Why is Machine Learning Trending in Medical Research but not in Our Doctor’s Offices?

by Melissa Pappas

Illustration of a robot in a white room with medical equipment.Machine learning (ML) programs computers to learn the way we do – through the continual assessment of data and identification of patterns based on past outcomes. ML can quickly pick out trends in big datasets, operate with little to no human interaction and improve its predictions over time. Due to these abilities, it is rapidly finding its way into medical research.

People with breast cancer may soon be diagnosed through ML faster than through a biopsy. Those suffering from depression might be able to predict mood changes through smart phone recordings of daily activities such as the time they wake up and amount of time they spend exercising. ML may also help paralyzed people regain autonomy using prosthetics controlled by patterns identified in brain scan data. ML research promises these and many other possibilities to help people lead healthier lives.

But while the number of ML studies grow, the actual use of it in doctors’ offices has not expanded much past simple functions such as converting voice to text for notetaking.

The limitations lie in medical research’s small sample sizes and unique datasets. This small data makes it hard for machines to identify meaningful patterns. The more data, the more accuracy in ML diagnoses and predictions. For many diagnostic uses, massive numbers of subjects in the thousands would be needed, but most studies use smaller numbers in the dozens of subjects.

But there are ways to find significant results from small datasets if you know how to manipulate the numbers. Running statistical tests over and over again with different subsets of your data can indicate significance in a dataset that in reality may be just random outliers.

This tactic, known as P-hacking or feature hacking in ML, leads to the creation of predictive models that are too limited to be useful in the real world. What looks good on paper doesn’t translate to a doctor’s ability to diagnose or treat us.

These statistical mistakes, oftentimes done unknowingly, can lead to dangerous conclusions.

To help scientists avoid these mistakes and push ML applications forward, Konrad Kording, Nathan Francis Mossell University Professor with appointments in the Departments of Bioengineering and Computer and Information Science in Penn Engineering and the Department of Neuroscience at Penn’s Perelman School of Medicine, is leading an aspect of a large, NIH-funded program known as CENTER – Creating an Educational Nexus for Training in Experimental Rigor. Kording will lead Penn’s cohort by creating the Community for Rigor which will provide open-access resources on conducting sound science. Members of this inclusive scientific community will be able to engage with ML simulations and discussion-based courses.

“The reason for the lack of ML in real-world scenarios is due to statistical misuse rather than the limitations of the tool itself,” says Kording. “If a study publishes a claim that seems too good to be true, it usually is, and many times we can track that back to their use of statistics.”

Such studies that make their way into peer-reviewed journals contribute to misinformation and mistrust in science and are more common than one might expect.

Read the full story in Penn Engineering Today.

CiPD Fellows Recognized with Research Awards

Members of the inaugural cohort of fellows in the Center for Innovation and Precision Dentistry (CiPD)’s NIDCR T90/R90 Postdoctoral Training Program have been recognized for their research activities with fellows receiving awards from the American Association for Dental, Oral, and Craniofacial Research (AADOCR), the Society for Biomaterials, and the Osteology Foundation. All four of the honored postdocs are affiliated with Penn Bioengineering.

Zhi Ren

Zhi Ren won first place in the Fives-Taylor Award at the AADOCR Mini Symposium for Young Investigators. A postdoctoral fellow in the labs of Dr. Hyun (Michel) Koo at Penn Dental Medicine (and member of the Penn Bioengineering Graduate Group) and Dr. Kathleen Stebe of Penn Engineering, Dr. Ren’s research focuses on understanding how bacterial and fungal pathogens interact in the oral cavity to form a sticky plaque biofilm on teeth, which gives rise to severe childhood tooth decay that affects millions of children worldwide. In his award-winning study, titled “Interkingdom Assemblages in Saliva Display Group-Level Migratory Surface Mobility”, Dr. Ren discovered that bacteria and fungi naturally present in the saliva of toddlers with severe decay can form superorganisms able to move and rapidly spread on tooth surfaces.

Justin Burrell

Justin Burrell won second place in the AADOCR Hatton Competition postdoctoral category for his research. Dr. Burrell has been working with Dr. Anh Le in Penn Dental Medicine’s Department of Oral Surgery/Pharmacology and Dr. D. Kacy Cullen of Penn Medicine and Penn Bioengineering. Together, their interdisciplinary team of clinician-scientists, biologists, and neuroengineers have been developing novel therapies to expedite facial nerve regeneration and increase meaningful functional recovery.

