BMI 702, Spring 24

_config.yml

@@ -29,7 +29,7 @@ heading_anchors: true
 permalink: pretty
 aux_links:
   Canvas:
-    - 'https://canvas.harvard.edu/courses/117878'
+    - 'https://canvas.harvard.edu/courses/134015'
   Harvard DBMI:
     - 'https://dbmi.hms.harvard.edu'
   Zitnik Lab:

_modules/week-01.md

@@ -4,10 +4,10 @@ title: Week 1
 
 Course overview and introduction to biomedical AI
 
-Jan 23
+Jan 25
 : **Lecture**{: .label .label-purple }[What makes biomedical problems unique](/BMI702/lectures/week01)
   : [Slides](/BMI702/assets/zitnik-BMI702-L1.pdf), [Reading List](/BMI702/lectures/week01)
 
-Jan 24
-: **Quiz**{: .label .label-green }[Week 2 pre-class quiz](#) (due Jan 29)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Jan 26
+: **Quiz**{: .label .label-green }[Week 2 pre-class quiz](#) (due Feb 1)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-02.md

@@ -4,10 +4,10 @@ title: Week 2
 
 Clinical research using EHR data, subtype discovery, disease diagnosis and prognosis prediction
 
-Jan 30
+Feb 1
 : **Module 1**{: .label .label-blue }**Lecture**{: .label .label-purple }[Clinical AI Part I](/BMI702/lectures/module1/week02)
-  : [Slides](/BMI702/assets/zitnik-BMI702-L2.pdf), [Reading List](/BMI702/lectures/module1/week02)
+  : [Slides](#), [Reading List](/BMI702/lectures/module1/week02)
 
-Jan 31
-: **Quiz**{: .label .label-green }[Week 3 pre-class quiz](#) (due Feb 5)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Feb 2
+: **Quiz**{: .label .label-green }[Week 3 pre-class quiz](#) (due Feb 8)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-03.md

@@ -2,12 +2,12 @@
 title: Week 3
 ---
 
-Multi-institutional EHR systems, transfer learning, federated learning, clinical workflows
+Multi-institutional EHR, transfer learning, federated learning
 
-Feb 6
+Feb 8
 : **Module 1**{: .label .label-blue }**Lecture**{: .label .label-purple }[Clinical AI Part II](/BMI702/lectures/module1/week03)
-  : [Slides](/BMI702/assets/zitnik-BMI702-L3.pdf), [Reading List](/BMI702/lectures/module1/week03)
+  : [Slides](#), [Reading List](/BMI702/lectures/module1/week03)
 
-Feb 7
-: **Quiz**{: .label .label-green }[Week 4 pre-class quiz](#) (due Feb 12)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Feb 9
+: **Quiz**{: .label .label-green }[Week 4 pre-class quiz](#) (due Feb 15)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-04.md

@@ -2,12 +2,12 @@
 title: Week 4
 ---
 
-Interpretability and explainability in biomedical AI
+Interpretability and explainability, bias and distribution shifts
 
-Feb 13
-: **Module 2**{: .label .label-blue }**Lecture**{: .label .label-purple }[Trustworthy AI Part I](/BMI702/lectures/module2/week04)
-  : [Slides](/BMI702/assets/zitnik-BMI702-L4.pdf), [Reading List](/BMI702/lectures/module2/week04)
+Feb 15
+: **Module 2**{: .label .label-blue }**Lecture**{: .label .label-purple }[Trustworthy & Efficient AI Part I](/BMI702/lectures/module2/week04)
+  : [Slides](#), [Reading List](/BMI702/lectures/module2/week04)
 
-Feb 13
-: **Quiz**{: .label .label-green }[Week 5 pre-class quiz](#) (due Feb 26)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Feb 16
+: **Quiz**{: .label .label-green }[Week 5 pre-class quiz](#) (due Feb 22)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-05.md

@@ -2,16 +2,16 @@
 title: Week 5
 ---
 
-Bias and fairness in biomedical AI
+Few-shot learning, scaling laws, generalization and robustness
 
