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Welcome New Faculty, Fellows, Students and Staff (Summer 2024)

June 20, 2024
by Shane Zhang

María Rodríguez Martínez, Associate Professor of Biomedical Informatics and Data Science

Maria Rodriguez Martinez is an associate professor at BIDS. She is originally from Spain and trained as a physicist, starting her academic journey in theoretical cosmology and earning her PhD in Paris. After her first postdoc at the Hebrew University, I transitioned to computational biology. “My current research interests lie in computational immunology, particularly in modeling T and B cells of the adaptive immune system. I employ a combination of mechanistic models and deep learning techniques. Within deep learning, I am particularly focused on developing interpretable approaches—models that can elucidate the underlying mechanisms driving a model's decisions. Interpretability is crucial to create trust in a model's predictions and for identifying potential biases and algorithmic errors.”

Maria came to Yale for its excellence in immunology and its support for work in data science. “I have been at BIDS for just a month, but my experience has been overwhelmingly positive. Everyone has been incredibly welcoming and eager to help us to get settled.” Her favorite part about New Haven is the combination of nature and urban life, with changing foliage and squirrels visible from city windows. If she were a technology, she’d be a noise-canceling device or a high-quality opera streaming service!

Claus Horn, Associate Research Scientist

Claus Horn grew up in Germany and has lived in Spain, France, Italy, Japan, California, and Switzerland over the years. At age 15, his favorite book was Gödel, Escher, Bach, which ignited his fascination with the interplay of philosophy, computation, and intelligence.

His passion for AI has led him to develop machine learning applications in diverse areas such as elementary particle physics, finance, insurance, and life sciences, with a recent focus on autonomous learning systems for life science applications and the design of enzymes for medical applications. When not working, his favorite activities include practicing sports outdoors, be it hiking, climbing, mountain biking, or skiing.

"Biomedical AI has a great future," says Claus. it's great to join BIDS right at the beginning and be part of a field that is expanding."

Brian Ondov, Associate Research Scientist

Brian Ondov is from northern New Jersey and joins us as an Associate Research Scientist. After getting his bachelors degree in Computer Science from RPI, he worked on video games for franchises like Spiderman and Guitar Hero. He left the industry to turn towards research, earning a master’s in Bioinformatics from Georgia Tech, and a doctorate in Computer Science from University of Maryland College Park. His research has spanned Computational Genomics, Machine Learning, and Human-Computer Interaction. He is currently working to apply this experience to explore how Large Language Models can help people interact with biomedical literature.

Asked about his experience at BIDS, he says “It is a very collegial and enthusiastic environment. On top of all the talent and resources, I feel like everyone here wants me to succeed, and it’s great to have that support.” His favorite part of New Haven is the architecture. “I love the contrast of majestic gothic buildings with bold mid-century modernism. Just walking through the city feels like visiting a museum, even down to the parking garages.”

Daniela (Ruey-Ling) Weng, Web Designer/Visual Design Specialist

Daniela, born and raised in Taiwan, joins BIDS as a web designer. She completed her undergraduate studies in Taiwan, majoring in Italian Languages and Culture with a minor in Advertising and Public Relations at Fu Jen Catholic University. Daniela holds two master's degrees: the first in International Luxury Management from NEOMA Business School in France and MIP Politecnico di Milano Business School in Italy, and the second in MS Information Design and Data Visualization from Northeastern University.

At BIDS, Daniela specializes in UI/UX design, focusing on creating accessible and engaging visual narratives and graphics for interfaces. Her expertise in business marketing helps her balance user needs with business objectives, building an environment for seamless communication between users and digital interfaces. Daniela chose to work at Yale for the educational resources, which support her continuous professional growth. "The community at BIDS is very friendly and welcoming."

Rui Zhu, Postdoctoral Associate

Originally from China, Rui completed an undergraduate degree at the University of Utah in Salt Lake City, majoring in math. After earning a master’s degree in statistics and PhD in computer science at Indiana University Bloomington, Rui joins BIDS as a postdoc supervised by Chair Lucila Ohno-Machado, MD, PhD, MBA. His primary fields of research are medical AI security and privacy. Rui says the experience at BIDS has been "so far, so good!" Around Yale's campus, he likes to admire Harkness Tower and describes himself as a "dog person". If Rui were a technology, he’d be a coffee machine—always buzzing with energy!

Tahseen Rabbani, Postdoctoral Associate

Born and raised in Richmond, Virginia, Tahseen graduated from the University of Virginia with a degree in mathematics, where he was very much interested in number theory and group theory. Following a stint as a software engineer at a large EMR company (Epic Systems), he began a PhD in pure mathematics at the University of Maryland before switching to computer science. Tahseen successfully defended his PhD in March earlier this year under Dr. Furong Huang. His thesis was focused on efficient, private, and distributed methods for AI/ML, and his primary areas of research are distributed learning, training efficiency, and compression. However, more recently Tahseen has also begun working on watermarks for generative imagery and few-shot machine translation. Since his background is in mathematics, he likes working out theoretical guarantees as well.

