Group Guide

Group guide for:
AI Laboratory for Biomolecular Engineering (AIBE)
Chalmers University of Technology
Section for Data Science and AI, Department of Computer Science and Engineering
ailab.bio

Note that this is a living document and some sections may change. Feedback welcome!

Group values

  1. Teamwork — AIBE is a team! This means that we not only work together to tackle challenging and impacful research questions, but also support each other in reaching our professional and personal goals. We lift each other up and create a positive workplace environment.
  2. Growth — Doing research involves exploring new ideas and tackling unsolved challenges. This means coming face-to-face with failure often. However, we don’t see failure as a negative thing, but rather as a positive experience from which we can grow and develop our abilities. We understand that if things are not going well, they will not stay that way forever, and we can work towards changing or improving our situation. We are not afraid to try a new approach, ask for help from a friend or colleague, or take time off to recharge when we’ve hit a wall. We practice a growth mindset.
  3. Diversity, equity, and inclusion — Diversity, equity, and inclusion (DEI) go hand-in-hand with excellence. A diverse community is able to generate diverse and creative ideas, which are critical in research and teaching. Diversity can refer to differences with respect to gender identity, sex, race, ethnicity, orientation, economic status, family status, neurodiversity, religion, cultural background, or any other aspect of personal identity. We recognize the inherent importance of DEI and are not only respectful of each other’s differences, but also advocate for each other and make an active effort to continuously educate ourselves on the principles of DEI and find better ways in which we can be inclusive.
  4. Open communication — We clearly and kindly communicate our ideas, thoughts, and expectations, as well as our disagreements. When prompted, we can clearly, effectively, and most importantly respectfully give feedback to other group members, whether positive or negative. However, we never critique something that a person cannot change and ensure all feedback is polite and constructive. We acknowledge that we all come from different backgrounds and have had different experiences, and that this can sometimes lead to miscommunications. We are not afraid to ask for help or clarifications when we do not understand something, and we are not afraid to share our ideas, however unusual they may sound. We are always open and willing to share our knowledge with each other.
  5. Improving society — The goal of making the world a better place for all underlies not only the research problems we choose (e.g., molecular engineering with therapeutic applications), but also how we present and report our findings (open-access) and publish the tools we build (open-source). We do not put up unnecessary barriers to our science. We behave ethically at all times. We are keenly aware that improving the world starts with improving our immediate environment. As such, we seek to create not only a positive work environment, but also a good environment in our division, department, and university.

Group overview

  • In AIBE, we are interested in developing methods for molecular engineering using artificial intelligence. By bridging machine learning and the life sciences, we hope to develop a better understanding of how molecules interact to form complex systems, and how we can use these insights to engineer molecular systems for therapeutic applications.
  • We are currently focused on applying our computational tools within the drug discovery and life science domains. In particular, we are interested in improving our understanding and the design of multi-target therapeutic modalities like PROTACs and molecular glues, which require large networks of proteins to come together and cooperate for the desired therapeutic effect to occur. We are also keenly interested in phenotype-guided molecular design. However, this does not mean we are not open to discussing new domains or new research directions and collaborations!
  • Close collaborations with leading academic and industrial groups in computational chemistry, bioinformatics, and computer science are very important to us. Furthermore, we value our collaborations with experimentalists, as working with experimentalists allows us to better understand the problems we are trying to solve, find limitations in the data we work with, and help design workflows for collecting relevant new data which may advance projects in AI-driven life science.
  • Our research covers the full spectrum of methods/algorithm development to applications. Where each member lies on this spectrum may evolve over time depending on each person’s interests and project needs.
  • We are strong advocates of open science. This means that, whenever possible, we submit our manuscripts as preprints to the arXiv, ChemRxiv, or BioRxiv, and we open source our code and data on GitHub or Zenodo. We make a deliberate effort to design tools which are easy to use and accessible (e.g., through thorough documentation, detailed installation instructions, tutorials, etc).
  • My current ideal steady state size for the group is ~4-8 (3-6 graduate students, 1-2 postdocs). This number will evolve over time, and, depending on the academic calendar, will include 6- to 12-month MSc students working on their thesis projects. As we grow, I hope that the senior members of the group will take an active role in onboarding and mentoring new members. New postdocs will be expected to have an interest in mentorship.
  • I aim to be as transparent as possible about the operations of the group. You are always welcome to ask me about hiring plans, current projects, finances, etc. I will be upfront about these things at the beginning of each academic year with a “State of the Group” presentation.

