Research Work
Research Interests
My doctoral research focused on the domains:
· Computational molecular biology
· Machine learning
· Algorithms
· NLP applied to biological sequences
· Unbiased processing of big data for ML
In my dissertation work, under the supervision of Prof. Mona Singh, I leveraged high-throughput genomic and proteomic data and developed machine learning algorithms to predict protein interaction sites. My work combined different data aggregation levels and different prior knowledge to construct predictive algorithms, guided by protein structural information. I also worked on applying NLP attention-based algorithms to protein sequences.
In my work, I put a great emphasis on appropriately handling big data for machine learning.
In addition to constructing useful prediction methods and identifying novel interaction sites, my doctoral work also highlights the importance of proper, unbiased construction of training datasets. A fundamental aspect of machine learning algorithms is the power to generalize towards unseen data. There are many pitfalls in constructing fair testing scenarios, and they can result in unintentional data leakage, rendering the performance estimation overly optimistic or completely invalid. My algorithm construction is accompanied by careful data preparation procedures that overcome many of these pitfalls.
Ph.D. dissertation defense
Ph.D. Final Public Oral (FPO), Virtual (due to the pandemic) | Zoom recording
Journal Publications
Anat Etzion-Fuchs, David A. Todd, and Mona Singh. "dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains." Nucleic Acids Research (2021): 49(13): e78
Website | Github | paper
Poster Presentations
· "De-novo Predictions of binding positions within protein domains", Anat Etzion-Fuchs, David A. Todd, and Mona Singh
Women in Machine Learning (WiML), and Machine Learning and Computational Biology (MLCB), Vancouver Canada (12/2019)
Recipient of the WiML workshop travel grant, for poster presenters and reviewers
· "De-novo Predictions of binding positions within protein domains", Anat Etzion-Fuchs, David A. Todd, and Mona Singh
RECOMB, Washington DC (05/2019)
· "Predicting and Characterizing the Functional Impact of Protein Domains' Positions", Anat Etzion-Fuchs, and Mona Singh
Quantitative Biology Meeting: Making Use of Emerging Technologies, Cold Spring Harbor, NY (08/2017)
· "Identifying Functional Protein Domains Positions Using Population Variation", Anat Etzion-Fuchs, and Mona Singh
Princeton Research Day (PRD), Princeton, NJ (04/2017) | Best Poster award (1st place) for graduate/post doctoral track
My doctoral research focused on the domains:
· Computational molecular biology
· Machine learning
· Algorithms
· NLP applied to biological sequences
· Unbiased processing of big data for ML
In my dissertation work, under the supervision of Prof. Mona Singh, I leveraged high-throughput genomic and proteomic data and developed machine learning algorithms to predict protein interaction sites. My work combined different data aggregation levels and different prior knowledge to construct predictive algorithms, guided by protein structural information. I also worked on applying NLP attention-based algorithms to protein sequences.
In my work, I put a great emphasis on appropriately handling big data for machine learning.
In addition to constructing useful prediction methods and identifying novel interaction sites, my doctoral work also highlights the importance of proper, unbiased construction of training datasets. A fundamental aspect of machine learning algorithms is the power to generalize towards unseen data. There are many pitfalls in constructing fair testing scenarios, and they can result in unintentional data leakage, rendering the performance estimation overly optimistic or completely invalid. My algorithm construction is accompanied by careful data preparation procedures that overcome many of these pitfalls.
Ph.D. dissertation defense
Ph.D. Final Public Oral (FPO), Virtual (due to the pandemic) | Zoom recording
Journal Publications
Anat Etzion-Fuchs, David A. Todd, and Mona Singh. "dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains." Nucleic Acids Research (2021): 49(13): e78
Website | Github | paper
Poster Presentations
· "De-novo Predictions of binding positions within protein domains", Anat Etzion-Fuchs, David A. Todd, and Mona Singh
Women in Machine Learning (WiML), and Machine Learning and Computational Biology (MLCB), Vancouver Canada (12/2019)
Recipient of the WiML workshop travel grant, for poster presenters and reviewers
· "De-novo Predictions of binding positions within protein domains", Anat Etzion-Fuchs, David A. Todd, and Mona Singh
RECOMB, Washington DC (05/2019)
· "Predicting and Characterizing the Functional Impact of Protein Domains' Positions", Anat Etzion-Fuchs, and Mona Singh
Quantitative Biology Meeting: Making Use of Emerging Technologies, Cold Spring Harbor, NY (08/2017)
· "Identifying Functional Protein Domains Positions Using Population Variation", Anat Etzion-Fuchs, and Mona Singh
Princeton Research Day (PRD), Princeton, NJ (04/2017) | Best Poster award (1st place) for graduate/post doctoral track
Ph.D. US Applications Process
The advice I'm about to share pertains mostly to Israeli students wishing to apply to P.hD. programs in the US but might help others around the globe. Over the years, I had many mentoring/conversations with Israeli students to help them with their P.hD. application process. Feel free to reach out if you need my help!