As a new postdoctoral associate in Annie Hartley's LiGHT lab, Tahseen will continue researching efficiency, privacy, and federated learning and mentor/supervise students at Yale and EPFL who can help drive these projects. He is looking forward to leading projects that will integrate DISCO with initiatives at WHO, ICRC, and Doctors Without Borders. "I truly believe that federated learning can be used to build powerful, global healthcare models while protecting user/patient privacy," Tahseen explains.

If Tahseen were a technology, he would want to be a sea floor rover—who knows what's down there! (Hopefully a sea monster or two.)

Tham Hoang, Postdoctoral Associate

Tham is a new postdoctoral associate joining the lab of Jihoon Kim at BIDS. Originally from Vietnam, Tham completed her PhD in computer science at University of Connecticut. Her research interests focus on genetics, immunology and multi-omics data analysis. "Yale has great sources and an environment to be successful," Tham says. "I have been here for more than a week and the experience [has been] excellent. Business office staff are helpful and welcoming." In New Haven, Tham is enjoying the historical architecture, and is thinking of adopting a puppy.

Bin Choi, Summer Fellow - Clinical NLP Lab

South Korean but raised in the Middle East, Bin is an undergraduate at Yale-NUS College in the computer science and Duke-NUS medical pathway. While on a leave of absence, Bin worked full-time as a software engineer in Korea for the last two years, primarily focused on the server/backend. Now joining Hua Xu's lab as a summer fellow, Bin is interested in learning more about machine learning research and software engineering in the biomedical domain.

"Looking ahead to my final summer as an undergraduate, I wanted to experience research at the intersection of medicine and computer science," says Bin. "I applied and was selected for the Yale College Dean’s Research Fellowship, and found Dr. Xu, who thankfully brought me onboard."

Although Bin has only been at BIDS for a few days, he has been enjoying his time. "It has been eye-opening to work alongside experts with a wealth of experience in my field of interest," he says. "I also visited the Yale libraries for the first time yesterday and it was beautiful. Being able to study and work on the Yale campus is a great perk!"

Abelardo A. Pérez Rosario, Postgraduate Associate

Abelardo A. Pérez Rosario, originally from Río Grande, Puerto Rico, holds a Bachelor of Sciences in Biology-Cell and Molecular Biology from the University of Puerto Rico Rio Piedras Campus and will start his second year at the Universidad Central del Caribe Medical School next year. Abelardo's academic interests are in diseases and genetic conditions and its application to understanding disease. He came to Yale this summer for his research on genetics and asthma, particularly within the Puerto Rican community. He’ll be working with Dr. Jihoon Kim as part of the Yale Summer Research Program at BIDS.

“My experience at BIDS has been incredibly enriching. The mentorship and resources available have provided me with a better understanding of the field, and I have enjoyed learning from a diverse and talented group of researchers,” he says. Abelardo’s favorite parts of New Haven are its architecture and sense of community.

Deyaneira Gonzalez Rodriguez, Postgraduate Associate

Deyaneira is currently a rising second year medical student at San Juan Bautista School of Medicine in Puerto Rico. She completed her undergraduate education at the University of Puerto Rico, majoring in biology. She joined the Biomedical Informatics & Data Science as part of a Summer Research Program with Yale School of Medicine. Her main interests are in the areas of neuroscience, neuroradiology and immunology. She is currently working under Dr. Kim’s team, assessing lung function test data of the Puertorrican population through All of Us. If she could be any technology she would be Chat GPT as she explained: “I would always be ready to help, full of information, and able to engage in interesting conversations at any time. Plus, it would be fun to have all the answers at my fingertips.”

Brittany Alexandra Herrera Contreras, Postgraduate Associate

Brittany Alexandra Herrera Contreras joins Yale this summer as a postgraduate associate mentored by Dr. Qingyu Chen. She completed her undergradutate at the University of Waterloo with a bachelor’s degree in biomedical science, a minor in computing, and a degree in Italian language. Currently, she’s a rising second-year medical student at San Juan Bautista School of Medicine. She was born in North Carolina, lived most of her life in Canada, and her background in Colombian. She has a forever cute senior Shih Tau in Canada named Toby.

This summer she’s working to generate SQL from input text to build a study cohort and associated dataset in the AoU/OMOP database using LLMs. In her free time, some of her hobbies are drawing, dancing, and walking in nature. Right now, she’s learning Hindi on Duolingo. “My favorite aspect of New Haven is how many trees there are when you walk in the city.”

