AI, science, education, & ethics
As a former mathematician, I was used to nobody reading what I wrote. So when I first began blogging in 2015, I never expected that several of my blog posts would go viral or to have multiple journalists contact me (including from NPR, Wired, and Fortune), make the front page of Hacker News (over 10 times), receive conference keynote invitations, and be interviewed on podcasts. I do not consider…
Most people catch many viruses in their lives– for example, over 90% of adults have Epstein-Barr virus , and adults catch the flu about once every 5 years. For a long time, catching frequent viruses was considered both inevitable and harmless. But it turns out that common, seemingly-mild viruses have disturbing long-term health impacts. Common respiratory viruses increase the risk of heart attacks…
I recently gave a talk tying together many of the topics I care about most: the potential of AI in immunology, racial and gender bias in medicine, harms of AI in society, the systemic dismissal of patient experience by doctors, and the promise of participatory, patient-led approaches. I hope you’ll watch my 29 minute talk in full here: Below is an edited transcript of the talk, with timestamps if…
Deep learning is glamorous and highly rewarded. If you train and evaluate a Transformer (a state-of-the-art language model) on a dataset of 22 million enzymes and then use it to predict the function of 450 unknown enzymes, you can publish your results in Nature Communications (a very well-regarded publication). Your paper will be viewed 22,000 times and will be in the top 5% of all research…
DNA sequencing hasn’t lived up to the hype Twenty to thirty years ago, politicians, scientific leaders, journalists, and even Nobel laureates predicted that sequencing the human genome would revolutionize how we treat disease. And while the advances in DNA sequencing that have occurred since then have improved recognition and treatment for some cancers and rare diseases, on the whole the field has…
Amidst the barrage of executive orders and announcements Trump made during his first week in office are two which highlight common misunderstandings and obfuscations about the relationship between data, AI, and power . These announcements contradict each other: He announced a freeze on communications from scientific and health agencies, stopping them from sharing health data with the public,…
The lavender images below show breast tissue . There are many questions doctors could want to answer using these images: They could want to know whether there are tumors present or not. If there is a tumor, doctors would want to classify its stage, make predictions about how likely the patient is to respond to treatment, and to detect whether the tumor has spread from another organ. All of these…
I spent close to 20 years focused on mathematics and data science, including cofounding the research lab fast.ai, which focused on the powerful family of AI algorithms known as deep learning. A few years ago, I decided to make a big pivot and return to school for immunology. What motivated my sudden change amidst a successful career? We are now living in a pandemicene , a period with increasingly…
“The human immune system is amazing, with an impressive range of techniques to protect against invaders.” I see this sentiment expressed frequently by everyone from doctors quoted in newspaper articles to online commentators in parenting groups. And I share it– I loved learning about the intricate processes our bodies deploy against invaders when I took graduate immunology. However, the point that…
My daughter is constantly creating– her passions include making art, writing fiction, coding interactive games, and composing music. Yet, I regularly see news articles and media pundits suggesting that my husband and I are doing things all wrong. The reason for these claims? My daughter uses screen-based tools, at least partially, and in some cases, entirely, to pursue the interests I listed in my…
AI is being used to tackle high-impact scientific problems, including searching for new antibiotics to combat antibiotic-resistance and predicting what foreign substances the immune system can recognize as invaders. Amidst the excitement, it is important to keep in mind the gaps and risks of how AI is applied in science. Recognizing these risks opens up new opportunities and can prevent us from…
That which doesn’t kill you… Some people compare the immune system to a muscle, suggesting that the more you use it, the stronger it gets. Who doesn’t love an analogy? But is this one accurate? We can see that not all obstacles make you stronger. Destroy the cartilage in your knee, and it may never fully recover, since cartilage doesn’t grow back. Some bacterial infections can permanently scar the…
This post is part 3 in a series on using AI to predict T cell binding. Here are part 1 and part 2 . Better understanding what T cells bind to is a crucial question; some researchers even call it “a holy grail of systems immunology” . While AI is already being used towards solutions, there is still much work to be done in this area! In part 1 of this series , we discussed the importance of…
This post can stand alone as a friendly introduction to neural nets, no background required. It is part 2 in my series on using AI to figure out what T cells can bind to. Here are part 1 and part 3 . What are Neural Networks? Neural networks are a type of machine learning algorithm that are currently in the limelight, powering chatbots like ChatGPT and image generators like Midjourney. Neural…
I’m studying the intersection of AI and immunology, two notoriously jargon-heavy fields – but it’s important that scientists share their work with a broader audience. This 3-part series is an experiment: an accessible introduction to AI immunology concepts. This post is part 1 in a series on using AI to predict T cell binding. Here are part 2 and part 3 . T cells are one of the most important cell…
This is part 2 in a series covering surprising facts about the microbiome. Be sure to check out part 1 here . A microbiome is the community of microorganisms found living together in a given habitat. The microbiome of the human gut can contribute to development of autoimmune disease . The microbiome of plant roots can include bacteria traveling on fungal super-highways . Scientists also study the…
This is part 1 in a series. You can read part 2 here . Humans co-evolved together with our microbiomes, the bacteria and fungi that colonize our intestines, coat our skin, and inhabit our mouths, throats, and numerous other body locations. Microbiomes are significant because they influence how we process nutrients, fight pathogens, and what diseases we are susceptible to. This is not just true of…
A Growing Threat The WHO estimates that antimicrobial resistance (AMR) contributed to approximately 5 million deaths worldwide in 2019 ( “Antimicrobial Resistance” 2023 ). In the USA, AMR results annually in 8 million additional days spent in the hospital and over $20 billion in healthcare costs ( Bush et al. 2011 ). The problem will only grow in magnitude as antibiotic resistant genes in bacteria…
AI has made remarkable strides in the medical field, with capabilities including the detection of Parkinson’s disease via retinal images , identification of promising drug candidates , and prediction of hospital readmissions . While these advance are exciting, I’m wary of the practical impact AI will have on patients. I recently watched a late-night talk show where skeptics and enthusiasts debated…
This post is part 2 in a series. Be sure to read part 1 here . A key obstacle hindering medical research for a range of diseases is our lack of understanding of the immune system. Harvard Professor Wayne Koff described his decades of HIV research, “ slowly, over time, we began to see that we understood a lot about HIV at the molecular level, but we didn’t know anything about ourselves. And the…