Publications
Our teams aspire to make discoveries that impact everyone, and core to our approach is sharing our research and tools to fuel progress in the field.
Our teams aspire to make discoveries that impact everyone, and core to our approach is sharing our research and tools to fuel progress in the field.
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1 - 15 of 10795 publications
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AI coding assistants are rapidly becoming integral to modern software development. A key challenge in this space is the continual need to migrate and modernize codebases in response to evolving software ecosystems. Traditionally, such migrations have relied on rule-based systems and human intervention. With the advent of powerful large language models (LLMs), AI-driven agentic frameworks offer a promising alternative—but their effectiveness remains underexplored. In this paper, we introduce FreshBrew, a novel benchmark for evaluating AI-based agentic frameworks on project-level Java migrations. We benchmark several such frameworks, powered by state-of-the-art LLMs, and compare their performance against established rule-based tools. Our evaluation of AI agents on this benchmark of 228 repositories shows that the top-performing model, Gemini 2.5 Flash, can successfully migrate 56.5% of projects to JDK 17. Our empirical analysis reveals novel insights into the critical strengths and limitations of current agentic approaches, offering actionable insights into their real-world applicability. By releasing FreshBrew publicly upon acceptance, we aim to facilitate rigorous, reproducible evaluation and catalyze progress in AI-driven codebase modernization.
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For many practical applications of quantum computing, the slowest and most costly steps involve coherently accessing classical data. We help address this challenge by applying mass production techniques, which can sometimes allow us to perform operations many times in parallel for a cost that is comparable to a single execution[1-3]. We combine existing mass-production results with modern approaches for loading classical data using ``quantum read-only memory.'' We show that quantum mass production techniques offer no benefit when we consider a cost model that focuses purely on the number of non-Clifford gates. However, analyzing the constant factors in a more nuanced cost model, we find that it may be possible to obtain a reduction in cost of an order or magnitude or more for a variety reasonably-sized fault-tolerant quantum algorithms. We present several applications of quantum mass-production techniques beyond naive parallelization, including a strategy for reducing the cost of serial calls to the same data loading step.
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Rapid Initial-State Preparation for the Quantum Simulation of Strongly Correlated Molecules
Dominic Berry
Yu Tong
Alec White
Tae In Kim
Lin Lin
Seunghoon Lee
Garnet Chan
PRX Quantum, 6 (2025), pp. 020327
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Studies on quantum algorithms for ground-state energy estimation often assume perfect ground-state preparation; however, in reality the initial state will have imperfect overlap with the true ground state. Here, we address that problem in two ways: by faster preparation of matrix-product-state (MPS) approximations and by more efficient filtering of the prepared state to find the ground-state energy. We show how to achieve unitary synthesis with a Toffoli complexity about 7 × lower than that in prior work and use that to derive a more efficient MPS-preparation method. For filtering, we present two different approaches: sampling and binary search. For both, we use the theory of window functions to avoid large phase errors and minimize the complexity. We find that the binary-search approach provides better scaling with the overlap at the cost of a larger constant factor, such that it will be preferred for overlaps less than about 0.003. Finally, we estimate the total resources to perform ground-state energy estimation of Fe-S cluster systems, including the FeMo cofactor by estimating the overlap of different MPS initial states with potential ground states of the FeMo cofactor using an extrapolation procedure. With a modest MPS bond dimension of 4000, our procedure produces an estimate of approximately 0.9 overlap squared with a candidate ground state of the FeMo cofactor, producing a total resource estimate of 7.3e10 Toffoli gates; neglecting the search over candidates and assuming the accuracy of the extrapolation, this validates prior estimates that have used perfect ground-state overlap. This presents an example of a practical path to prepare states of high overlap in a challenging-to-compute chemical system.
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Passive Heart Rate Monitoring During Smartphone Use in Everyday Life
Shun Liao
Paolo Di Achille
Jiang Wu
Silviu Borac
Jonathan Wang
Eric Teasley
Lawrence Cai
Daniel McDuff
Hao-Wei Su
Brent Winslow
Anupam Pathak
Shwetak Patel
Jim Taylor
Jamie Rogers
(2025)
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Resting heart rate (RHR) is an important biomarker of cardiovascular health and mortality, but tracking it longitudinally generally requires a wearable device, limiting its availability. We present PHRM, a deep learning system for passive heart rate (HR) and RHR measurements during ordinary smartphone use, using facial video-based photoplethysmography. Our system was developed using 225,773 videos from 495 participants and validated on 185,970 videos from 205 participants in laboratory and free-living conditions – the largest validation study of its kind. Compared to reference electrocardiogram, PHRM achieved a mean absolute percentage error (MAPE) <10% for HR measurements across three skin tone groups of light, medium and dark pigmentation; MAPE for each skin tone group was non-inferior versus the others. Daily RHR measured by PHRM had a mean absolute error <5 bpm compared to a wearable HR tracker, and was associated with known risk factors. These results highlight the potential of smartphones to enable passive and equitable heart health monitoring.
