Lecture tomorrow | |
Hi, Tomorrow will be our second to last lesson. Our subject tomorrow is "Machine Learning in Healthcare", a field that many bioinformaticians are now involved in. In the first lesson, we will introduce the fascinating world of clinical informatics and causal inference. In the second lesson, I want to share with you few of the recent studies we published (or about to publish) in this field. They are very diverse - two studies on cancer treatments, another on labor complications, on stroke, on chronic kidney disease and on medical cannabis. They also use very different methodologies, from classic ML to deep-learning to counterfactual predictions to LLMs. The problem is that I don't know which of them chose, so I'm passing the ball to you - please rank the studies you want to hear about tomorrow in this google form: https://forms.gle/S7qEM6ZBvdLby3SM8 Note that you can only choose one column (1-6) per study. See you tomorrow. There will be no recording of the lesson tomorrow. Best, Dvir |
עדכון אחרון ב-26/3/2024, 22:08:02 Last updated on 26/3/2024, 22:08:02 Последняя модификация26/3/2024, 22:08:02 تمت الحتلنة الأخيرة ب-26/3/2024, 22:08:02 |
HW3 is published and tutorial 8 recording | |
Dear students, Please note that HW3 is now available. In addition, I have uploaded the recording for Tutorial 8. Best, Almog |
עדכון אחרון ב-7/3/2024, 17:40:58 Last updated on 7/3/2024, 17:40:58 Последняя модификация7/3/2024, 17:40:58 تمت الحتلنة الأخيرة ب-7/3/2024, 17:40:58 |
Lecture tomorrow | |
Hi, Unfortunately, I'm sick and won't be able to come to the Technion tomorrow. To ensure that we stay on track, we decided to share with you the recordings from this class taken two years ago. Almog will organize a joint viewing session of these recordings during our regular class time. It is important that you watch these recordings before the tutorial, as the tutorial will be based on the assumption that you are already familiar with GWAS. Part 1: https://www.youtube.com/watch?v=Et9IVyqFNw8 Part 2: https://www.youtube.com/watch?v=PPGJMMGbLAI Best, Dvir |
פורסם ב-5/3/2024, 13:51:48 Created on 5/3/2024, 13:51:48 Создано5/3/2024, 13:51:48 تم النشر ب-5/3/2024, 13:51:48 |
HW feedback and tutorial 7 recording | |
Dear students, 1. To discuss HW1 and HW2 please contact Ziv - uzcatcampus.technion.ac.il 2. For HW3 and 4 you can contact me as I will be the one checking. 3. If needed, feel free to watch the new recording of tutorial 7 here - https://www.youtube.com/watch?v=o1ifj4EeEe4 Best, Almog |
פורסם ב-29/2/2024, 15:19:20 Created on 29/2/2024, 15:19:20 Создано29/2/2024, 15:19:20 تم النشر ب-29/2/2024, 15:19:20 |
Taub 6 - new classroom Wednesday's tutorials | |
Dear student, From now on Wednesday's tutorial will take place in Taub 6. Best, Almog |
פורסם ב-28/2/2024, 12:44:10 Created on 28/2/2024, 12:44:10 Создано28/2/2024, 12:44:10 تم النشر ب-28/2/2024, 12:44:10 |
New classroom for today's tutorial (Wednesday 21 Feb) | |
Dear students, I changed today's classroom to Taub 6 to avoid technical problems. |
פורסם ב-21/2/2024, 14:08:15 Created on 21/2/2024, 14:08:15 Создано21/2/2024, 14:08:15 تم النشر ب-21/2/2024, 14:08:15 |
A few clarifications about homework 1 | |
Dear students, 1. In the step saying to "deal" with NAs, what I meant is simply to remove those rows. 2. The dates in the "death" column should be considered as 1 (or dead). 3. To check normality you need to run the "Shapiro-Wilk normality test" as presented in the tutorial 4. There is a problem running the "msaR" function, I trust you to find the correct function and fix it. 5. There is a typing mistake in the last question regarding the phylogenetic tree. This question is canceled since some people already submitted the HW. Best, Almog |
פורסם ב-13/2/2024, 11:36:48 Created on 13/2/2024, 11:36:48 Создано13/2/2024, 11:36:48 تم النشر ب-13/2/2024, 11:36:48 |
Cancellation of Today's Tutorial Session - Thursday February 8 | |
Dear students, Unfortunately, I am unable to conduct today's tutorial as planned. I will upload a recording of this lesson. Best, Almog |
פורסם ב-8/2/2024, 08:25:15 Created on 8/2/2024, 08:25:15 Создано8/2/2024, 08:25:15 تم النشر ب-8/2/2024, 08:25:15 |
New paper on sequence alignment | |
I told you yesterday that there are not much new things that are happening in sequence alignment research, but apparently, this paper was published yesterday: "Exact global alignment using a* with chaining seed heuristic and match pruning" https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae032/7587511 I think it's pretty cool that you should be able to understand it now. Best, Dvir |
פורסם ב-25/1/2024, 09:11:45 Created on 25/1/2024, 09:11:45 Создано25/1/2024, 09:11:45 تم النشر ب-25/1/2024, 09:11:45 |