Lorier Bernes Atabonfack, Postgraduate Associate - BIDSIES

Atabonfack joins Yale as part of the inaugural cohort of Biomedical Informatics and Data Science International Exchange for Students. Originally from Cameroon, he earned a bachelor’s degree in Software Engineering at the University of Buéa’s College of Technology, and now lives in Rwanda undertaking a master's degree in Artificial Intelligence Engineering at Carnegie Mellon University Africa. Atabonfack is interested in applications of AI in health, particularly with regards to bioimaging, image processing and the development of machine learning models. He is also interested in natural language processing. Most recently, Atabonfack worked on research involving brain tumor segmentation using MRI images.

Passionate about AI in healthcare, Atabonfack is glad to be at Yale and hopes to nurture this passion to benefit his "immediate community and the world at large." He is eager to explore New Haven culture and visit Payne Whitney Gym.

Wendy Essuman, Postgraduate Associate - BIDSIES

Originally from Ghana, Wendy earned her bachelor’s degree in Computer Science from African Leadership University with Honors. She is particularly adept at using her computer skills in data analysis and technology to enhance learning experiences and educational outcomes. Wendy is currently working on a research project titled "Transforming Math Olympiad in Africa through Automated Solutions". The project involves using AI to enhance students’ online learning experiences in mathematics.

“I'm thrilled to be joining Yale this summer as part of the Africa exchange program,” Wendy says. “I look forward to collaborating with and learning from the brilliant minds in the Yale community.” Wendy hopes to gain exposure to research in biomedical informatics and data science, and to build connections that will support my future research endeavors.

When she isn’t coding and researching, Wendy is crafting, cooking and learning how to ride a bicycle. Wendy’s superpower is her ability to fall asleep within minutes. “When I lay my head on my pillow,” she says, “I can drift off into dreamland in less than 5 minutes flat.”

Scovia Achan, Postgraduate Associate - BIDSIES

After graduating with a degree in computer engineering, Scovia now undertakes a master’s program in Information Technology at Carnegie Mellon University Africa. Hailing from Kampala, Uganda, Scovia is interested in AI applications for healthcare, particularly leveraging AI to address pressing healthcare needs in Africa.

“I am coming to Yale because of its exceptional resources and expertise in the field of data science and machine learning within the Bioinformatics and Data Science department,” says Scovia. “I am eager to learn from renowned faculty members who are leaders in their respective fields, like Dr. Mary-Anne Hartley.”

Scovia recently worked on a project to map cholera hotspots in developing countries using machine learning (ML) techniques. The project leveraged ML to identify the best predictor variables, and used K-means clustering to classify regions into low, medium and high levels of risk of cholera infection.

Scovia is looking forward to visiting historic museums and art galleries around New Haven. As she arrives on Yale’s campus, she is particularly excited about the opportunity to travel beyond Africa.

Peter Ahumuza, Postgraduate Associate - BIDSIES

A software developer from Uganda, Peter earned his Bachelor's Degree in Information Systems at Makerere University and now brings a strong foundation in technology to his summer research at Yale. With an eye for industry, he is passionate about smart city implementation in Africa and leveraging automation to streamline business processes and efficiency. “I am particularly interested in understanding the unique needs and challenges faced by businesses in Africa,” says Peter, “and identifying opportunities for automation to drive growth, productivity, and competitiveness.”

As a BIDSIES Postgraduate Associate, Peter will work with Annie Hartley, MD, PhD, MPH, to develop a pedagogical tool designed to empower medical professionals in leveraging AI for enhanced patient care. Additionally, he will collaborate with a dynamic team on the development of the Massive Online Open Validation and Evaluation (MOOVE) project, a pioneering platform designed to facilitate global evaluation of Hartley’s medical large language models.

“I aim to deepen my understanding of complex healthcare challenges and innovative solutions, particularly in the realm of artificial intelligence and its applications in improving patient care and outcomes,” says Peter. “I also look forward to networking with experts in the field, engaging in meaningful discussions, and contributing to impactful projects that have the potential to shape the future of healthcare.”

Arriving on campus in June with the inaugural cohort of BIDSIES fellows, Peter is excited to sample New Haven’s diverse food and scenery.

Joshua Freeman, Postgraduate Associate - BIDSIES

After completing a bachelor’s degree at Swiss Federal Institute of Technology Lausanne (EPFL), Joshua is now pursuing a master's degree at ETH Zürich. Traveling to Yale as part of the inaugural BIDSIES cohort, Joshua’s skills include writing clean code for developing around and benchmarking large language models.

“I have a good friend not too far away from here that I thought might like a 4-month visit,” Joshua says, about traveling 4,000 miles to perform biomedical informatics research at Yale. Back home Joshua has a dog at his parents' place, named Muffin.

Submitted by Akio Tamura-Ho on May 08, 2024