Marshall Padilla

Marshall Padilla earned third place at the Society for Biomaterials Postdoctoral Recognition Award Competition for a project titled, “Branched lipid architecture improves lipid-nanoparticle-based mRNA delivery to the liver via enhanced endosomal escape”. Padilla was also a finalist in the AADOCR Hatton Award Competition, presenting on a separate project titled, “Lipid Nanoparticle Optimization for mRNA-based Oral Cancer Therapy”. Both projects employ lipid nanoparticles, the same delivery vehicles used in the mRNA COVID-19 vaccine technology. A postdoctoral fellow in the lab of Dr. Michael J. Mitchell of Penn’s Department of Bioengineering, Dr. Padilla’s research focuses on developing new ways to enhance the efficacy and safety of lipid nanoparticle technology and its applications in dentistry and biomedicine. He has been working in collaboration with Dr. Shuying (Sheri) Yang and Dr. Anh Le in Penn Dental Medicine.

Dennis Sourvanos

Dennis Sourvanos (GD’23, DScD’23) was the recipient of the Trainee Travel Grant award through the Osteology Foundation (Lucerne Switzerland). Dr. Sourvanos will be presenting his research related to medical dosimetry and tissue regeneration at the International Osteology Symposium in Barcelona, Spain (April 27th – 29th 2023). He also presented at the 2023 AADOCR/CADR Annual Meeting for his project titled, “Validating Head-and-Neck Human-Tissue Optical Properties for Photobiomodulation and Photodynamic Therapies.” Dr. Sourvanos has been working with Dr. Joseph Fiorellini in Penn Dental Medicine’s Department of Periodontics and Dr. Timothy Zhu in the Hospital of the University of Pennsylvania’s Department of Radiation Oncology and the Smilow Center for Translational Research (and member of the Penn Bioengineering Graduate Group).

Read the full announcement in Penn Dental Medicine News.

Safe and Sound: Sonura Supports Newborn Development by Sequestering Disruptive Noise

by Nathi Magubane

Recipients of the 2023 President’s Innovation Prize, team Sonura, five bioengineering graduates from the School of Engineering and Applied Science, have created a device that filters out disruptive environmental noises for infants in neonatal intensive care units. Their beanie offers protection and fosters parental connection to newborns while also supporting their development.

Machines beeping and whirring in a rhythmic chorus, the droning hum of medical equipment, and the bustles of busy health care providers are the familiar sounds of an extended stay at a hospital. This cacophony can create a sense of urgency for medical professionals as they move about with focused determination, closely monitoring their patients, but for infants in neonatal intensive care units (NICU) this constant noise can be overwhelming and developmentally detrimental.

Enter Tifara Boyce, from New York City; Gabriela Cano, from Lawrenceville, New Jersey; Gabriella Daltoso, from Boise, Idaho; Sophie Ishiwari, from Chicago, and Caroline Magro, from Alexandria, Virginia, bioengineering graduates from the School of Engineering and Applied Science, who have created the Sonura Beanie. Their device filters out harmful noises for NICU infants while supporting cognitive and socioemotional development by allowing parents to send voice messages to their newborns.

The Sonura team members are recipients of the 2023 President’s Innovation Prize, which includes an award of $100,000 and an additional $50,000 living stipend per team member. The recent graduates will spend the year developing their product.

“The Penn engineers behind Sonura are determined to make a difference in the world,” says President Liz Magill. “They identified a substantial medical challenge that affects many parents and their newborn children. With the guidance of their mentors, they are taking key steps to address it and in doing so are improving the developmental prospects for children in the NICU. I am proud the University is able to support their important work.”

The Sonura Beanie’s creation began in the Stephenson Foundation Educational Laboratory and Bio-MakerSpace as a part of the Bioengineering Senior Design class project.

Prototype of the Sonura Beanie. (Image: Courtesy of the Sonura team)

She was particularly struck by the noisiness of the environment and considered the neurodevelopmental outcomes that may arise following long-term exposure to the harsh sounds at a critical developmental stage for infants. This concern prompted Magro to consult her team about potential solutions.

“I was really eager to tackle this problem because it bears some personal significance to me,” says Cano, who works on the device’s mobile application. “My sister was a NICU baby who was two months premature, so, when Caroline and I started talking about the issues a disruptive environment could cause, it seemed like the pieces of a puzzle started to come together.”

Read the full story in Penn Today.

