## W1D4: Projects Day!
 
 This is a full day dedicated to projects! The goals are threefold: perform a literature search, refine your question, and try to find a good dataset.
@@ -97,7 +91,7 @@ Then,
 * You should now have as many copies of your abstract as there are students in your group. Put them all into the same google doc, and try to see what you all did the same / differently. What sounds better? Pick and choose different sentences from different abstracts.
 
 
-Try to schedule a meeting with your project TA and/or mentor during this day and show them your abstract. Try to get explicit feedback and edit the abstract together in a google doc.
+Try to schedule a meeting with your project TA during this day and show them your abstract. Try to get explicit feedback and edit the abstract together in a google doc.
 
 Likewise, it is always revealing to present your research to someone who has never heard about it. Take turns in your pod to read the other group's abstract and provide feedback. What did you understand and what didn't make sense? Give detailed writing feedback if you can (use "suggestion mode" in google docs). If there is no other project group in your pod, ask your TA to reach out to other pods to find a group you can workshop your abstract with.
 
@@ -120,7 +114,7 @@ At the end of W3D4, you should also submit your slides via this [Airtable link](
 
 Please see final day schedule and shared calendars for timing details: [https://deeplearning.neuromatch.io/tutorials/Schedule/daily_schedules.html#w3d5-final-day-of-course](https://deeplearning.neuromatch.io/tutorials/Schedule/daily_schedules.html#w3d5-final-day-of-course)
 
-This is the day where you present your project to other groups. Your mentor and your project TAs can be invited too, but they are busy so they might not make it. The groups will take turns to share their screens. You can use figures and other graphics, but this is meant to be told as a story, and everyone from your group should take a turn telling a part of the story. Tell us about the different hypotheses you’ve had at different points and how you refined them using some of the tools we taught.
+This is the day where you present your project to other groups. Your project TAs can be invited too, but they are busy so they might not make it. The groups will take turns to share their screens. You can use figures and other graphics, but this is meant to be told as a story, and everyone from your group should take a turn telling a part of the story. Tell us about the different hypotheses you’ve had at different points and how you refined them using some of the tools we taught.
 
 ### Schedule
 

diff --git a/_sources/tutorials/intro.ipynb b/_sources/tutorials/intro.ipynb
diff --git a/prereqs/DeepLearning.html b/prereqs/DeepLearning.html
@@ -1404,7 +1404,7 @@ <h2> Contents </h2>
 
   <section class="tex2jax_ignore mathjax_ignore" id="prerequisites-and-preparatory-materials-for-nma-deep-learning">
 <h1>Prerequisites and preparatory materials for NMA Deep Learning<a class="headerlink" href="#prerequisites-and-preparatory-materials-for-nma-deep-learning" title="Permalink to this heading">#</a></h1>
-<p>Welcome to the <a class="reference external" href="https://academy.neuromatch.io/">Neuromatch Academy</a>! We’re really excited to bring deep learning to such a wide and varied audience. We’re preparing an amazing set of lectures and tutorials for you!</p>
+<p>Welcome to the <a class="reference external" href="https://neuromatch.io/deep-learning-course/">Neuromatch Academy</a>! We’re really excited to bring deep learning to such a wide and varied audience. We’re preparing an amazing set of lectures and tutorials for you!</p>
 <section id="preparing-yourself-for-the-course">
 <h2>Preparing yourself for the course<a class="headerlink" href="#preparing-yourself-for-the-course" title="Permalink to this heading">#</a></h2>
 <p>People are coming to this course from a wide range of disciplines and with varying levels of background, and we want to make sure everybody is able to follow and enjoy the school from day 1. This means you need to know the basics of programming in Python and some core math concepts. Below we provide more details.</p>

