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 10467 publications
Heterogeneous graph neural networks for species distribution modeling
Christine Kaeser-Chen
Keith Anderson
Michelangelo Conserva
Elise Kleeman
Maxim Neumann
Matt Overlan
Millie Chapman
Drew Purves
arxiv (2025)
Preview abstract
Species distribution models (SDMs) are necessary for measuring and predicting occurrences and habitat suitability of species and their relationship with environmental factors. We introduce a novel presence-only SDM with graph neural networks (GNN). In our model, species and locations are treated as two distinct node sets, and the learning task is predicting detection records as the edges that connect locations to species. Using GNN for SDM allows us to model fine-grained interactions between species and the environment. We evaluate the potential of this methodology on the six-region dataset compiled by National Center for Ecological Analysis and Synthesis (NCEAS) for benchmarking SDMs. For each of the regions, the heterogeneous GNN model is comparable to or outperforms previously-benchmarked single-species SDMs as well as a feed-forward neural network baseline model.
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Ransomware over Modern Web Browsers: A Novel Strain and A New Defense Mechanism
Harun Oz
Ahmet Aris
Leonardo Babun
Selcuk Uluagac
Abbas Acar
ACM Transactions on the Web (2025)
Preview abstract
Ransomware is an increasingly prevalent form of malware targeting end-users, governments, and businesses. As it has evolved,
adversaries added new capabilities to their arsenal. Throughout the ransomware evolution, the adversaries propose a next-generation
browser-based ransomware, RøB, that performs its malicious actions via emerging web technologies, File System Access API (FSA) and
WebAssembly (Wasm). RøB uses this API through the victims’ browsers; hence, it does not require the victims to download and install
malicious binaries. We performed extensive evaluations with 3 different OSs, 23 file formats, 29 distinct directories, 5 cloud providers,
and 4 antivirus solutions. Our evaluations show that RøB can encrypt various types of files in the local and cloud-integrated directories,
external storage devices, and network-shared folders of victims. Our experiments also reveal that popular cloud solutions, Box
Individual and Apple iCloud can be severely affected by RøB. Moreover, we conducted tests with commercial antivirus software such
as AVG, Avast, Kaspersky, Malware Bytes that perform sensitive directory and suspicious behavior monitoring against ransomware.
We verified that RøB can evade these antivirus software and encrypt victim files. Moreover, existing ransomware detection solutions
in the literature also cannot be a remedy against RøB due to its distinct features. Therefore, in this paper, we also propose broguard,
a new detection system for RøB-like attacks. broguard monitors the web applications that use the FSA API via function hooking and
uses a machine learning classifier to detect RøB-like attacks in real-time without any file loss. Performance evaluations of broguard
on a comprehensive dataset show that broguard can detect RøB-like browser-based ransomware attacks with over 99% accuracy and
minimal overhead.
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Explainable Artificial Intelligence Techniques for Software Development Lifecycle: A phase-specific survey
Shashank Kapoor
Aman Raj
IEEE Compsac (2025)
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Artificial Intelligence (AI) is rapidly expanding and integrating more into daily life to automate tasks, guide decision-making and enhance efficiency. However, complex AI models, which make decisions without providing clear explanations (known as the "black-box problem"), currently restrict trust and widespread adoption of AI.
Explainable Artificial intelligence (XAI) has emerged to address the black-box problem of making AI systems more interpretable and transparent so stakeholders can trust, verify, and act upon AI-based outcomes. Researcher have come up with various techniques to foster XAI in Software Development Lifecycle. However, there are gaps in the application of XAI in Software Engineering phases. Literature shows that 68% of XAI in Software Engineering research focused on maintenance as opposed to 8% on software management and requirements [7].
In this paper we present a comprehensive survey of the applications of XAI methods (e.g., concept-based explanations, LIME/SHAP, rule extraction, attention mechanisms, counterfactual explanations, example-based explanations) to the different phases of Software Development Lifecycles (SDLC) mainly requirements elicitation, design and development, testing and deployment, and evolution.
To the best of our knowledge, this paper presents the first comprehensive survey of XAI techniques for every phase of the Software Development Life Cycle (SDLC). In doing so, we aim to promote explainable AI in Software Engineering and facilitate the use of complex AI models in AI-driven software development.