Michael Mitchell and Kyle Vining Win IDEA Prize from CiPD and Penn Health-Tech

Michael J. Mitchell
Kyle Vining

 Michael J. Mitchell, J. Peter and Geri Skirkanich Assistant Professor of Innovation in Bioengineering, and Kyle Vining, Assistant Professor in Materials Science and Engineering and in Penn Dental Medicine and member of the Penn Bioengineering Graduate Group, have been awarded the second-annual IDEA (Innovation in Dental Medicine and Engineering to Advance Oral Health) Prize, issued by the Center for Innovation & Precision Dentistry (CiPD) and Penn Health-Tech.

“Through their collaborative research, they are aiming to develop next-generation treatments for dental caries (tooth-decay) using lipid nanoparticles, the same delivery vehicles employed in the mRNA COVID-19 vaccine technology.

‘This project shows the type of innovative ideas and collaborations that we are kickstarting through the IDEA prize,’ says Dr. Michel Koo, co-director of the CiPD and Professor at Penn Dental Medicine. ‘This is a great example of synergistic interaction at the interface of engineering and oral health’ adds Dr. Kate Stebe, co-director of the CiPD and Professor at Penn Engineering.”

Read the full announcement in Penn Dental Medicine News.

Franklin Medal Laureate Nader Engheta Honored at Sculpting Waves Symposium

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(Left to Right) Vijay Kumar, Nemirovsky Family Dean of Penn Engineering, Nader Engheta, H. Nedwill Ramsey Professor in Electrical and Systems Engineering, and Michele Marcolongo, Drosdick Endowed Dean of Villanova University’s College of Engineering

On April 26, scholars from all over the world gathered at Villanova University to celebrate extraordinary innovation in the physics and technology of light.

The Franklin Institute Awards Laureate Symposium honored Nader Engheta, H. Nedwill Ramsey Professor in Electrical and Systems Engineering, Bioengineering, Materials Science and Engineering in the School of Engineering and Applied Science and in Physics and Astronomy in the College of Arts & Sciences at the University of Pennsylvania . The event heralded the awards gala held on April 27, where Engheta received the Benjamin Franklin Medal in Electrical Engineering from the Franklin Institute in Philadelphia, Pennsylvania.

The symposium, titled “Sculpting Waves with Complex Materials,” explored the richness and breadth of Engheta’s impact.

In a glass-paneled lecture hall nestled between flowering dogwoods and limber pines, speakers attested to Engheta’s technical acumen and intellectual creativity, describing his pathbreaking work in light-matter interaction.

Andrea Alù, Distinguished Professor at the City University of New York, Einstein Professor of Physics at the Graduate Center, CUNY and former Penn Engineering postdoctoral fellow, cited Engheta as “one of the original pioneers of the field of complex electromagnetic structures and modern metamaterials,” and the “father” of four influential fields: analog computing with metamaterials, plasmonic cloaking, non-zero-index metamaterials and optical nanocircuits.

Read the full story in Penn Engineering Today.

Watch the recording of the 2023 Franklin Institute Awards Ceremony on the Institute’s Youtube page.

Penn Medicine and Independence Blue Cross Eliminate Preapprovals for Imaging Tests

Brian Litt, MD

Brian Litt, Professor in Bioengineering in Penn Engineering and in Neurology in the Perelman School of Medicine, spoke to Neurology Today about the advances in technology for detecting and forecasting seizures.

The Litt Lab for Translational Neuroengineering translates neuroengineering research directly into patient care, focusing on epilepsy and a variety of research initiatives and clinical applications.

“Dr. Litt’s group is working with one of a number of startups developing ‘dry’ electrode headsets for home EEG monitoring. ‘They are still experimental, but they’re getting better, and I’m really optimistic about the possibilities there.'”

Read “How Detecting, Identifying and Forecasting Seizures Has Evolved” in Neurology Today.

Read more stories featuring Litt in the BE Blog.

2023 Senior Design Project Competition Winners Announced

Each year, Penn Engineering’s seniors present their Senior Design projects, a year-long effort that challenges them to test and develop solutions to real-world problems, to their individual departments. The top three projects from each department go on to compete in the annual Senior Design Competition, sponsored by the Engineering Alumni Society, which involves pitching projects to a panel of judges who evaluate their potential in the market.

We are proud that two of the four awards went to Penn Bioengineering teams!

This year’s panel included over forty judges, and each winning team received a $2,000 prize, generously sponsored by Penn Engineering alumnus Kerry Wisnosky.

Congratulations to all of the 2023 participants and winners!

Technology & Innovation Award

This award recognized the team whose project represents the highest and best use of technology and innovation to leverage engineering principles.

Team BAMBI poses with Dean Vijay Kumar.