Applications timeline
The US applications all have a standardized timeline. Usually, applications are submitted around December. Invitations for interviews (in natural science programs, e.g., Biology, Chemistry, Physics) are sent around January-February, and post-acceptance visit days are usually in March (in Engineering programs, e.g., Computer Science, Electrical Engineering). Yes, that's right, for science programs there is an extra step of in-person interviews (pending pandemic restrictions), whereas for engineering programs, the acceptance is based solely upon your application.
A major common deadline is April 15. By that time, you should have gotten accept/reject notices from all the P.hD. programs you have applied to, and the ball is in your hand. You need (or want :) ) to reply affirmative response to one program and reject all others by that date. In April, you know which university you will attend and can spend the next few months making logistical preparations to move there before the Fall semester starts.
Note: Fall semester starting date depends on the university, but it is usually much earlier than in Israel. For instance, Princeton University started its Fall semester for many years shortly after the Labor day holiday (~second week of September), and it recently changed its schedule and starts the Fall semester at the end of August.
The US applications all have a standardized timeline. Usually, applications are submitted around December. Invitations for interviews (in natural science programs, e.g., Biology, Chemistry, Physics) are sent around January-February, and post-acceptance visit days are usually in March (in Engineering programs, e.g., Computer Science, Electrical Engineering). Yes, that's right, for science programs there is an extra step of in-person interviews (pending pandemic restrictions), whereas for engineering programs, the acceptance is based solely upon your application.
A major common deadline is April 15. By that time, you should have gotten accept/reject notices from all the P.hD. programs you have applied to, and the ball is in your hand. You need (or want :) ) to reply affirmative response to one program and reject all others by that date. In April, you know which university you will attend and can spend the next few months making logistical preparations to move there before the Fall semester starts.
Note: Fall semester starting date depends on the university, but it is usually much earlier than in Israel. For instance, Princeton University started its Fall semester for many years shortly after the Labor day holiday (~second week of September), and it recently changed its schedule and starts the Fall semester at the end of August.
Preparing your application
A P.hD. application in most places consists of the following main components:
A little more detail/tips on each of these application components.
A P.hD. application in most places consists of the following main components:
- GRE (Graduate Record Examination) and TOEFL (Test Of English as a Foreign Language) exams.
- Personal essay
- Recommendation letters from Professors.
A little more detail/tips on each of these application components.
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GRE and TOEFL
GRE is taken by everyone, including American students. You only need TOEFL if you've never studied any of your previous higher education in an English-speaking institution, which is true for most Israeli students. I do not wish to thoroughly review these tests (you can google them easily); I do want to say that for science and engineering P.hD. programs, they do not have a big effect on the acceptance status. In my opinion, a long preparation course Psychometry-style (Israel's SAT equivalent) is unnecessary. For the GRE, all you need to do is focus on not getting a really embarrassing grade in the quantitative part. The English part is hard even for native speakers, and you really don't need to spend months memorizing all these words. Personally, I just studied from books and got a satisfying grade in the GRE quant. part. |
https://brightlinkprep.com/how-important-is-the-gre-for-graduate-school/
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Personal essay
Often referred to as "Statement of Purpose," this essay is one of the main components that will determine your acceptance, more than any single course/exam. The majority of the applications do not require a CV document. Instead, this is the only place where you can describe your previous experience in detail. You can download here my statement of purpose for Princeton University. |
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The essay should answer about three main questions:
1) Why do you want to a P.hD.?
2) Why do you want to a P.hD. now?
3) Why do you want to do a P.hD. here?
It should be a carefully crafted story about how your whole life and experiences brought you to this singular moment in time where a P.hD. program is the best thing for you personally, and for the program, and maybe even for science and humanity as a whole. Yes, you need to think big :)
The best way to write your essay is by reading many examples online. Many people are happy to share their essays/writing advice. After lots of reading, the conclusions I reached about writing this essay are as follows:
For the Israeli students, I want to note that the standard in American writing for this type of essays is to use a lot more superlatives, excitement, and exaggeration than what we are used to. If you try to write in a neutral way in fear of bragging, to the American ear it may sound as if you are not excited enough or serious enough about your intentions.
For international students in general, I want to note that as non-native speakers, we need to make sure our writing level is near-perfect. Personally, I wrote my essays alone and then used the (paid) service of an English technical writer in Technion to fix some grammatical errors. I also gave my essay to friends and family to read, but take others' advice with a grain of salt if they are not familiar with writing American academic essays.
1) Why do you want to a P.hD.?
2) Why do you want to a P.hD. now?
3) Why do you want to do a P.hD. here?