Communication

  • I check my Chalmers email rocio.mercado@chalmers.se and AIBE email rocio@ailab.bio daily and prefer the latter for most communications, including scheduling meetings and sharing important documents. Regarding work matters, I prioritize emails from group members. However, I am occasionally not great at responding, particularly when travelling. If it ever seems I have missed your email, please write me again to remind me. For extremely urgent matters, please call me (phone number in my email signature).
  • If you need me to do something (e.g., provide a signature, give feedback on a manuscript), try to make this clear in the email through the use of bold text, along with the date by which you need me to complete the task. I will do the same for you: if there is something with a specific deadline, I will let you know in my message.
  • If you would like to schedule a meeting with me, my calendar availability can be easily found here. I recommend all group members use either Google Calendar or Outlook to create event invitations to make it easy for myself and others to add the event to our calendars (or quickly see any potential conflicts).
  • We also have a group calendar in Gmail where we can keep track of group events, like group meetings, seminars, and socials.
  • For more technical conversations or back-and-forth discussions on a manuscripr or research project, I recommend to use the AIBE Slack as it provides a semi-permanent record of scientific conversations. We often have similar problems in our research, and Slack makes it easy for other group members to participate in a discussion and see what others think (as well as contribute your own thoughts).
  • Don’t ever feel that you’re wasting my time or bothering me! You can let me know if I’m too slow to respond and it’s urgent (e.g., an impending deadline), either in person, via email, or in a private Slack message.
  • While we should all strive to be as responsive to each other as possible, I definitely don’t expect you to respond to messages outside of normal working hours (M-F 8-5) nor should you expect this from other team members. Similarly, do not feel obliged to respond to emails/Slack messages on weekends.

Resolving conflict

  • If you are uncomfortable with the statements or behavior of another member of the team or division, please don’t hesitate to come to me so that we may discuss it privately and identify the best way to resolve it.
  • For any situation that directly involves me, you can reach out to the DSAI division head Kolbjörn Tunström (kolbjorn.tunstrom@chalmers.se).
  • In work related matters, the Chalmers external occupational healthcare service (arbetsmiljo.stodet@chalmers.se) may also assist you.

One-on-one meetings

  • I’d like to have one-on-one meetings once every week with every group member for whom I am the sole/main advisor, and at least once every two weeks for every co-advised group member (e.g., industry PhD and MSc students). These would ideally be scheduled for 30 minutes but we can always increase or decrease the duration/frequency as needed. They can always be rescheduled or canceled, but let’s aim to have something on the calendar. I’m happy to allocate more or less time for our meetings as needed.
  • What we discuss at each 1:1 meeting will vary as you progress through your time in the group, and will have slightly different focuses for MSc students, PhD students, and postdocs. Most meetings, we’ll talk about recent research progress, challenges, and ideas (new results, planned tasks/experiments, unexpected obstacles, etc). For these types of meetings, it is helpful if you prepare a few slides to guide our discussion. Other meetings might focus on planning, drafting, revising manuscripts, or revising fellowship applications. Others might focus on career development opportunities and long-term planning for your future career. We can also take this time to talk more generally about your experience in the group/division/department, align expectations, and provide two-way feedback to each other.
  • We will be able to use our meeting time most efficiently if you have thought about what you hope to get out of it in advance, so try to come prepared.

