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Molecule Maker Lab Newsletter - Issue 35
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Happy September! We have several updates this month including: more details about our annual retreat, MMLi's accomplishments and travels from this past summer, two new MMLI spotlights, and more! Remember that we LOVE submissions for MMLI newsletters, and we would love to feature news and opportunities from our external advisory board and partners as well! National Postdoctoral Appreciation Week (NPAW) is from September 16th-20th, and recognizes the significant contributions of postdoctoral fellows. We hope you will join us in thanking and appreciating all of our MMLI postdocs. Virtual events for postdocs in honor of NPAW can be found here. |
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In this issue: - Call for submissions
- In MMLI's Orbit
- MMLI Updates & Reminders
- A Summer of MMLI: Publications, Conferences, and awards.
- MMLI Spotlight: Learn about your colleagues and collaborators!
- Upcoming opportunities
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In MMLI's Orbit: Snippets from the lives of Molecule Makers outside of the lab
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Pet of the month: Name: Lucca Owner: Costas Maranas Lucca (she) is a mischievous frisbee-obsessed manipulator of humans. |
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Molecular Inspirations Artist: Nelle Planey, age 5 This may be James Planey's last month with us at the Molecule Maker Lab, but he is raising a molecule maker of his own! The artist, Nelle Planey, describes this as her depiction of the Molecule Maker featuring a machine to test whether or not molecular outputs are toxic. |
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All MMLI trainees, staff, and faculty are strongly encouraged to attend, and we would love to see as many industry partners and advisory board members as possible join us in person as well! Registration is now open - please register by September 26th. Everyone: Join us for an evening of fun and networking on Thursday, December 4th to try your hand at the MMLI escape room and debrief or just catch up with everyone at the evening happy hour! Industry Partners: Please join us to represent your company at our "Speed Networking" event by providing an elevator pitch about your company and up to 4 representatives to network with MMLI trainees along with faculty. Join us at the end of the conference for a half day professional development period (details TBD, ideas welcome!). Industry partners are also welcome and encouraged to present posters during the poster session. Advisory Board members: Please join us for our in-person EAB meeting, participate as mentors in our speed networking event and join the PD session if you are interested! Advisory board members are welcome and encouraged to present posters during the poster session. Trainees: Trainees are highly encouraged to present posters, as well as to join us at the end of the conference for a half day professional development period (details TBD, ideas welcome!). |
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Highlights from a Summer of Molecule Making
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Message from Director, Huimin Zhao: Thank you for your submissions - please continue
to submit your accomplishments so that we can be proud of the MMLI community together.
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A group of Lab 217 Escape Room Escapees at ACS Fall 2024, Denver, CO. |
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The MMLI escape room team explore Meow Wolf, Denver. |
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Ayush Kumar Shah presented his and Bryan Amador's journal track (ICDAR/IJDAR) paper at ICDAR 2024 in Athens, Greece. |
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Conferences & Publications SciMON: Scientific Inspiration Machines Optimized for Novelty Qingyun Wang published his recent ACL paper in which he and his co-authors explore and enhance the ability of neural language models to generate novel scientific directions grounded in literature. [PDF] “Biological Synthesis of Chemicals and Fuels.” 29th Biotechnology and Biochemical Engineering Society of Taiwan (BEST) annual symposium, Jingmeng, Taiwan, June 22, 2024 - Huimin Zhao. “A Journey Towards the Development of a Cloud Biofoundry.” ECI Biochemical and Molecular Engineering Conference XXIII, Dublin, Ireland, July 22, 2024 - Huimin Zhao. “New Tools and Strategies for Protein Engineering.” Gordon Research Conference on Enzymes, Coenzymes and Metabolic Pathways, Waterville Valley, NH, July 28, 2024 -Huimin Zhao. During the first week of September, Ayush Kumar Shah presented his and Bryan Amador's journal track (ICDAR/IJDAR) paper at ICDAR 2024 in Athens, Greece. Their paper details the ChemScraper born-digital and visual molecular diagram parsers. Shah, A.K., Amador, B., Dey, A., Creekmore, M., Ocampo, B., Denmark, S., and Zanibbi, R. ChemScraper: leveraging PDF graphics instructions for molecular diagram parsing. IJDAR 27, 395–414 (2024). (PDF: https://link.springer.com/content/pdf/10.1007/s10032-024-00486-7.pdf ) "Application of Chemoinformatics and Machine Learning to Discover and Optimize Enantioselective Catalysts” - Scott Denmark.