Winner: Team BAMBI
Department: Bioengineering
Team Members: Ria Dawar, Pallavi Jonnalagadda, Jessica Ling, Grace Qian
Mentor: Erin Anderson
Instructors: Erin Berlew, Sevile Mannickarottu, and David Meaney
Abstract: BAMBI (Biointelligent Apnea Monitor for Bradycardia-Prone Infants) is a tripartite system that leverages machine learning and automated mechanical stimulation to detect and treat apnea of prematurity in the NICU.

Judges’ Choice Award

Team StablEyes poses with Dean Vijay Kumar.This award recognizes the group whose all-around presentation captures the best of the senior design program’s different facets:  ideation, scope of project, team problem-solving, execution and presentation.

Winner: Team StablEyes
Department: Bioengineering
Team Members: Ella Atsavapranee, Jake Becker, Ruoming Fan, Savan Patel
Mentor: Erin Anderson, Dr. Drew Scoles and Dr. Tomas Aleman (Children’s Hospital of Philadelphia, Penn Medicine)
Instructors: Erin Berlew, Sevile Mannickarottu, and David Meaney
Abstract: StablEyes consists of a stabilization mount that provides fine, motorized control of the handheld OCT to improve ease of use for physicians and machine learning-based software to aid in diagnosis from retinal images.

Read the full list of SEAS Senior Design Competition Award winners in Penn Engineering Today.

Read more about all the Class of 2023 Penn Bioengineering Senior Design Teams in the Penn BE Labs website.

Daeyeon Lee: Evan C Thompson Lecture and American Chemical Society Award

 Daeyeon Lee, Professor and Evan C Thompson Term Chair for Excellence in Teaching in the Department of Chemical and Biomolecular Engineering and member of the Penn Bioengineering Graduate Group, is the recipient of two recent honors.

Surrounded by his supportive research team, fellow faculty, students, School of Engineering and Applied Science Dean Vijay Kumar, and Interim Provost Beth Winkelstein, Lee recently delivered the 2023 Evan C Thompson Chair Lecture about—fittingly enough—establishing a sense of community as we return from the isolating days of the pandemic.

Daeyeon Lee of the School of Engineering and Applied Science delivers the 2023 Thompson Chair Lecture on April 4, 2023. He spoke about reconnecting in the classroom and building community.

“Students who feel connected with instructors and among peers will invest more time, work harder, and retain information better, because they feel comfortable and safe being in the classroom and making space,” Lee said in his opening remarks. “So, there are clearly lots of positive benefits to having this connectedness among students in the classroom.”

Lee’s lecture, titled “(Re)connecting in the Classroom,” was inspired by the “Great Disengagement” referenced in an article published in The Chronicle of Higher Education last year. It portrayed students as more disconnected and uncertain as they re-entered the campus environment.

Read more about Lee’s “(Re)connecting in the Classroom” in Penn Today.

In addition, Lee has received the 2022 Outstanding Achievement Award in Nanoscience from the American Chemical Society (ACS).

The annual award recognizes exceptional achievements in nanoscience research and notable leadership in the area of colloidal nanoparticles and application. Lee was chosen from a large group of extraordinary nominees among the invited speakers, “for pioneering research in development of factory-on-a-chip and its application for large scale nanoparticle synthesis and functionalization.”

Read more about this award in Penn Engineering Today.

Penn Bioengineering Senior Design Team “Sonura” Wins 2023 President’s Innovation Prize

Gabriella Daltoso, Sophie Ishiwari, Gabriela Cano, Caroline Amanda Magro, and Tifara Eliana Boyce pose on College Green.
Sonura

University of Pennsylvania President Liz Magill announced on April 21, the recipients of the 2023 President’s Engagement and Innovation Prizes.

Awarded annually, the Prizes empower Penn students to design and undertake post-graduation projects that make a positive, lasting difference in the world. Each Prize-winning project will receive $100,000, as well as a $50,000 living stipend per team member. The Prizes are the largest of their kind in higher education. All Prize recipients collaborate with a Penn faculty mentor.

A team of fourth-year Bioengineering majors, Gabriella Daltoso, Sophie Ishiwari, Gabriela Cano, Caroline Amanda Magro, and Tifara Eliana Boyce, have received the President’s Innovation Prize for their project, Sonura.

“This year’s President’s Engagement and Innovation Prize recipients are fueled by a desire to make a difference—in their community, across the country, and around the world,” Magill said. “Communities for Childbirth, Act First, and Sonura embody an inspiring blend of passion and purpose. They are addressing consequential challenges with compelling solutions, and their dedication and smarts are exemplary. I congratulate them and wish them success as they launch and grow their ventures.”