Group meeting

  • Group meetings will take place weekly and will be scheduled for 1.5 hours, except during holidays and summer months. The time for group meeting will vary throughout the academic calendar depending on everyone’s availibility.
  • For PhD students and postdocs, attendance at group meetings is required.
  • While MSc students are not required to attend, you are of course welcome.
  • During each meeting, one group member will give a semi-formal presentation on either (a) an introduction to their research project, (b) their research progress since their last group meeting presentation, or (c) a practice talk for an upcoming presentation.
    • These presentations should be planned for around 30-45 minutes, leaving plenty of time at the end for discussion. Everyone should strive to be an active participant in these discussions and feel comfortable interjecting with questions or suggestions during the talk.
    • Presenting your own research will help you reflect on what you have been working on and how it fits into the overall narrative of your project and the research we do in the group.
    • When introducing a new project, be sure to provide an overview of the field and summarize the relevant literature.
    • When presenting on your research progress, make sure to remind us of the context for your work, why it is important, who has worked on it before, what the state-of-the-art is, what your approach is, how it is different, how you’ve progressed, any challenges you are facing, and what the next steps you planned are.
    • Your group meeting presentation is the best opportunity to ask for direct feedback on your approach, particularly if you’re encountering any challenges or seeing poor/unexpected results.
  • The goal of these meetings is not only to educate the rest of the group on what you’re working on, but also for you to get feedback on the talk along with fresh ideas on how to move forward with your project. To get the most out of group meetings, both as a presenter and as an audience member, I expect all atendees to be active participants.
  • When others are presenting, you as the audience are expected to be critical but constructive. Ask probing questions and challenge any missing baselines, assumptions, and model choices (politely — do not become adversarial). This will strengthen the science that we do, as well as help prepare the presenter for comments during conference presentations or peer review.
  • At the beginning of each academic term, we’ll all select an appropriate time that works for everyone’s course/teaching schedules (some time between 9-5 on a weekday).
  • After a presentation, slides from group meetings should be placed in the group Box folder (private, available to group members only). This will be helpful for returning to something a member has previously presented, as well as for me to easily borrow slides for seminar and conference presentations.

Wellness, work hours, and expectations

  • Sweden has comparably strict work environment acts and regulations relative to other countries. PhD students, for instance, are typically employed at Chalmers and have the same rights and obligations as all employees.
  • While we should strive to do impactful, ambitious research, we shouldn’t do so at the expense of our well-being and happiness!
  • Academia offers a lot of flexibility. It’s important to keep a healthy work-life balance and use that flexibility to our advantage. More time spent working does not always translate into increased productivity.
  • There is a lot of work in our field that can be done remotely or at home. Nonetheless, I hope most of you will be able to keep relatively normal working hours in the office during most weekdays, arriving between 8-11 am and leaving 4-8 pm. I would like 11-4 to be a time of maximal overlap when most people are present. It’s nice to be in the office at the same time as your colleagues, both socially and so that you can quickly ask each other questions throughout the day. However, I realize that everyone’s work style and family obligations are different and you should communicate to me what works best for you.
  • On days I come into the office (typically MWTh), I usually arrive in the office around 9am and stay until 5:30pm. Once or twice a week I tend to work from home.
  • On days you are working from home, try to indicate so in your Slack status.
  • If you are planning on working remotely for an extended period of time, try to indicate this in the group calendar.
  • Over the course of any project, there will be slow periods and there will be fast periods. If you’re at a point in your project where things are going well and you are highly motivated to push forward and make progress, then please do so. If you’re in a slower period and you’re feeling idle, unmotivated, or overwhelmed, take a break and try to come back refreshed. I want you to feel comfortable communicating with me and your colleagues during these times so we can figure out how best to move forward.
  • Personal health is more important than work. Just focus on resting up and recovering when you are sick. Sick days are not vacation days.
  • You aren’t expected to work evenings or weekends, especially if we aren’t running up against immovable deadlines and if you’re managing your time well during the week.
  • Chalmers provides opportunities for preventive wellness activities. For instance, the Chalmers Student Support page has many nice online resources. The Chalmers Studentkår also has a page with many useful tips and resources, as well as the Chalmers Doctoral Students Guild (support for PhD students page). For options on disability or functional accommodations, you can find more general information here, and more software-specific information here.
  • Additional information on health, safety, and the workplace environment can be found on the Chalmers intranet.
  • There are many opportunities at Chalmers for extracurricular activities and involvement in student groups or affinity groups. These can enrich your experience and you are encouraged to pursue them for your professional development (e.g., pedagogical courses, writing seminars, etc.) and other intrinsic benefits, but we should talk about it first if you believe that your involvement would significantly hinder research progress. More information on professional development resources at Chalmers can be found on the Chalmers intranet.