-Feb 27
-: **Module 2**{: .label .label-blue }**Lecture**{: .label .label-purple }[Trustworthy AI Part II](/BMI702/lectures/module2/week05)
-  : [Slides](/BMI702/assets/zitnik-BMI702-L5.pdf), [Reading List](/BMI702/lectures/module2/week05)
+Feb 22
+: **Module 2**{: .label .label-blue }**Lecture**{: .label .label-purple }[Trustworthy & Efficient AI Part II](/BMI702/lectures/module2/week05)
+  : [Slides](#), [Reading List](/BMI702/lectures/module2/week05)
 
-Feb 28
-: **Quiz**{: .label .label-green }[Week 6 pre-class quiz](#) (due Mar 5)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Feb 23
+: **Quiz**{: .label .label-green }[Week 6 pre-class quiz](#) (due Feb 29)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)
 
-Mar 1
-: **PSet released**{: .label .label-yellow }[PSet 1: Bias, explainability, and fairness](#)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Feb 23
+: **PSet released**{: .label .label-yellow }[PSet 1: Bias, trustworthiness, and fairness](#)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-06.md

@@ -4,10 +4,10 @@ title: Week 6
 
 Foundations of geometric deep learning, graph representation learning, link prediction, node classification, graph clustering, graph classification, semi-supervised learning, label propagation, network medicine, disease modules and endotypes
 
-Mar 6
+Feb 29
 : **Module 3**{: .label .label-blue }**Lecture**{: .label .label-purple }[Biomedical graph learning Part I](/BMI702/lectures/module3/week06)
-  : [Slides](/BMI702/assets/zitnik-BMI702-L6.pdf), [Reading List](/BMI702/lectures/module3/week06)
+  : [Slides](#), [Reading List](/BMI702/lectures/module3/week06)
 
-Mar 7
-: **Quiz**{: .label .label-green }[Week 7 pre-class quiz](#) (due Mar 12)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Mar 1
+: **Quiz**{: .label .label-green }[Week 7 pre-class quiz](#) (due Mar 7)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-07.md

@@ -4,14 +4,14 @@ title: Week 7
 
 Machine learning with heterogeneous graphs, multimodal learning, graph neural networks, knowledge graph embeddings, reasoning over knowledge graphs
 
-Mar 20
+Mar 7
 : **Module 3**{: .label .label-blue }**Lecture**{: .label .label-purple }[Biomedical graph learning Part II](/BMI702/lectures/module3/week07)
-  : [Slides - Part 1](/BMI702/assets/zitnik-BMI702-L7-Part-1.pdf), [Slides - Part 2](/BMI702/assets/li-BMI702-L7-Part-2.pdf), [Reading List](/BMI702/lectures/module3/week07)
+  : [Slides - Part 1](#), [Slides - Part 2](#), [Reading List](/BMI702/lectures/module3/week07)
 
-Mar 21
-: **Quiz**{: .label .label-green }[Week 8 pre-class quiz](#) (due Mar 26)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Mar 8
+: **Quiz**{: .label .label-green }[Week 8 pre-class quiz](#) (due Mar 21)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)
 
-Mar 22
-: **PSet due**{: .label .label-yellow }[PSet 1: Bias, explainability, and fairness](#)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Mar 8
+: **PSet due**{: .label .label-yellow }[PSet 1: Bias, trustworthiness, and fairness](#)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-08.md

@@ -4,14 +4,14 @@ title: Week 8
 
 Foundations of natural language processing and understanding
 
-Mar 27
+Mar 21
 : **Module 4**{: .label .label-blue }**Lecture**{: .label .label-purple }[Medical language modeling Part I](/BMI702/lectures/module4/week08)
-  : [Slides](/BMI702/assets/li-BMI702-L8.pdf), [Reading List](/BMI702/lectures/module4/week08)
+  : [Slides](#), [Reading List](/BMI702/lectures/module4/week08)
 
-Mar 28
-: **Quiz**{: .label .label-green }[Week 9 pre-class quiz](#) (due Apr 2)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Mar 22
+: **Quiz**{: .label .label-green }[Week 9 pre-class quiz](#) (due Mar 28)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)
 
-Mar 29
-: **PSet released**{: .label .label-yellow }[PSet 2: Biomedical networks and graph embeddings](#)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Mar 22
+: **PSet released**{: .label .label-yellow }[PSet 2: Knowledge graphs and geometric deep learning](#)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-09.md

@@ -4,10 +4,10 @@ title: Week 9
 
 Clinical trial site identification, patient trial matching, clinical trial recruitment
 