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A Scalable Framework for Evaluating Health Language Models
Neil Mallinar
Tony Faranesh
Brent Winslow
Nova Hammerquist
Ben Graef
Cathy Speed
Mark Malhotra
Shwetak Patel
Xavi Prieto
Daniel McDuff
Ahmed Metwally
(2025)
Preview abstract
Large language models (LLMs) have emerged as powerful tools for analyzing complex datasets. Recent studies demonstrate their potential to generate useful, personalized responses when provided with patient-specific health information that encompasses lifestyle, biomarkers, and context. As LLM-driven health applications are increasingly adopted, rigorous and efficient one-sided evaluation methodologies are crucial to ensure response quality across multiple dimensions, including accuracy, personalization and safety. Current evaluation practices for open-ended text responses heavily rely on human experts. This approach introduces human factors and is often cost-prohibitive, labor-intensive, and hinders scalability, especially in complex domains like healthcare where response assessment necessitates domain expertise and considers multifaceted patient data. In this work, we introduce Adaptive Precise Boolean rubrics: an evaluation framework that streamlines human and automated evaluation of open-ended questions by identifying gaps in model responses using a minimal set of targeted rubrics questions. Our approach is based on recent work in more general evaluation settings that contrasts a smaller set of complex evaluation targets with a larger set of more precise, granular targets answerable with simple boolean responses. We validate this approach in metabolic health, a domain encompassing diabetes, cardiovascular disease, and obesity. Our results demonstrate that Adaptive Precise Boolean rubrics yield higher inter-rater agreement among expert and non-expert human evaluators, and in automated assessments, compared to traditional Likert scales, while requiring approximately half the evaluation time of Likert-based methods. This enhanced efficiency, particularly in automated evaluation and non-expert contributions, paves the way for more extensive and cost-effective evaluation of LLMs in health.
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Fast electronic structure quantum simulation by spectrum amplification
Guang Hao Low
Robbie King
Dominic Berry
Qiushi Han
Albert Eugene DePrince III
Alec White
Rolando Somma
arXiv:2502.15882 (2025)
Preview abstract
The most advanced techniques using fault-tolerant quantum computers to estimate the ground-state energy of a chemical Hamiltonian involve compression of the Coulomb operator through tensor factorizations, enabling efficient block-encodings of the Hamiltonian. A natural challenge of these methods is the degree to which block-encoding costs can be reduced. We address this challenge through the technique of spectrum amplification, which magnifies the spectrum of the low-energy states of Hamiltonians that can be expressed as sums of squares. Spectrum amplification enables estimating ground-state energies with significantly improved cost scaling in the block encoding normalization factor $\Lambda$ to just $\sqrt{2\Lambda E_{\text{gap}}}$, where $E_{\text{gap}} \ll \Lambda$ is the lowest energy of the sum-of-squares Hamiltonian. To achieve this, we show that sum-of-squares representations of the electronic structure Hamiltonian are efficiently computable by a family of classical simulation techniques that approximate the ground-state energy from below. In order to further optimize, we also develop a novel factorization that provides a trade-off between the two leading Coulomb integral factorization schemes-- namely, double factorization and tensor hypercontraction-- that when combined with spectrum amplification yields a factor of 4 to 195 speedup over the state of the art in ground-state energy estimation for models of Iron-Sulfur complexes and a CO$_{2}$-fixation catalyst.
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Triaging mammography with artificial intelligence: an implementation study
Sarah M. Friedewald
Sunny Jansen
Fereshteh Mahvar
Timo Kohlberger
David V. Schacht
Sonya Bhole
Dipti Gupta
Scott Mayer McKinney
Stacey Caron
David Melnick
Mozziyar Etemadi
Samantha Winter
Alejandra Maciel
Luca Speroni
Martha Sevenich
Arnav Agharwal
Rubin Zhang
Gavin Duggan
Shiro Kadowaki
Atilla Kiraly
Jie Yang
Basil Mustafa
Krish Eswaran
Shravya Shetty
Breast Cancer Research and Treatment (2025)
Preview abstract
Purpose
Many breast centers are unable to provide immediate results at the time of screening mammography which results in delayed patient care. Implementing artificial intelligence (AI) could identify patients who may have breast cancer and accelerate the time to diagnostic imaging and biopsy diagnosis.
Methods
In this prospective randomized, unblinded, controlled implementation study we enrolled 1000 screening participants between March 2021 and May 2022. The experimental group used an AI system to prioritize a subset of cases for same-visit radiologist evaluation, and same-visit diagnostic workup if necessary. The control group followed the standard of care. The primary operational endpoints were time to additional imaging (TA) and time to biopsy diagnosis (TB).