Holidays and vacations

  • PhD students and postdocs at Chalmers have the right to vacation days, and your vacation entitlement is as follows:
    • 28 days until and including the year in which you turn 29 years old,
    • 31 days from and including the year in which you turn 30 years old,
    • and 35 days from and including the year in which you turn 40 years old.
  • Employees are entitled to 20 days of vacation during the summer months of June–August. If you prefer, you can schedule your vacation at a different time of year, but know that you are legally required to use at least 20 days of vacation per year, and you should take these 100% guilt free.
  • Many folks take additional time, often in the form of 3- or 4-day weekends throughout the year.
  • Please let me know about planned vacations when you book them if they are longer in duration (i.e., multiple days) and add them to the group calendar. If you are planning on being away for more than a week, try to let me know ahead of time for planning purposes.
  • If it is something you are interested in, I fully support tacking on personal vacation days to the ends of conferences if your schedule allows, since your flight costs will already be covered. Unless there is a significant price difference, you’re welcome to book your flights to arrive/depart a couple days early/late (keep screenshots of flight prices to include in your reimbursement report).
  • For the most up-to-date information regarding holidays, see the Chalmers intranet.

Defining research projects

  • My expectation is that we will work together to identify meaningful and worthwhile projects that are suited to your interests and current/desired skills. I am here to provide as much guidance as needed, particularly toward the beginning of your research career. However, as you progress, I hope to give you more and more intellectual freedom to define your own research directions.
  • Generally speaking, projects should have a clear path to publication when they are started, whether it be as an article, blog, software package, and/or toolkit. Even if the project fails, it should be defined in a way that we learn something meaningful from that failure. You should have a meaningful motivation for your project that aligns with our group values.
  • I find it to be a good idea for most students to have at least two research projects: one with shorter-term goals (weeks/months) and one with longer-term goals (months/years). The long-term project should be designed such that you are able to break it down into many more managable short-term goals.
  • I encourage you to work together on projects! Take advantage of each other’s complementary skill sets. Research is much more fun when done as a team.
  • You should have an idea of what “major problem” in the field your project is addressing. However, you don’t have to solve this “major problem” with each of your projects; making incremental steps towards helping us solve it is also progress.
  • As you get more comfortable and experienced with the research process, I hope to encourage you to take riskier and riskier projects (high risk, high reward). Of course we can work together to define what this means for you.
  • Sometimes, our choice of research topics will be constrained by the grants we have secured and/or the grant opportunities we are eligible to apply for (especially for postdocs). Certain grants will have more specific deliverables that will guide what we do.
  • It can be helpful to keep an eye out for fellowships and grant opportunities that will offer us the flexibility we need to do the research we are most interested in (more on that later).

Documenting work

  • It is important that we keep careful notes of our work for the sake of publications, patent filings, reproducibility, and later reference by future members of the group once you depart. You’re welcome to use whatever format you find most convenient: a written journal, an electronic word document (e.g., using Notion, Obsidian), etc. I have a preference for electronic documents so that we can archive them and back them up.
  • Keep backups of everything, and remember to back-up regularly! I personally do 99% of my work either in GitHub repositories that I manually sync or in Notion/Overleaf documents that automatically sync.
  • For projects involving code, you should actively maintain private (before publication) GitHub repositories for all of your projects. When dealing with large datasets, try to maintain copies across multiple servers when possible.
  • I recommend following a strict naming convention for all presentations and documents. In my opinion, “YYMMDD [Filename]” is the best choice; electronic files following this convention will be easy to sort in chronological order.
  • If you do not already use a password manager, I strongly recommend you start. LastPass, Bitwarden, and Keeper are popular choices.