It should be a carefully crafted story about how your whole life and experiences brought you to this singular moment in time where a P.hD. program is the best thing for you personally, and for the program, and maybe even for science and humanity as a whole. Yes, you need to think big :)
The best way to write your essay is by reading many examples online. Many people are happy to share their essays/writing advice. After lots of reading, the conclusions I reached about writing this essay are as follows:
- It should tell a story about who you are in an interesting way that will catch the eye.
- It should demonstrate a great passion for the domain you want to research.
- It should highlight all your most significant professional achievements.
- It should include a rather detailed description of your previous research experience.
For the Israeli students, I want to note that the standard in American writing for this type of essays is to use a lot more superlatives, excitement, and exaggeration than what we are used to. If you try to write in a neutral way in fear of bragging, to the American ear it may sound as if you are not excited enough or serious enough about your intentions.
For international students in general, I want to note that as non-native speakers, we need to make sure our writing level is near-perfect. Personally, I wrote my essays alone and then used the (paid) service of an English technical writer in Technion to fix some grammatical errors. I also gave my essay to friends and family to read, but take others' advice with a grain of salt if they are not familiar with writing American academic essays.
Recommendation letters
A minimum of three letters is required by most of the applications I've seen.
If you are applying after completing a Master's degree, one of these letters should be from your academic advisor (if not, it would raise a red flag).
If you are applying straight from undergrad (like me), it might be challenging to get letters from many Professors at your university. Yes, it needs to be Professors and not your boss from a Tech company or your commander from military service. Of course, it is better to have something than nothing. Still, the people who are reading and assessing your application are Professors, and they expect to read a letter from their peers, and even more preferably, someone they know, or at least heard of.
The best way to achieve familiarity that can lead to a good recommendation letter is through course projects. Another option is getting a paid research assistantship in one of the university's labs.
Either way, a strong recommendation letter would come after joint work with someone that can attest to your ability in doing research. Remember that one component of your personal essay is previous research experience; therefore, a research project before completing your undergraduate studies would serve both.
Note: In the US, good students travel every summer to a different research institution and engage in research that sometimes even leads to publications. By the time they graduate from their college/undergraduate university, many students have accumulated several research experiences under their belt.
In order to ask for a recommendation letter from someone you know, my best advice is simply to schedule a meeting with them, tell them about your plans to apply and ask for advice and relevant pointers in different universities. I had received extremely helpful tips from my mentors who also wrote my letters, including which Professors they recommend me to work with and who I should try to stay away from. Networking plays a big role in academia, and a word from someone influential can go a long way.
After getting your letter, don't forget to update your mentors from time to time about your application process, and most importantly, don't forget to thank them when it's all over and they have helped you achieving your dream! :)
A minimum of three letters is required by most of the applications I've seen.
If you are applying after completing a Master's degree, one of these letters should be from your academic advisor (if not, it would raise a red flag).
If you are applying straight from undergrad (like me), it might be challenging to get letters from many Professors at your university. Yes, it needs to be Professors and not your boss from a Tech company or your commander from military service. Of course, it is better to have something than nothing. Still, the people who are reading and assessing your application are Professors, and they expect to read a letter from their peers, and even more preferably, someone they know, or at least heard of.
The best way to achieve familiarity that can lead to a good recommendation letter is through course projects. Another option is getting a paid research assistantship in one of the university's labs.
Either way, a strong recommendation letter would come after joint work with someone that can attest to your ability in doing research. Remember that one component of your personal essay is previous research experience; therefore, a research project before completing your undergraduate studies would serve both.
Note: In the US, good students travel every summer to a different research institution and engage in research that sometimes even leads to publications. By the time they graduate from their college/undergraduate university, many students have accumulated several research experiences under their belt.
In order to ask for a recommendation letter from someone you know, my best advice is simply to schedule a meeting with them, tell them about your plans to apply and ask for advice and relevant pointers in different universities. I had received extremely helpful tips from my mentors who also wrote my letters, including which Professors they recommend me to work with and who I should try to stay away from. Networking plays a big role in academia, and a word from someone influential can go a long way.
After getting your letter, don't forget to update your mentors from time to time about your application process, and most importantly, don't forget to thank them when it's all over and they have helped you achieving your dream! :)
Helpful links
- The grad Cafe: https://www.thegradcafe.com/ (Anonymous admission results and a very active forum)
- GPA calculator: http://www.scholaro.com/gpa-calculator/ (converting international GPA to the American letter code system)
- Graduate school application advice: https://sites.google.com/site/gradappadvice/
- Many grad school and academia career advice: https://theprofessorisin.com/ including:
- Handling the campus visit: https://theprofessorisin.com/category/the-campus-visit/
- Ph.D. poverty: https://theprofessorisin.com/category/ph-d-poverty/