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Improving simulation-based origin-destination demand calibration using sample segment counts data
Arwa Alanqary
Yechen Li
The 12th Triennial Symposium on Transportation Analysis conference (TRISTAN XII), Okinawa, Japan (2025)
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This paper introduces a novel approach to demand estimation that utilizes partial observations of segment-level track counts. Building on established simulation-based demand estimation methods, we present a modified formulation that integrates sample track counts as a regularization term. This approach effectively addresses the underdetermination challenge in demand estimation, moving beyond the conventional reliance on a prior OD matrix. The proposed formulation aims to preserve the distribution of the observed track counts while optimizing the demand to align with observed path-level travel times. We tested this approach on Seattle's highway network with various congestion levels. Our findings reveal significant enhancements in the solution quality, particularly in accurately recovering ground truth demand patterns at both the OD and segment levels.
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Gemini & Physical World: Large Language Models Can Estimate the Intensity of Earthquake Shaking from Multi-Modal Social Media Posts
Marc Stogaitis
Tajinder Gadh
Richard Allen
Alexei Barski
Robert Bosch
Patrick Robertson
Youngmin Cho
Nivetha Thiruverahan
Aman Raj
Geophysical Journal International (2025), ggae436
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This paper presents a novel approach for estimating the ground shaking intensity using real-time social media data and CCTV footage. Employing the Gemini 1.5 Pro’s (Reid et al. 2024) model, a multi-modal language model, we demonstrate the ability to extract relevant information from unstructured data utilizing generative AI and natural language processing. The model’s output, in the form of Modified Mercalli Intensity (MMI) values, align well with independent observational data. Furthermore, our results suggest that beyond its advanced visual and auditory understanding abilities, Gemini appears to utilize additional sources of knowledge, including a simplified understanding of the general relationship between earthquake magnitude, distance, and MMI intensity, which it presumably acquired during its training, in its reasoning and decision-making processes. These findings raise intriguing questions about the extent of Gemini's general understanding of the physical world and its phenomena. Gemini’s ability to generate results consistent with established scientific knowledge highlights the potential of LLMs like Gemini in augmenting our understanding of complex physical phenomena such as earthquakes. More specifically, the results of this study highlight the potential of LLMs like Gemini to revolutionize citizen seismology by enabling rapid, effective, and flexible analysis of crowdsourced data from eyewitness accounts for assessing earthquake impact and providing crisis situational awareness. This approach holds a great promise for improving early warning systems, disaster response, and overall resilience in earthquake-prone regions. This study provides a significant step toward harnessing the power of social media and AI for earthquake disaster mitigation.
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Exploring Optimization Techniques For Finding Contraction Paths
Salvatore Mandra
(2025)
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In my talk, I will present a historical overview of the different numerical methods used to find optimal contraction paths. I will introduce TNSA, which has been used for the optimization of the contraction used for [Nature, 634 (8033), 2024], and TNCO, which is an ongoing effort to build upon TNSA.
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During remote communication, participants often share both digital and physical content, such as product designs, digital assets, and environments, to enhance mutual understanding. Recent advances in augmented communication have facilitated users to swiftly create and share digital 2D copies of physical objects from video feeds into a shared space. However, conventional 2D representations of digital objects limits spatial referencing in immersive environments. To address this, we propose Thing2Reality, an Extended Reality (XR) meeting platform that facilitates spontaneous discussions of both digital and physical items during remote sessions. With Thing2Reality, users can quickly materialize ideas or objects in immersive environments and share them as conditioned multiview renderings or 3D Gaussians. Thing2Reality enables users to interact with remote objects or discuss concepts in a collaborative manner. Our user studies revealed that the ability to interact with and manipulate 3D representations of objects significantly enhances the efficiency of discussions, with the potential to augment discussion of 2D artifacts.