Good coding practices

  • AIBE consists of members with a range of programming experience. If you feel that you would like to improve your programming skills upon joining, there are some nice online resources for getting up to speed on these things (see the introductory tutorials linked in the onboarding guide).
  • Regardless of your background, I highly recommend the online course “The Missing Semester of Your CS Education” from MIT CSAIL.
  • Most of our code will be likely be written in Python. You should familiarize yourself with PEP 8 guidelines and use tools like Pylint to enforce good style. I also strongly recommend that everyone in the group use (optional) type hints in their code so that others can more easily understand what you have written. Google has a comprehensive style guide for Python code.
  • While working in Jupyter notebooks is a great way to analyze experiments and provide tutorials of code, rigorous testing and reproducible research is more easily conducted with a well-organized and documented codebase. For examples on how to structure your codebase, you can have a look at the dl-chem-101 repo.
  • There is no “right way” to structure your code as long as it is easy to run, and your calculations reproducible. However, try to follow accepted conventions when possible. Reading codebases for other packages is one of the best ways to see and learn good coding practices (as well as bad). You can also have a look at common cookiecutters, such as this one from MolSSI.
  • An excellent way of looking at how you can improve your code and the accompanying documentation is to imagine yourself looking at your codebase 6 months from now. Would you be able to reproduce what you did?
  • When you are ready to publish and open source your code, you should triple check that the repository does not contain any proprietary information (private data, passwords, etc., which should never be pushed to a repo in the first place) before making the repository public. It is also common to create a new clean repository and push your finalized code all at once. We will create a fork of your public repository in the AIBE group GitHub.
  • I would encourage you to have someone else in the group review your GitHub repo before publication. If they are not able to run your code, then it is unlikely that other folks, less familiar with your work, will be able to do so. This may take a long time depending on the size of the codebase so make sure to properly acknowledge those who help out in the review process (and, ideally, pay it forward sometime).
  • For reproducibility, you should always use a dependency manager like Conda or Mamba. For more complex dependencies beyond Python packages, use Docker containers.
  • Version your code, especially upon publication. This way you can always reference and/or return to the exact version used in specific publication.
  • Best practices in software development change, so we should all inform each other of useful resources, packages, and new tools. The group Slack is a good place for this.
  • If you’re not sure what your development workflow should be, or how to use certain tools like GitHub, please just ask! We all had to learn this for the first time in our lives at some point, and there is no shame in asking.

