Dafflon, Jessica
Recent Advances, Applications and Open Challenges in Machine Learning for Health: Reflections from Research Roundtables at ML4H 2024 Symposium
Adibi, Amin, Cao, Xu, Ji, Zongliang, Kaur, Jivat Neet, Chen, Winston, Healey, Elizabeth, Nuwagira, Brighton, Ye, Wenqian, Woollard, Geoffrey, Xu, Maxwell A, Cui, Hejie, Xi, Johnny, Chang, Trenton, Bikia, Vasiliki, Zhang, Nicole, Noori, Ayush, Xia, Yuan, Hossain, Md. Belal, Frank, Hanna A., Peluso, Alina, Pu, Yuan, Shen, Shannon Zejiang, Wu, John, Fallahpour, Adibvafa, Mahbub, Sazan, Duncan, Ross, Zhang, Yuwei, Cao, Yurui, Xu, Zuheng, Craig, Michael, Krishnan, Rahul G., Beheshti, Rahmatollah, Rehg, James M., Karim, Mohammad Ehsanul, Coffee, Megan, Celi, Leo Anthony, Fries, Jason Alan, Sadatsafavi, Mohsen, Shung, Dennis, McWeeney, Shannon, Dafflon, Jessica, Jabbour, Sarah
The fourth Machine Learning for Health (ML4H) symposium was held in person on December 15th and 16th, 2024, in the traditional, ancestral, and unceded territories of the Musqueam, Squamish, and Tsleil-Waututh Nations in Vancouver, British Columbia, Canada. The symposium included research roundtable sessions to foster discussions between participants and senior researchers on timely and relevant topics for the ML4H community. The organization of the research roundtables at the conference involved 13 senior and 27 junior chairs across 13 tables. Each roundtable session included an invited senior chair (with substantial experience in the field), junior chairs (responsible for facilitating the discussion), and attendees from diverse backgrounds with an interest in the session's topic.
Super-Resolution without High-Resolution Labels for Black Hole Simulations
Helfer, Thomas, Edwards, Thomas D. P., Dafflon, Jessica, Wong, Kaze W. K., Olson, Matthew Lyle
Generating high-resolution simulations is key for advancing our understanding of one of the universe's most violent events: Black Hole mergers. However, generating Black Hole simulations is limited by prohibitive computational costs and scalability issues, reducing the simulation's fidelity and resolution achievable within reasonable time frames and resources. In this work, we introduce a novel method that circumvents these limitations by applying a super-resolution technique without directly needing high-resolution labels, leveraging the Hamiltonian and momentum constraints--fundamental equations in general relativity that govern the dynamics of spacetime. We demonstrate that our method achieves a reduction in constraint violation by one to two orders of magnitude and generalizes effectively to out-of-distribution simulations.
Large language models surpass human experts in predicting neuroscience results
Luo, Xiaoliang, Rechardt, Akilles, Sun, Guangzhi, Nejad, Kevin K., Yรกรฑez, Felipe, Yilmaz, Bati, Lee, Kangjoo, Cohen, Alexandra O., Borghesani, Valentina, Pashkov, Anton, Marinazzo, Daniele, Nicholas, Jonathan, Salatiello, Alessandro, Sucholutsky, Ilia, Minervini, Pasquale, Razavi, Sepehr, Rocca, Roberta, Yusifov, Elkhan, Okalova, Tereza, Gu, Nianlong, Ferianc, Martin, Khona, Mikail, Patil, Kaustubh R., Lee, Pui-Shee, Mata, Rui, Myers, Nicholas E., Bizley, Jennifer K, Musslick, Sebastian, Bilgin, Isil Poyraz, Niso, Guiomar, Ales, Justin M., Gaebler, Michael, Murty, N Apurva Ratan, Loued-Khenissi, Leyla, Behler, Anna, Hall, Chloe M., Dafflon, Jessica, Bao, Sherry Dongqi, Love, Bradley C.
Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors.
Transformer-based normative modelling for anomaly detection of early schizophrenia
Da Costa, Pedro F, Dafflon, Jessica, Mendes, Sergio Leonardo, Sato, Joรฃo Ricardo, Cardoso, M. Jorge, Leech, Robert, Jones, Emily JH, Pinaya, Walter H. L.
Despite the impact of psychiatric disorders on clinical health, early-stage diagnosis remains a challenge. Machine learning studies have shown that classifiers tend to be overly narrow in the diagnosis prediction task. The overlap between conditions leads to high heterogeneity among participants that is not adequately captured by classification models. To address this issue, normative approaches have surged as an alternative method. By using a generative model to learn the distribution of healthy brain data patterns, we can identify the presence of pathologies as deviations or outliers from the distribution learned by the model. In particular, deep generative models showed great results as normative models to identify neurological lesions in the brain. However, unlike most neurological lesions, psychiatric disorders present subtle changes widespread in several brain regions, making these alterations challenging to identify. In this work, we evaluate the performance of transformer-based normative models to detect subtle brain changes expressed in adolescents and young adults. We trained our model on 3D MRI scans of neurotypical individuals (N=1,765). Then, we obtained the likelihood of neurotypical controls and psychiatric patients with early-stage schizophrenia from an independent dataset (N=93) from the Human Connectome Project. Using the predicted likelihood of the scans as a proxy for a normative score, we obtained an AUROC of 0.82 when assessing the difference between controls and individuals with early-stage schizophrenia. Our approach surpassed recent normative methods based on brain age and Gaussian Process, showing the promising use of deep generative models to help in individualised analyses.
Analysis of an Automated Machine Learning Approach in Brain Predictive Modelling: A data-driven approach to Predict Brain Age from Cortical Anatomical Measures
Dafflon, Jessica, Pinaya, Walter H. L, Turkheimer, Federico, Cole, James H., Leech, Robert, Harris, Mathew A., Cox, Simon R., Whalley, Heather C., McIntosh, Andrew M., Hellyer, Peter J.
The use of machine learning (ML) algorithms has significantly increased in neuroscience. However, from the vast extent of possible ML algorithms, which one is the optimal model to predict the target variable? What are the hyperparameters for such a model? Given the plethora of possible answers to these questions, in the last years, automated machine learning (autoML) has been gaining attention. Here, we apply an autoML library called TPOT which uses a tree-based representation of machine learning pipelines and conducts a genetic-programming based approach to find the model and its hyperparameters that more closely predicts the subject's true age. To explore autoML and evaluate its efficacy within neuroimaging datasets, we chose a problem that has been the focus of previous extensive study: brain age prediction. Without any prior knowledge, TPOT was able to scan through the model space and create pipelines that outperformed the state-of-the-art accuracy for Freesurfer-based models using only thickness and volume information for anatomical structure. In particular, we compared the performance of TPOT (mean accuracy error (MAE): $4.612 \pm .124$ years) and a Relevance Vector Regression (MAE $5.474 \pm .140$ years). TPOT also suggested interesting combinations of models that do not match the current most used models for brain prediction but generalise well to unseen data. AutoML showed promising results as a data-driven approach to find optimal models for neuroimaging applications.