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Unprecedented Insights into Maternal Sleep: A Large-scale Longitudinal Analysis of Real-world Wearable Device Data Before, During, and After Pregnancy
Nichole Young-Lin
Conor Heneghan
Logan Schneider
Logan Niehaus
Ariel Haney
Karla Gleichauf
Jacqueline Shreibati
Belen Lafon
Lancet eBioMedicine (2025)
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Introduction: Current understanding of pregnancy and postpartum sleep is driven by limited lab or self-reported data. Consumer wearable devices may help reveal longitudinal, real-world sleep patterns.
Methods: We analyzed de-identified wearable device data from 2,540 users in the United States and Canada who met strict wear-time requirements (≥80% daily usage for ≥80% of the time periods of interest [12 weeks prepregnancy, throughout pregnancy, and 20 weeks immediately postpartum]). We tracked sleep time and staging using Fitbit devices.
Results: Compared to prepregnancy, total sleep time (TST) increased from an average of 425.3±43.5 min to a peak of 447.6±47.6 min at gestational week 10 with ongoing declines throughout pregnancy. Time in bed (TIB) followed a similar pattern. Increased light sleep drove the initial TST rise. Deep and REM sleep decreased significantly throughout pregnancy, with maximum reductions of 19.2±13.8 min (p<0.01) and 9.0±19.2 min (p<0.01) respectively by pregnancy end. Sleep efficiency also declined slightly during pregnancy (median drop from 88.3% to 86.8%). After delivery, TIB remained below the prepregnancy baseline by 14.7±45.7 min at one year postpartum and 15.2±47.7 min at 1.5 years postpartum.
Conclusion: This unprecedented look at large-scale, real-world sleep and pregnancy patterns revealed a previously unquantified initial increase in sleep followed by decreases in both quantity and quality as pregnancy progresses. Sleep deficits persist for at least 1.5 years postpartum. These quantified trends can assist clinicians and patients in understanding what to expect.
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ZAPBench: A Benchmark for Whole-Brain Activity Prediction in Zebrafish
Alexander Immer
Alex Bo-Yuan Chen
Mariela D. Petkova
Nirmala A. Iyer
Luuk Willem Hesselink
Aparna Dev
Gudrun Ihrke
Woohyun Park
Alyson Petruncio
Aubrey Weigel
Wyatt Korff
Florian Engert
Jeff W. Lichtman
Misha B. Ahrens
International Conference on Learning Representations (ICLR) (2025)
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Data-driven benchmarks have led to significant progress in key scientific modeling domains including weather and structural biology. Here, we present the Zebrafish Activity Prediction Benchmark (ZAPBench), which quantitatively measures progress on the problem of predicting cellular-resolution neural activity throughout an entire vertebrate brain. The benchmark is based on a novel dataset containing 4d light-sheet microscopy recordings of more than 70,000 neurons in a larval zebrafish brain, along with motion stabilized and voxel-level cell segmentations of these data that facilitate development of a variety of forecasting methods. Initial results from a selection of time series and volumetric video modeling approaches achieve better performance than naive baseline methods, but also show room for further improvement. The specific brain used in the activity recording is also undergoing synaptic-level anatomical mapping, which will enable future integration of detailed structural information into ZAP forecasting methods.
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Simulation-Based Inference: A Practical Guide
Michael Deistler
Jan Boelts
Peter Steinbach
Guy Moss
Thomas Moreau
Manuel Gloeckler
Pedro L. C. Rodriguez
Julia Linhart
Janne K. Lappalainen
Benjamin Kurt Miller
Pedro J. Goncalves
Cornelius Schröder
Jakob H. Macke
arXiv (2025)
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A central challenge in many areas of science and engineering is to identify model parameters that are consistent with empirical data and prior knowledge. Bayesian inference offers a principled framework for this task, but can be computationally prohibitive when models are defined by stochastic simulators. Simulation-Based Inference (SBI) provides a suite of methods to overcome this limitation and has enabled scientific discoveries in fields such as particle physics, astrophysics and neuroscience. The core idea of SBI is to train neural networks on data generated by a simulator, without requiring access to likelihood evaluations. Once trained, the neural network can rapidly perform inference on empirical observations without requiring additional optimization or simulations. In this tutorial, we provide a practical guide for practitioners aiming to apply SBI methods. We outline a structured SBI workflow and offer practical guidelines and diagnostic tools for every stage of the process--from setting up the simulator and prior, choosing the SBI method and neural network architecture, training the inference model, to validating results and interpreting the inferred parameters. We illustrate these steps through examples from astrophysics, psychophysics, and neuroscience. This tutorial empowers researchers to apply state-of-the-art SBI methods, facilitating efficient parameter inference for scientific discovery.