Manuscripts

  • Publishing in academic journals and conferences is one of the primary ways that we communicate our research with the broader community. While we should never see publishing as a numbers game, we should be aware that the quality of our publications is a major way in which we are evaluated as scientists, for better of for worse.
  • Typical publication venues that I anticipate will be relevant to our group’s research include (but are not limited to) conferences such as ICML, ICLR, AISTATS, and NeurIPS, conference workshops such as AI4Science and ML4Molecules, and journals such as JCIM, J. Cheminf., Machine Learning: Science and Technology, Nature Machine Intelligence, etc. We should also strive to publish our work concurrently on the arXiv, ChemRxiv, or BioRxiv when possible so as to maximise the accessibility and reach of our research.
  • Deciding authorship order and inclusion is not always straightforward. More often than not, it will be clear who is leading the project. In those cases, I will work with the lead author to discuss the contributions of other members of the group and propose an author list for everyone involved to review. We should have conversations about authorship as early as possible, even at the start of a project, to avoid misaligned expectations when it comes time to write a first draft.
  • The quality of a manuscript and whether the right audience reads it is more important than the sheer number of papers we publish or the impact factors of the journals we publish in. With the sheer volume of publications coming out each day in out field, I also feel it is important not to “litter” the literature with mediocre manuscripts, and we should do our best to avoid this practice.
  • Before you start writing a manuscript, you should prepare a draft outline for us to review together. A good paper outline will contain the following elements:
    • Abstract: A short paragraph that concisely describes the narrative of the entire paper. You might find the article “How to construct a Nature summary paragraph” useful when preparing an abstract (I frequently reference it, both for preparing conference and publication abstracts).
    • Introduction: A couple of paragraphs describing the problem being addressed, how others have tried addressing it in the past, and what you are doing differently. You should also include a few sentences here on how your new method is different/better.
    • Contributions: A short section (usually bullet points) summarizing the 2-5 main take-aways from the manuscript.
    • Methods: A couple of paragraphs, ideally divided into subsections, discussing the technical details of the method(s) you have developed, the data you are working with, the various experiments you ran, etc. However, do not present or discuss results in this section.
    • Results: A couple paragraphs summarizing the key results of your study. Here, you should be strategic about how you present the results, particularly in the figures (a well-done figure is much more enjoyable to read than a wall of text).
    • Discussion: Here, you can go a bit more into a detailed analysis of your results. You can discuss , for instance, if something was surprising/unexpected, what the advantages and limitations of your method are, etc.
    • Conclusion: A short paragraph or two summarizing the narrative of the paper, with an emphasis on the outlook of the work (i.e., what do you plan to do in the future? what questions remain unanswered?).
    • Code and data availability: One of the most important sections of the paper. Here, make sure to include links to your code (typically on GitHub) and any data necessary to run or reproduce your results from the paper. If the data is too large for a GitHub repo, one alternative is to upload your data to Zenodo.
    • Acknowledgements: Please acknowledge our funding sources (there is usually specific guidelines for how we must do so — check with me if unclear). Also, acknowledge others who have helped you out with your project but perhaps with smaller contributions than a fellow co-author.
    • Appendix: Can contain additional data or details that an interested reader might reference, but that would be clunky or disrupt the general narrative of the paper if included in the main text.
  • However, note that the specific outline and required sections will depend on the venue you plan to submit to. For instance, chemistry journals don’t typically expect a separate “Contributions” section, and different journals have different required sections (and word/page limits). Most journals and conferences provide a pre-formatted LaTeX/MS Word template which you can download and use as a starting point for your manuscript.
  • After we work on an outline together, I would like you to prepare the initial draft. We will likely go through many iterations together, so don’t worry about getting it 100% polished before showing me the first draft. However, do try to make sure there aren’t significant distracting typos or placeholders. As we get closer to finalizing the content of a manuscript, my comments will shift from high-level organizational changes to suggesting more specific wording changes. When you share a draft with me, you can specify what kind of comments or feedback you’re looking for.
  • I would like us to use Overleaf for every manuscript unless a target journal explicitly forbids it. It might take some time to get used to writing in LaTeX if you are not familiar with it, but the ease of formatting figures, tables, references, and cross-referencing these in the text makes it worth it — especially for MSc and PhD students who plan to reuse parts of the text in their theses.
  • Figures should look clean and professional (even draft figures), using consistent font families (sans serif) and font sizes. Make sure all text in a figure is legible (e.g., the axes labels, tick labels, etc.). I recommend using Adobe Illustrator for making figures. It is a steep learning curve but worth your while, as you will likely be making many figures throughout your scientific career.
  • Chemical structures should always be drawn in ChemDraw, preferably using the ACS style or a modification thereof.
  • Graphs should be prepared programmatically using tools like seaborn, matplotlib, or similar programs (not MS Excel — it’s not a good aesthetic).
  • When assembling multipanel figures in Python with Matplotlib, figures should be exported at the figure size intended in publication or poster.
  • Please do not ever submit work for publication (abstracts, posters, papers) without making sure I’ve had a chance to look it over.
  • While chemistry-focused journals do not have strict deadlines, computer science conferences and workshops do and we should all be conscious of those dates and deadlines. We’ll all likely be working a little bit harder in the weeks leading up to a major conference deadline if we are preparing a submission.
  • When planning for deadlines, do not forget that if we have work co-authored with collaborators outside the group — especially from industry — then there is likely an internal review process the material to be published needs to undergo (usually at least 2 weeks). So please budget for this time. It usually applies for any archival publication, including the abstract.
  • Here are some additional resources for scientific writing:

Grants

  • Writing proposals and securing funding for the group is one of my primary main as PI, but it is also good practice for you to develop your research and communication skills. If you would like to be involved in grant writing while in the group, graduate students and especially postdocs are welcome help write grant proposals for the lab as long as it doesn’t significantly detract from the time you spend on your research. This includes brainstorming, writing text, making figures, and attending meetings with potential collaborators, etc.
  • Tell me if you have a particularly active interest in grant writing, e.g., to prepare for an academic career.