-Apr 3
+Mar 28
 : **Module 4**{: .label .label-blue }**Lecture**{: .label .label-purple }[Medical language modeling Part II](/BMI702/lectures/module4/week09)
-  : [Slides](/BMI702/assets/zitnik-BMI702-L9.pdf), [Reading List](/BMI702/lectures/module4/week09)
+  : [Slides](#), [Reading List](/BMI702/lectures/module4/week09)
 
-Apr 4
-: **Quiz**{: .label .label-green }[Week 10 pre-class quiz](#) (due Apr 9)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Apr 29
+: **Quiz**{: .label .label-green }[Week 10 pre-class quiz](#) (due Apr 4)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-10.md

@@ -4,14 +4,14 @@ title: Week 10
 
 Foundations of biomedical imaging, self-supervised learning, analysis of radiology images
 
-Apr 10
+Apr 4
 : **Module 5**{: .label .label-blue }**Lecture**{: .label .label-purple }[Biomedical imaging Part I](/BMI702/lectures/module5/week10)
-  : [Slides](/BMI702/assets/rajpurkar-BMI702-L10.pdf), [Reading List](/BMI702/lectures/module5/week10)
+  : [Slides](#), [Reading List](/BMI702/lectures/module5/week10)
 
-Apr 11
-: **Quiz**{: .label .label-green }[Week 11 pre-class quiz](#) (due Apr 16)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Apr 5
+: **Quiz**{: .label .label-green }[Week 11 pre-class quiz](#) (due Apr 11)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)
 
-Apr 12
-: **PSet due**{: .label .label-yellow }[PSet 2: Biomedical networks and graph embeddings](#)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Apr 5
+: **PSet due**{: .label .label-yellow }[PSet 2: Knowledge graphs and geometric deep learning](#)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-11.md

@@ -4,14 +4,14 @@ title: Week 11
 
 Multimodal learning, analysis of histopathology slides, quantitative pathology in cancer diagnosis and prognosis
 
-Apr 17
+Apr 11
 : **Module 5**{: .label .label-blue }**Lecture**{: .label .label-purple }[Biomedical imaging Part II](/BMI702/lectures/module5/week11)
-  : [Slides](https://drive.google.com/file/d/1w6ED8dOF8DKFgFdFbmwPNYZRT9z2HwCY/view?usp=share_link), [Reading List](/BMI702/lectures/module5/week11)
+  : [Slides](#), [Reading List](/BMI702/lectures/module5/week11)
 
-Apr 18
-: **Quiz**{: .label .label-green }[Week 12 pre-class quiz](#) (due Apr 23)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Apr 12
+: **Quiz**{: .label .label-green }[Week 12 pre-class quiz](#) (due Apr 18)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)
 
-Apr 19
+Apr 12
 : **PSet released**{: .label .label-yellow }[PSet 3: Biomedical imaging methods and applications](#)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-12.md

@@ -2,12 +2,12 @@
 title: Week 12
 ---
 
-Overview of drug discovery and development, AI-guided drug design, small-molecule generation, molecule optimization, identification and characterization of therapeutic targets, high-throughput chemical and genetic perturbations
+AI-guided drug design, small-molecule generation, molecule optimization, identification and characterization of therapeutic targets, design of chemical and genetic perturbations
 
-Apr 24
-: **Module 6**{: .label .label-blue }**Lecture**{: .label .label-purple }[Therapeutic science and drug discovery Part I](/BMI702/lectures/module6/week12)
-  : [Slides](/BMI702/assets/zitnik-BMI702-L12.pdf), [Reading List](/BMI702/lectures/module6/week12)
+Apr 18
+: **Module 6**{: .label .label-blue }**Lecture**{: .label .label-purple }[Generative AI Part I](/BMI702/lectures/module6/week12)
+  : [Slides](#), [Reading List](/BMI702/lectures/module6/week12)
 
-Apr 25
-: **Quiz**{: .label .label-green }[Week 13 pre-class quiz](#) (due Apr 30)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Apr 19
+: **Quiz**{: .label .label-green }[Week 13 pre-class quiz](#) (due Apr 25)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-13.md

@@ -2,16 +2,16 @@
 title: Week 13
 ---
 
-Label-efficient learning, few-shot learning, biomarker discovery, indication inference, drug repurposing, adverse event prediction
+Protein design and digital twins 
 