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ECG-Nest-FM: A Frequency-Focused ECG Foundation Model with Nested Embeddings
Abhishek Sharma
Lin Yang
ICLR 2025 Workshop MLGenX (2025)
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Electrocardiograms (ECGs) are fundamental to cardiac diagnostics, providing noninvasive insights into cardiovascular conditions. Recent advancements in deep learning have led to foundation models (FMs) capable of learning powerful representations of ECG signals. However, these models often fail to fully exploit the periodic nature and diagnostic frequency bands of ECGs, leading to inefficiencies in computational cost and interpretability. We propose a novel ECG foundation model that learns nested embeddings, where each subset of dimensions encodes progressively higher-frequency information. By explicitly modeling frequency structures and applying a correlation penalty, the method achieves compact, high-rank representations that reduce model size without sacrificing performance. We evaluate our approach on two large-scale datasets for embedding redundancy and prediction performance on downstream clinical tasks such as arrhythmia classification, and cardiac condition detection. We observe similar prediction performance AUROC scores and lower embedding redundancy, offering a computationally efficient and interpretable framework for ECG analysis. Finally, the representations obtained from our model in UK Biobank data capture known cardiovascular variants and detect novel loci, which can be applied to drug discovery.
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Generative AI for medical education: Insights from a case study with medical students and an AI tutor for clinical reasoning
Amy Wang
Roma Ruparel
Paul Jhun
Julie Anne Seguin
Patricia Strachan
Renee Wong
2025
Preview abstract
Generative Artificial Intelligence (AI), particularly Large Language Models (LLMs), have demonstrated significant potential in clinical reasoning skills such as history-taking and differential diagnosis generation—critical aspects of medical education. This work explores how LLMs can augment medical curricula through interactive learning. We conducted a participatory design process with medical students, residents and medical education experts to co-create an AI-powered tutor prototype for clinical reasoning. As part of the co-design process, we conducted a qualitative user study, investigating learning needs and practices via interviews, and conducting concept evaluations through interactions with the prototype. Findings highlight the challenges learners face in transitioning from theoretical knowledge to practical application, and how an AI tutor can provide personalized practice and feedback. We conclude with design considerations, emphasizing the importance of context-specific knowledge and emulating positive preceptor traits, to guide the development of AI tools for medical education.
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AI and Generative AI Transforming Disaster Management: A Survey of Damage Assessment and Response Techniques
Aman Raj
IEEE Compsac 2025 (2025)
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Natural disasters, including earthquakes, wildfires and cyclones, bear a huge risk on human lives as well as infrastructure assets. An effective response to disaster depends on the ability to rapidly and efficiently assess the intensity of damage. Artificial Intelligence (AI) and Generative Artificial Intelligence (GenAI) presents a breakthrough solution, capable of combining knowledge from multiple types and sources of data, simulating realistic scenarios of disaster, and identifying emerging trends at a speed previously unimaginable. In this paper, we present a comprehensive review on the prospects of AI and GenAI in damage assessment for various natural disasters, highlighting both its strengths and limitations. We talk about its application to multimodal data such as text, image, video, and audio, and also cover major issues of data privacy, security, and ethical use of the technology during crises. The paper also recognizes the threat of Generative AI misuse, in the form of dissemination of misinformation and for adversarial attacks. Finally, we outline avenues of future research, emphasizing the need for secure, reliable, and ethical Generative AI systems for disaster management in general. We believe that this work represents the first comprehensive survey of Gen-AI techniques being used in the field of Disaster Assessment and Response.
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As large language models (LLMs) improve in their capacity to serve as personal AI assistants, their ability to output uniquely tailored, personalized responses that align with the soft preferences of their users is imperative for maximizing user satisfaction and retention. However, lay users are notoriously bad at prompt specification and often struggle with conveying their latent preferences to AI assistants. To resolve this, we demonstrate that activation steering, an inference-time method, can effectively control the response of the LLMs towards expressing different preferences. In contrast to memory-based personalization methods that require long user history, steering is extremely lightweight and easily-controllable via an interpretable linear strength factor. We further conduct a within-subjects user study (n=14) to investigate how end users personalize their conversations through three different steerable chatbot interfaces. The results demonstrate the effectiveness of preference-based steering for aligning real-world conversations with user preferences, and we discuss qualitative findings on how diverse values around control, transparency, and usability of personalization lead users to prefer different interfaces.
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