-7th International School of Process Chemistry, Gargnano, Italy; May 26-29, 2024
-34th International Symposium on Chirality, Kyoto, Japan, August 26-29, 2024. Thrust 5 represented MMLI at the American Chemical Society national conference in Denver, August 18-22nd by bringing Lab 217, the MMLI themed escape room as a conference experience. James Planey, Rachel Switzky, Sabrina Abdulla, Carter Boyce, and Shreya Sachdev transported and built the escape room within the walls of the Denver convention center and hosted the experience for 130 ACS participants.
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Awards and Recognition Huimin Zhao: Heng Ji: - A joint paper by PIs Heng Ji and Ying Diao has been accepted by the 33rd ACM International Conference on Information and Knowledge Management (CIKM 2024):
GLaD: Synergizing Molecular Graphs and Language Descriptors for Enhanced Power Conversion Efficiency Prediction in Organic Photovoltaic Devices Thao Nguyen, Tiara Torres-Flores, Changhyun Hwang, Carl Edwards, Ying Diao and Heng Ji - Selected as "Young Scientist" by the World Laureates Association 2024
Jiawei Han: Ying Diao: |
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MMLI in the News Molecule Maker Lab institute Unveils Upgrades to Alphasynthesis platform, Carl R. Woese Institute for Genomic Biology, UIUC, June 6, 2024. "Bringing Chemistry, AI, and Design Together: Molecular Maker Lab Institute’s Escape Room." ACS Network, July 11, 2024. Discover The Midwest’s AI Powerhouse: The University Of Illinois, Forbes, July 11, 2024 “New Additive Process Can Make Better and Greener High-Value Chemicals.” DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), UIUC, July 23, 2024. “NSF funds new iBioFoundry at Illinois.” Illinois News Bureau, UIUC, August 28, 2024. "Breaking open the AI black box, team finds key chemistry for solar energy and beyond.", Science Daily, August 2024. "Unlocking Teamwork: Lessons Learned from an AI-Assisted Escape Room Experience." LinkedIn, Shreya Sachdev, August 29, 2024. Seed Grant awardee feature: "Using machine learning to speed up simulations of irregularly shaped particles." Chemical & Biomolecular Engineering, UIUC, September 3, 2024.
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Do you remember your first experience in the lab? For many of us, it was a fundamental point in our careers. MMLI will be working with summer research programs to mentor summer research students, and we are looking for Faculty and Trainee mentors to work with these students. Please submit a short blurb (~100 words) about a possible project or lab description, Name of PI, Name of Trainee, and number of students you can accept this summer. Please send submissions to abdulla3@illinois.edu. |
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Follow MMLI on Social Media Help the Molecule Maker Lab institute launch its way to internet fame (or at least just presence...) by following us on social media and tagging MMLI in any relevant stories! LinkedIn: Molecule Maker Lab Institute Twitter/X: @Molecule_Maker Instagram: @moleculemaker (MMLI as a whole) and @mmlispc (Student Postdoc Council) Coming soon: MMLI on Youtube. Interested in contributing or brainstorming ideas? E-mail Sabrina at abdulla3@illinois.edu to join the Youtube brainstorming committee. |
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Faculty Spotlight:Heng Ji Heng Ji is a professor at Computer Science Department and part of Thrust 1 in MMLI. Her esearch focuses on Natural Language Processing, especially on Multimedia Multilingual Information Extraction, Knowledge-enhanced Large Language Models and Vision-Language Models, AI for Science and Science-inspired AI. There exist approximately 166 billion small molecules, with 970 million deemed druglike. Despite this vast pool, only a tiny portion of molecules are currently approved across global healthcare systems. This scarcity underscores the urgent need for innovative approaches, motivating me to contribute significantly to molecule function discovery with advanced AI technologies. Many of these technologies can be applied to other domains such as new material discovery. My favorite part of MMLI is the people. It’s a wonderful privilege to be able to work with wonderful chemists such as Profs. Martin Burke, Ying Diao and Huimin Zhao. They are extremely intelligent, open-minded, kind and generous, and have become my close collaborators and good friends. Outside of the lab, Heng regularly does yoga and Zumba indoor, and has been enjoying outdoor activities in the countryside, especially cycling and hiking in the forests. She has been traveling to 30+ countries in six continents.