Tutorial recordings | |
Dear Students, I uploaded the recording of the first tutorial to my YouTube channel. You can find the link on the course website. The recording of our second tutorial will be shared with you tomorrow. Please note! I find it very important to see you all in person so I can answer questions, start discussions, and understand where you need extra help in understanding the course material. In other words, the recording should not replace your attendance at the tutorials. Dvir and I value your active participation and engagement in class and we may need to reconsider the availability of these recordings based on attendance. Best regards, Almog |
פורסם ב-24/1/2024, 21:17:44 Created on 24/1/2024, 21:17:44 Создано24/1/2024, 21:17:44 تم النشر ب-24/1/2024, 21:17:44 |
Change of Location for This Wednesday's Tutorial: Taub 7 | |
Dear students, This Wednesday's tutorial will take place in Taub 7. Best, Almog |
פורסם ב-21/1/2024, 20:30:08 Created on 21/1/2024, 20:30:08 Создано21/1/2024, 20:30:08 تم النشر ب-21/1/2024, 20:30:08 |
R Markdown File and Data for Our First Tutorial Available Now | |
Dear students, I have uploaded the R Markdown file and the associated data for our first tutorial to the course website. A friendly reminder to bring a laptop that R and RStudio installed with the 'tidyverse' package. Please do not hesitate to reach out if you have problems with the installation. I look forward to seeing you this Wednesday. Best, Almog |
פורסם ב-15/1/2024, 20:09:17 Created on 15/1/2024, 20:09:17 Создано15/1/2024, 20:09:17 تم النشر ب-15/1/2024, 20:09:17 |
Requirements for the tutorials and some recommendations | |
Dear students, I am excited to be your TA for "Introduction to Bioinformatics" this semester. This course is a unique opportunity to delve into the fascinating intersection of biology, medicine, data, and computer science. Our primary tool for this exploration will be R, a powerful and popular programming language among, statisticians, data scientists and bioinformaticians. To ensure you are well-prepared for our first session, please: 1. Install R and Rstudio (a user-friendly IDE for R) by following the instructions below: https://rstudio-education.github.io/hopr/starting.html 2. Learn About R Packages: Packages significantly extend R's capabilities, please take a few minutes to understand the concept of packages as described at: https://rstudio-education.github.io/hopr/packages2.html For starters, we'll use the 'tidyverse' package collection. Install it in RStudio using install.packages("tidyverse"). You can discover more about these packages on the tidyverse website: https://www.tidyverse.org/packages/ Familiarize Yourself with R: While our first tutorial will introduce R and RStudio, prior exposure is highly recommended. Explore R tutorials on YouTube to find one that suits your learning style. Bring Your Laptop to Classes: It's highly recommended to bring your laptop for hands-on coding exercises. A day before the tutorial I will upload to the course website an R markdown file with the code we will use. You should download this file before the class begins and install the required packages. Course Schedule and Homework: I uploaded the schedule for this semester's tutorials and homework. Please review it to stay informed about the topics we will cover and important deadlines. For any questions or assistance, feel free to reach out to me at ualmog.angelatcampus.technion.ac.il. Best wishes, Almog Angel PhD Candidate The Aran Lab - Biomedical Data Science |
פורסם ב-13/1/2024, 21:36:01 Created on 13/1/2024, 21:36:01 Создано13/1/2024, 21:36:01 تم النشر ب-13/1/2024, 21:36:01 |
Welcome to Intro 2 bioinformatics (236523) | |
Hi all, Welcome to the Introduction to Bioinformatics course. We are happy to have you join us this semester where we will delve into the fascinating science of biology, data science, and the exciting interface between them. It is expected to be a challenging semester, but we hope that you will find this course both intellectually stimulating and highly rewarding. We're committed to providing a supportive learning environment and encourage you to actively engage with the material. For those who are currently on reserve duty, or expect to be called for such duty during the semester, we kindly request that you inform us as soon as possible. This will allow us to make the necessary arrangements. Please send an email to our TA, Almog Angel, at [ualmog.angelatcampus.technion.ac.il]. Looking forward to a productive and enjoyable semester with all of you! Best regards, Dvir |
פורסם ב-7/1/2024, 22:17:50 Created on 7/1/2024, 22:17:50 Создано7/1/2024, 22:17:50 تم النشر ب-7/1/2024, 22:17:50 |