diff --git a/projects/ComputerVision/data_augmentation.html b/projects/ComputerVision/data_augmentation.html
@@ -1763,8 +1763,8 @@ <h2>Cutout<a class="headerlink" href="#cutout" title="Permalink to this heading"
 <section id="mixup">
 <h2>Mixup<a class="headerlink" href="#mixup" title="Permalink to this heading">#</a></h2>
 <p>Mixup is a data augmentation technique that combines pairs of examples via a convex combination of the images and the labels. Given images <span class="math notranslate nohighlight">\(x_i\)</span> and <span class="math notranslate nohighlight">\(x_j\)</span> with labels <span class="math notranslate nohighlight">\(y_i\)</span> and <span class="math notranslate nohighlight">\(y_j\)</span>, respectively, and <span class="math notranslate nohighlight">\(\lambda \in [0, 1]\)</span>, mixup creates a new image <span class="math notranslate nohighlight">\(\hat{x}\)</span> with label <span class="math notranslate nohighlight">\(\hat{y}\)</span> the following way:</p>
-<div class="amsmath math notranslate nohighlight" id="equation-a4a0abc1-1bbd-472d-8c3f-025daccdd721">
-<span class="eqno">(128)<a class="headerlink" href="#equation-a4a0abc1-1bbd-472d-8c3f-025daccdd721" title="Permalink to this equation">#</a></span>\[\begin{align}
+<div class="amsmath math notranslate nohighlight" id="equation-14356126-e765-4652-94c2-a8e36873215c">
+<span class="eqno">(128)<a class="headerlink" href="#equation-14356126-e765-4652-94c2-a8e36873215c" title="Permalink to this equation">#</a></span>\[\begin{align}
 \hat{x} &amp;= \lambda x_i + (1 - \lambda) x_j \\
 \hat{y} &amp;= \lambda y_i + (1 - \lambda) y_j
 \end{align}\]</div>