The 2023 Prize recipients—selected from an applicant pool of 76—will spend the next year implementing the projects:

Gabriella Daltoso, Sophie Ishiwari, Gabriela Cano, Caroline Amanda Magro, and Tifara Eliana Boyce for Sonura: Daltoso, from Boise, Idaho; Ishiwari, from Chicago; Cano, from Lawrenceville, New Jersey; Magro, from Alexandria, Virginia; and Boyce, from Jamaica, Queens, New York, are bioengineering majors in the School of Engineering and Applied Science. Their startup, Sonura, is developing a beanie that promotes the cognitive and socioemotional development of newborns in the NICU by protecting them from the auditory hazards of their environments while fostering parental connection. The Sonura Beanie is composed of a frequency-dependent filter and a mobile application. The Sonura team is mentored by Brian Halak, a lecturer in the Engineering Entrepreneurship program. Sonura was developed in Penn’s Stephenson Foundation Bio-MakerSpace and was part of their Bioengineering Senior Design class.

To learn more about the 2023 President’s Engagement and Innovation Prizes, visit Penn Today.

2023 Undergraduate Awards for Bioengineering Students

Congratulations to the Bioengineering student recipients of undergraduate awards from the School of Engineering and Applied Science  for the 2022-2023 academic year. These  awards are given annually by the school and the department in recognition of outstanding scholarship and service. Read the full list of Bioengineering undergraduate award winners below.

The Wolf-Hallac Award: Sofia Mouchtaris. This award was established in October 2000 to recognize the graduating female senior from across Penn Engineering’s departments who is seen as a role model, has achieved a high GPA (in the top 10% of their class), and who has demonstrated a commitment to school and/or community.

The Management and Technology Scholarship Award: Savan Patel. This prize is awarded by the SEAS faculty to that member of the senior class in the Jerome Fisher Management and Technology Program who has created an innovative system and attained high scholastic achievement.

The Hugo Otto Wolf Memorial Prize: Joshua Freedman & Le He. This prize is awarded to one or more members of each department’s senior class, distinguishing students who meet with great approval of the professors at large through “thoroughness and originality” in their work.

The Herman P. Schwan Award: Laila Norford. This department award honors a graduating senior who demonstrates the “highest standards of scholarship and academic achievement.”

Exceptional Service Awards recognize students for their outstanding service to the University and their larger communities: Dylan Hurok, Julia Lottman, Caroline Magro & Grace Qian.

The Student Leadership Award: Moses Zeidan. This award is given annually to a student in Bioengineering who has demonstrated, through a combination of academic performance, service, leadership, and personal qualities, that they will be a credit to the Department, the School, and the University.

Additionally, the Bioengineering Department  also presents a single lab group with the Albert Giandomenico Award which reflects their “teamwork, leadership, creativity, and knowledge applied to discovery-based learning in the laboratory.” This year’s group consists of Ella Atsavapranee, Jake Becker, Ruoming Fan & Savan Patel, aka Team StablEyes.

The awardees above were recognized at the annual Penn Engineering Awards Ceremony held Wednesday, March 29, 2023 in the Harrison Auditorium, Penn Museum.

Three Bioengineering Senior Design teams were chosen for recognition in the Bioengineering Senior Design Competition:

Team BAMBI: Ria Dawar, Pallavi Jonnalagadda, Jessica Ling, & Grace Qian. BAMBI (Biointelligent Apnea Monitor for Bradycardia-Prone Infants) is a tripartite system that leverages machine learning and automated mechanical stimulation to detect and treat apnea of prematurity in the NICU.

Team StablEyes: Ella Atsavapranee, Jake Becker, Ruoming Fan, & Savan Patel. StablEyes consists of a stabilization mount that provides fine, motorized control of the handheld OCT to improve ease of use for physicians and machine learning-based software to aid in diagnosis from retinal images.

Team inSPIRE: Jackson Dooley, Joshua Freedman,Yi-An Hsieh, Isabella Mirro, & Parth Mody. inSPIRE is the first smart incentive spirometer, used post-operatively to improve patient outcomes and reduce costs associated with complications and readmissions.

These teams will compete in the Penn Engineering Senior Design Competition on Friday, April 28, 2023.

Research for these projects was conducted in the George H. Stephenson Foundation Education Laboratory & Bio-Maker Space. Learn about all the 2023 Senior Design projects and view their final presentations on the Stephenson Bio-MakerSpace website here.

A full list of Penn Engineering award descriptions and recipients can be found here.