Fun fact (or extremely average fact) about yourself. I’m very creative in terms of making dumplings. |
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Trainee Spotlight: Bryan Amador Bryan is a graduate student in the Computing and Information Science PhD program at Rochester Institute of Technology, where he is currently in his third year and a member of the Document and Pattern Recognition Lab (DPRL). In the DPRL lab, they research systems that recognize and retrieve information from documents, images, and videos. Bryan’s area of research is Math Information Retrieval, where the goal is to develop tools that facilitate users' access to mathematical content. Right now, he is most excited to work on modeling the task of formula search as a graph embedding and retrieval problem taking advantage of the visual and semantic content of formulas. The DPRL lab easily connected to MMLI, as they have been working by recognizing math formulas from documents. That is, given a formula image, infer the symbols and the structure of them so that they can be used in downstream tasks as retrieval. So they thought similar techniques can be applied to molecular diagrams. With this in mind, ChemScraper was created. The main goal of this tool is to extract molecules from documents and export them to formats that can be used by chemists for their needs. For instance, produce SMILES from molecules in chemical papers that can be further indexed and searched to facilitate reaction planning. Outside of the lab, Bryan loves to play football. If he had more time, he would like to continue learning to play guitar (his old guitar is probably full of dust back home). He like to visit places where he can appreciate natural wonders, to cook and try new dishes whenever he can, and sometimes play video games as well. Fun fact (or extremely average fact) about yourself you would like to share: I love tulips. I wish one day I can have my own tulip garden. |
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Upcoming Opportunities: Volunteering & Science Communication - 10/14 & 10/15: MMLI at IGB's World of Genomics, Museum of Science and Industry Chicago
- Help museum explorers create their own protein by joining MMLI's booth! Join for one or both days. (2-4 volunteers needed)
- 10/19, 10/26: Imagine STEM with Molecule Maker Lab
- 9:30am-12:30pm, topics TBD & open for discussion. (1-2 volunteers needed)
Escape Room Leadership & Volunteering Experience - Help run the MMLI Escape Room: Want to help run the MMLI escape room? Join the volunteer database or sign-up to help at specific events by e-mailing abdulla3@illinois.edu. Volunteers will be trained and work with experienced escape room-hosts.
- 10/6-10/12: Lab 217 at Reimagining the Classroom Symposium at SCD. Escape room running all week, symposium on October 9th. (All volunteers welcome, slots will be scheduled according to your schedule).
- 11/4, 5pm-10pm: Lab 217 Escape Room with U Chicago College Readiness Students (2-6 volunteers needed).
- 12/5, 1pm-6pm: Have you already done the MMLI escape room? Excited to see how you colleagues fare? Help run the escape room for the MMLI retreat on 12/4, 1pm-6pm!
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September in AI, Chemistry, and Culture
September 4, 1987: AI Pioneer McCarthy Born. John McCarthy, whose many contributions to the field of computer science included the language LISP, is born in Boston. LISP -- the first computer language designed for writing Artificial Intelligence (AI) programs -- while a professor at MIT.
September 20, 1954: First FORTRAN Program Runs. FORTRAN, which is an acronym for "FORmula TRANslator," was invented at IBM by a group led by John Backus. FORTRAN's purpose was to simplify the programming process by allowing the programmer ("coder") to use simple algebra-like expressions when writing software. FORTRAN is still in use today in scientific and engineering applications, making it one of the oldest programming languages still in use (COBOL is another).[Source]
September 21st: Birth of the Prophet Muhammad (Shia Islam). Born in 570 CE, Prophet Muhammad’s [peace be upon him] birthday is commemorated by Muslims around the world during the month of Rabi’ Al-Awal. Mawlid an-Nabi – literally, The Birth of the Prophet – is often referred to as the Mawlid. September 22nd-29th: M abon (Autumn Equinox) (Wicca). The Autumn Equinox is a time for giving thanks and for reflection. At Mabon, the day and the night are equal in length, in sublime balance. For many locations, Mabon coincides with the final harvest of grain, fruits, and vegetables. Mabon, also called Harvest Home, is the time of thanksgiving. September 26th: First of Mashiyyat (Will) (Baha'i). At the beginning of each Bahá'í month, Bahá'ís gather for an observance called the 19-Day Feast. The First of Mashiyyat (Will) begins at sunset of the first day and ends at sunset of the last day. It is a three-part observance with devotions, community consultation, and a social portion. Some students or employees may request schedule adjustments in order to observe.
September 28th: Leil Selichot (Judaism). Jewish students or employees often observe Leil Selichot by praying for forgiveness in preparation for the High Holidays.
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Thanks for reading! Want to request a topic for the October newsletter, or have papers, conferences, or other accomplishments to feature? Submissions for October are open until October 9th - use the form below or e-mail abdulla3@illinois.edu. Industry partners and external advisory board members are encouraged to submit relevant info and features as well (we want to see your pets too!) |
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