Literature

  • It can be challenging to keep up with the literature in such a fast-moving field. It feels like every week there is a new groundbreaking paper. We should help each other stay on top of the state of the field as best we can by sharing papers with each other and discussing them.
  • We have a #papers channel in the AIBE Slack where you should post anything that looks interesting and broadly relevant to the group, whether it be an article, blog post, or recorded talk. If possible, read it before you post so you can provide a few bullet points summarizing the main results. Usually such a summary can help help kick-off a thread discussion.
  • When it comes to your own research project, it’s good to begin with a thorough understanding of what has been done before so we don’t end up accidentally reinventing the wheel. As the number of distinct research projects in the group grows, I will have to rely more and more on you to help me stay up to date.
  • To stay on top of the literature, you can also set up RSS feeds, Google Scholar alerts, or follow relevant feeds on social networking platforms like LinkedIn, Twitter, and Mastodon.
  • Make sure you have a good reference manager. I personally use Paperpile and its Chrome extension that lets me quickly download papers I have open. Other popular choices include Mendeley and Zotero (open-source).

Fellowships and awards

  • Keep an eye out for fellowships that you’re eligible to apply for. We can work together to help prepare a competitive application for you. When preparing any fellowship application, pay close attention to deadlines and special requirements (e.g., you may need to secure a departmental nomination or administrative approval).
  • For any of you who are funded by the WASP program, I encourage you to take advantage of the available opportunities they provide for graduate students.
  • I also maintain my own list of fellowships and opportunities on my personal website, which you can feel free to browse. With time I will move those resources here.
  • Applying for fellowships will not only help your own career, but help with the group budget. I am willing to spend a lot of time working with you to craft your proposals and statements. Group members are also encouraged to share their application materials regardless of whether they were successful. There is no shame in getting an application rejected; sometimes it is simply bad luck but usually we can learn from the process and improve our proposal based on the reviewer’s comments.
  • Always read clearly the evaluation criteria and, if possible, understand who will be evaluating your application. It can be helpful to put yourself in their shoes when reading through your application to see if you have included everything they would be looking for.
  • You should also be on the lookout for internal and external awards. If you find one that’s relevant to you and you would like to be nominated, please don’t hesitate to ask me or a colleague to nominate you!
  • Try to give me at least a couple weeks notice to prepare a recommendation letter if I don’t already have a recent one on file. It’s helpful if you also send me your CV, any materials related to the application, and anything you would like me to highlight in my letter (see Recommendation Letters).

Internships

  • While it is quite common for graduate students in computer science programs abroad to pursue summer internships, it is not such a common practice here in Sweden. However, I believe such experiences can be invaluable, especially if you know you would like to pursue an industrial career after your PhD, or if you are undecided between academia and another career path.
  • Please let me know if this is something you would be interested in and we can figure out how to go about it. I can also help you reach out to people at various companies, especially if I have a connection there.
  • For WASP-funded graduate students, there is generous funding available for research stints abroad or international study visits. I encourage you to take advantage of these opportunities!
  • Note, if you are a student from abroad reading this and would like to visit my group as part of your MSc thesis, please read up on Erasmus guidelines at your university as that is the easiest way for you to do a research stay in my group.

Conferences and schools

  • Attending conferences is an essential part of your professional development!
  • If there is a conference or winter/summer school you would like to attend, please talk to me as early as possible. I expect that international machine learning conferences like ICML, ICLR, and NeurIPS will be popular in our group. However, take advantage of local opportunities as well, such as the Gothenburg AI Alliance (GAIA) annual conference and the Nordic Conference on Computational Chemistry (at AstraZeneca), as well as European conferences such as the RDKit User Group Meeting and the German Cheminformatics Conference. There are also several focused Gordon conferences throughout the year which may be relevant.
  • Keep an eye out also for relevant conference workshops, such as the ELLIS ML4Molecules and AI4Science workshops, as well as affinity groups like Queer in AI, Women in Machine Learning, and LatinX in AI. These are not only great opportunities to present your work but also for networking.
  • Local events are terrific opportunities because there will be no or few transportation/lodging costs, there are no challenges with obtaining a visa, and you can avoid being gone from home for extended periods (for instance, maybe you don’t want to travel due to family reasons). Online symposia are also nice for these reasons, with the added benefit that registration is often free.
  • For WASP-funded students and postdocs, the annual WASP Winter Conference is a great opportunity for networking and learning about cutting-edge AI research going on in Sweden.
  • Many conferences have specific travel awards you could be eligible for, so make sure to do some research when looking into the potential costs.
  • At each of these conferences (except local or low-cost conferences) you should be presenting your original research in a poster or oral format, so make sure to submit an abstract in good time. If you are scheduled to give a presentation or poster at an upcoming conference, we can set aside time to go over what you plan to present, especially if it is your first time at a major conference. For oral presentations, we can also book a time slot for you to practice your presentation for the group; this is a good chance to get valuable feedback from group members in a low-stakes, non-threatening setting.
  • For poster presentations, I would like to see a draft of your poster before it is printed. However, once it is printed, you are encouraged to reuse it, especially if you have two or more back-to-back conferences or workshops.
  • Remember that how you communicate your work is a reflection of not just you, but the whole group, so always take it seriously and help each other out.
  • For an amazing resource on how to prepare engaging scientific talks, I highly recommend this “How to Speak” lecture from the late Patrick Winston.