-May 1
-: **Module 6**{: .label .label-blue }**Lecture**{: .label .label-purple }[Therapeutic science and drug discovery Part II](/BMI702/lectures/module6/week13)
-  : [Slides](/BMI702/assets/zitnik-BMI702-L13.pdf), [Reading List](/BMI702/lectures/module6/week13)
+Apr 25
+: **Module 6**{: .label .label-blue }**Lecture**{: .label .label-purple }[Generative AI Part II](/BMI702/lectures/module6/week13)
+  : [Slides](#), [Reading List](/BMI702/lectures/module6/week13)
 
-May 2
-: **Quiz**{: .label .label-green }[Week 14 pre-class quiz](#) (due May 7)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+Apr 26
+: **Quiz**{: .label .label-green }[Week 14 pre-class quiz](#) (due May 2)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)
 
-May 3
+Apr 26
 : **PSet due**{: .label .label-yellow }[PSet 3: Biomedical imaging methods and applications](#)
-  : [Canvas](https://canvas.harvard.edu/courses/117878)
+  : [Canvas](https://canvas.harvard.edu/courses/134015)

_modules/week-14.md

@@ -4,7 +4,7 @@ title: Week 14
 
 Introduction to ethical frameworks, data privacy, regulation and liability aspects of AI
 
-May 8
+May 2
 : **Lecture**{: .label .label-purple }[Ethical and legal considerations for biomedical AI ](/BMI702/lectures/week14)
-  : [Slides](/BMI702/assets/gerke-BMI702-L14.pdf), [Reading List](/BMI702/lectures/week14)
+  : [Slides](#), [Reading List](/BMI702/lectures/week14)
 

_sass/color_schemes/harvardred.scss

@@ -7,7 +7,7 @@ $body-font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helve
 // Layout
 $gutter-spacing: $sp-6;
 $gutter-spacing-sm: $sp-4;
-$nav-width: 250px;
+$nav-width: 300px;
 $content-width: 950px;
 
 // Components

_schedules/weekly.md

@@ -23,32 +23,27 @@ timeline:
 schedule:
   - name: 
   - name: Monday
-    events:
-      - name: Lecture
-        start: 1:00 PM
-        end: 3:00 PM
-        location: Armenise Modell 100A, 200 Longwood Ave
-      - name: OH Prof Zitnik
-        start: 3:00 PM
-        end: 4:00 PM
-        location: Countway 309, 10 Shattuck St
   - name: Tuesday
     events:
-      - name: OH Chen
-        start: 5:00 PM
-        end: 6:00 PM
-        location: Countway 423/424 Open area
+    - name: OH Ullanat
+      start: 3:00 PM
+      end: 4:00 PM
+      location: Countway 423/424
   - name: Wednesday
   - name: Thursday
     events:
-      - name: OH Huang
-        start: 3:00 PM
+      - name: Lecture
+        start: 2:00 PM
         end: 4:00 PM
-        location: Countway 423/424 Open area
+        location: Countway 403
+      - name: OH Prof Zitnik
+        start: 4:00 PM
+        end: 5:00 PM
+        location: Countway 309
   - name: Friday
     events:
       - name: OH Ektefaie
-        start: 10:00 AM
-        end: 11:00 AM
-        location: Countway 423/424 Open area
+        start: 11:00 AM
+        end: 12:00 PM
+        location: Countway 423/424
 ---

_staffers/marinka.md

@@ -4,5 +4,5 @@ role: Instructor
 email: [email protected]
 website: https://zitniklab.hms.harvard.edu
 photo: marinka.png
-office-hours: Mo, 3pm - 4pm
+office-hours: Thu, 4pm - 5pm
 ---

_staffers/varun.md

@@ -0,0 +1,8 @@
+---
+name: Varun Ullanat
+role: Staff
+email: [email protected]
+website: https://dbmi.hms.harvard.edu/people/varun-ullanat
+photo: varun.png
+office-hours: Tue, 3pm - 4pm 
+---

_staffers/yasha.md

@@ -4,5 +4,5 @@ role: Staff
 email: [email protected]
 website: https://www.yashaektefaie.com
 photo: yasha.png
-office-hours: Fri, 10am - 11am
+office-hours: Fri, 11am - 12pm
 ---