diff --git a/projects/docs/project_guidance.html b/projects/docs/project_guidance.html
@@ -1396,11 +1396,6 @@ <h2> Contents </h2>
    Project TAs
   </a>
  </li>
- <li class="toc-h2 nav-item toc-entry">
-  <a class="reference internal nav-link" href="#project-mentors">
-   Project Mentors
-  </a>
- </li>
  <li class="toc-h2 nav-item toc-entry">
   <a class="reference internal nav-link" href="#week-1-getting-started">
    Week 1: Getting started
@@ -1497,15 +1492,11 @@ <h2>Project TAs<a class="headerlink" href="#project-tas" title="Permalink to thi
 <p>Project TAs are your friendly topic experts to consult with on all issues related to your project. They can help with brainstorming, literature searches and coding. You will have meetings with them approximately every two days. During this time, they will help you refine your question and hypothesis into something that can be answered with deep learning. Sometimes they may miss a meeting or arrive late (busy schedules, lots of meetings!). In those cases, please stop what you were doing to have the meeting, and then resume your work when the project TA leaves.</p>
 <p>Sometimes the project TAs might need to schedule meetings slightly earlier or later. Please try to be flexible, they are doing a lot of “virtual footwork” to make sure all the groups have enough support during projects. We also encourage you to reach out to them for extra meetings whenever you need them, and to post questions on discord in the #topic channels.</p>
 </section>
-<section id="project-mentors">
-<h2>Project Mentors<a class="headerlink" href="#project-mentors" title="Permalink to this heading">#</a></h2>
-<p>Project mentors are more senior figures in the field, typically senior postdocs, professors, or industry researchers. Each project group will have a mentor to help them refine their hypotheses and navigate the scientific process. They won’t be around as often as the TAs, but they are another source of guidance and perspective.</p>
-</section>
 <section id="week-1-getting-started">
 <h2>Week 1: Getting started<a class="headerlink" href="#week-1-getting-started" title="Permalink to this heading">#</a></h2>
 <p>Depending on your time slot, you may or may not have project time on the first day of the course. Regardless of whether your first project meeting is day 1 or day 2, spend your first session doing the following:</p>
 <ul class="simple">
-<li><p>Split into groups alphabetically. First sort yourselves by the first letter of your name. The first half of the students are in group 1, the second in group 2. If the split is not well-balanced, move one or two people around.</p></li>
+<li><p>Split into groups. We recommend intentionally creating groups with diverse skill sets. Groups should have students who are very confident in Python and those who are just learning. Through the project, students can work together to strengthen each other’s skills. We want to make sure that all members of each group get a chance to do all parts of the project. We ask that folks who are good with Python share what they know and hand off tasks to peers who are learning so they can improve their skills.</p></li>
 <li><p>Introductions (30 min = 2 min/student): say a few things about yourself, then about your research area or research interests. What are you really curious about, that you might explore in your NMA project?</p></li>
 <li><p>Listen carefully as others talk about their interests.</p></li>
 <li><p>Individual reading time (30 min): browse the projects booklet which includes this guide (skim the entire thing) + 16 project templates with slides and code + docs with further ideas and datasets</p></li>
@@ -1521,7 +1512,6 @@ <h2>Week 1: Getting started<a class="headerlink" href="#week-1-getting-started"
 <li><p>If you are using a project template, your goal is to translate the information from the slide and colab notebook into the 10-steps format. Some information might not be readily available in the slide or notebook, and you might have to find it in your literature review later this day.</p></li>
 <li><p>Try to write down a few sentences for each of the two steps applied to your project. Putting thoughts into well-defined sentences and paragraphs helps at all stages of a project.</p></li>
 </ul>
-<p><em>Stay tuned for your mentor assignments. Once you receive them, reach out to your mentor to set up a first meeting this week. Also try to arrange a meeting for W2D1, ideally the second half of the day, when their feedback on your abstract could be useful.</em></p>
 </section>
 <section id="w1d4-projects-day">
 <h2>W1D4: Projects Day!<a class="headerlink" href="#w1d4-projects-day" title="Permalink to this heading">#</a></h2>
@@ -1559,7 +1549,7 @@ <h2>W3D2: Half project day!<a class="headerlink" href="#w3d2-half-project-day" t
 <li><p>Edit the abstract individually in your own google doc. At this stage, it is also important to control the flow of the abstract, in addition to keeping the structure from the 10 rules-paper. The flow relates to the “writing style”, which is generally no different for researchers than for other writers. Most importantly, make sure each sentence continues from where the previous one left, and do not use jargon without defining it first. Check out this book about writing if you have time (<a class="reference external" href="https://sites.duke.edu/niou/files/2014/07/WilliamsJosephM1990StyleTowardClarityandGrace.pdf">book</a>, especially chapter 3 about “cohesion” and flow.</p></li>
 <li><p>You should now have as many copies of your abstract as there are students in your group. Put them all into the same google doc, and try to see what you all did the same / differently. What sounds better? Pick and choose different sentences from different abstracts.</p></li>
 </ul>
-<p>Try to schedule a meeting with your project TA and/or mentor during this day and show them your abstract. Try to get explicit feedback and edit the abstract together in a google doc.</p>
+<p>Try to schedule a meeting with your project TA during this day and show them your abstract. Try to get explicit feedback and edit the abstract together in a google doc.</p>
 <p>Likewise, it is always revealing to present your research to someone who has never heard about it. Take turns in your pod to read the other group’s abstract and provide feedback. What did you understand and what didn’t make sense? Give detailed writing feedback if you can (use “suggestion mode” in google docs). If there is no other project group in your pod, ask your TA to reach out to other pods to find a group you can workshop your abstract with.</p>
 <p>Finally, with your group, has the abstract refined or changed your question? Use the rest of this day to make a concrete plan for the final week of your project. If you already answered your question, then you will need to plan for control analyses, maybe including some simulated data that you need to also generate yourself.</p>
 <p>Once you are done, please submit the abstract <a class="reference external" href="https://airtable.com/appoh6RKyBvxgiJ89/shrUeDqzGe8Cplk8u">here</a>.</p>
@@ -1578,7 +1568,7 @@ <h2>W3D3 and W3D4 (3h/day): Results<a class="headerlink" href="#w3d3-and-w3d4-3h
 <section id="w3d5-final-presentations">
 <h2>W3D5: Final Presentations<a class="headerlink" href="#w3d5-final-presentations" title="Permalink to this heading">#</a></h2>
 <p>Please see final day schedule and shared calendars for timing details: <a class="reference external" href="https://deeplearning.neuromatch.io/tutorials/Schedule/daily_schedules.html#w3d5-final-day-of-course">https://deeplearning.neuromatch.io/tutorials/Schedule/daily_schedules.html#w3d5-final-day-of-course</a></p>
-<p>This is the day where you present your project to other groups. Your mentor and your project TAs can be invited too, but they are busy so they might not make it. The groups will take turns to share their screens. You can use figures and other graphics, but this is meant to be told as a story, and everyone from your group should take a turn telling a part of the story. Tell us about the different hypotheses you’ve had at different points and how you refined them using some of the tools we taught.</p>
+<p>This is the day where you present your project to other groups. Your project TAs can be invited too, but they are busy so they might not make it. The groups will take turns to share their screens. You can use figures and other graphics, but this is meant to be told as a story, and everyone from your group should take a turn telling a part of the story. Tell us about the different hypotheses you’ve had at different points and how you refined them using some of the tools we taught.</p>
 <section id="schedule">
 <h3>Schedule<a class="headerlink" href="#schedule" title="Permalink to this heading">#</a></h3>
 <ul class="simple">
@@ -1712,11 +1702,6 @@ <h3>Questions:<a class="headerlink" href="#questions" title="Permalink to this h
    Project TAs
   </a>
  </li>
- <li class="toc-h2 nav-item toc-entry">
-  <a class="reference internal nav-link" href="#project-mentors">
-   Project Mentors
-  </a>
- </li>
  <li class="toc-h2 nav-item toc-entry">
   <a class="reference internal nav-link" href="#week-1-getting-started">
    Week 1: Getting started