Opportunities for mentorship and outreach

  • Group members are highly encouraged to organize and participate in outreach activities! Please let me know if you hear of events where the group can participate.
  • Examples of programs which may organize recurring outreach events include, but are not limited to, the WASP Diversity and Inclusion Group and GENIE.
  • If mentorship is a skill you are particularly looking to build in your time at AIBE, let me know. More senior PhD students and postdocs will be expected to take on more mentorship responsibility for junior group members as time goes on. There may also be the opportunity to mentor students outside AIBE.

Professional development and career guidance

  • I would like all new members of the group to fill out an Individual Development Plan (IDP) upon joining and to set up a meeting early on to discuss their professional development plans with me. This way I can best provide guidance throughout your time in the group. More details about this, and the IDP template, can be found in the onboarding guide.
  • One of my primary goals is to make sure you are set up to succeed the next stage of your career and that you have all of the support and connections you need. I will provide my network of connections from academia and industry to each of you. It is also in your best interest to periodically discuss your career goals with me at least once per year, that way we can make sure you’re on the best course for achieving these. Note that your goals may change during your PhD, and that is okay!

Group socials and fika

  • The relationships we build both in and outside the lab can add value to our life and help build a positive environment for us to thrive in. Although our research is awesome and certainly a large part of our lives, it should go without saying that there is more to life than research!
  • One way to foster a fun, collegial environment that we look forward to coming to every day is through regular group socials and fika. If you don’t know what fika is, don’t worry, you will learn.
  • We can have group fika on a weekly basis, and we will choose a time in the afternoon when everyone is available (after group meeting would be one option). The fika room is on the 6th floor of the EDIT building.
  • For group socials, we will organize semi-regular events where we meet up outside of work about once a month for activities like group dinner, hikes, pub quiz, etc. If you have any ideas feel free to suggest them, or even organize a social yourself, but remember to ensure that organized group socials are inclusive of all lab members who want to join. You are of course welcome to bring any guests to these events.
  • Don’t ever hesitate to ask anyone in the group or division to lunch. This is one of the easiest ways to meet your colleagues, and everyone is very friendly and will almost certainly say yes. There is a café, Linsen, in the EDIT building where you can get lunch at a relatively good price, but you will find that most people bring lunchboxes from home and heat them upstairs (the fika room doubles as a lunch room). There are a few good restaurants in and around campus as well, for when one is feeling more adventurous.
  • The division organizes an annual group retreat which is a great place to meet our colleagues outside of AIBE in a less formal setting.
  • Finally, there are many great student organizations around campus that regularly organize socials, and I encourage you to ask more senior group members about these and participate if you are so inclined.

Links

  1. Group website: ailab.bio
  2. Group GitHub: github.com/ailab-bio
  3. Group Slack: [see onboarding guide, group members only]
  4. Group Box: [see onboarding guide, group members only]
  5. Group calendar: [see onboarding guide, group members only]
  6. Chalmers intranet: intranet.chalmers.se
  7. AI conference deadlines: aideadlin.es
  8. Chalmers Doctoral Studies Support (need Chalmers ID to access)

Acknowledgements

This group guide was modeled after the Coley group public group guide, available at coley.mit.edu.