Results
The final cohort included 463 experimental and 392 control participants. The one-sided Mann-Whitney U test was employed for analysis of TA and TB. In the control group, the TA was 25.6 days [95% CI 22.0–29.9] and TB was 55.9 days [95% CI 45.5–69.6]. In comparison, the experimental group's mean TA was reduced by 25% (6.4 fewer days [one-sided 95% CI > 0.3], p<0.001) and mean TB was reduced by 30% (16.8 fewer days; 95% CI > 5.1], p=0.003). The time reduction was more pronounced for AI-prioritized participants in the experimental group. All participants eventually diagnosed with breast cancer were prioritized by the AI.
Conclusions
Implementing AI prioritization can accelerate care timelines for patients requiring additional workup, while maintaining the efficiency of delayed interpretation for most participants. Reducing diagnostic delays could contribute to improved patient adherence, decreased anxiety and addressing disparities in access to timely care.
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Preview abstract
Large language models (LLMs), optimized through human feedback, have rapidly emerged as a leading paradigm for developing intelligent conversational assistants. However, despite their strong performance across many benchmarks, LLM-based agents might still lack conversational skills such as disambiguation -- when they are faced with ambiguity, they often overhedge or implicitly guess users' true intents rather than asking clarification questions. Under task-specific settings, high-quality conversation samples are often limited, constituting a bottleneck for LLMs' ability to learn optimal dialogue action policies. We propose Action-Based Contrastive Self-Training (ACT), a quasi-online preference optimization algorithm based on Direct Preference Optimization (DPO), that enables data-efficient dialogue policy learning in multi-turn conversation modeling. We demonstrate ACT's efficacy under data-efficient tuning scenarios, even when there is no action label available, using multiple real-world conversational tasks: tabular-grounded question-answering, machine reading comprehension, and AmbigSQL, a novel task for disambiguating information-seeking requests for complex SQL generation towards data analysis agents. Additionally, we propose evaluating LLMs' ability to function as conversational agents by examining whether they can implicitly recognize and reason about ambiguity in conversation. ACT demonstrates substantial conversation modeling improvements over standard tuning approaches like supervised fine-tuning and DPO.
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Concerns Beyond the Accuracy of AI Output
DORA, Google (2025)
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Generative AI's potential for hallucinations and inaccuracies are by far the most discussed limitation in AI-assisted software development. But, whether developers have other concerns about using generative AI in their coding practice has not been thoroughly explored. This article describes the results of in-depth interviews with developers about their other concerns about generative AI in coding, beyond the tools accuracy, and discusses related policy implications for organizations developing software.
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PreFix: Optimizing the Performance of Heap-Intensive Applications
Chaitanya Mamatha Ananda
Rajiv Gupta
Han Shen
CGO 2025: International Symposium on Code Generation and Optimization, Las Vegas, NV, USA (to appear)
Preview abstract
Analyses of heap-intensive applications show that a small fraction of heap objects account for the majority of heap accesses and data cache misses. Prior works like HDS and HALO have shown that allocating hot objects in separate memory regions can improve spatial locality leading to better application performance. However, these techniques are constrained in two primary ways, limiting their gains. First, these techniques have Imperfect Separation, polluting the hot memory region with several cold objects. Second, reordering of objects across allocations is not possible as the original object allocation order is preserved. This paper presents a novel technique that achieves near perfect separation of hot objects via a new context mechanism that efficiently identifies hot objects with high precision. This technique, named PreFix, is based upon Preallocating memory for a Fixed small number of hot objects. The program, guided by profiles, is instrumented to compute context information derived from
dynamic object identifiers, that precisely identifies hot object allocations that are then placed at predetermined locations in the preallocated memory. The preallocated memory region for hot objects provides the flexibility to reorder objects across allocations and allows colocation of objects that are part of a hot data stream (HDS), improving spatial locality. The runtime overhead of identifying hot objects is not significant as this optimization is only focused on a small number of static hot allocation sites and dynamic hot objects. While there is an increase in the program’s memory foot-print, it is manageable and can be controlled by limiting the size of the preallocated memory. In addition, PreFix incorporates an object recycling optimization that reuses the same preallocated space to store different objects whose lifetimes are not expected to overlap. Our experiments with 13 heap-intensive applications yields reductions in execution times ranging from 2.77% to 74%. On average PreFix reduces execution time by 21.7% compared to 7.3% by HDS and 14% by HALO. This is due to PreFix’s precision in hot object identification, hot object colocation, and low runtime overhead.
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Preview abstract
Recent work suggested utilizing inference compute, showing that scaling of number of samples consistently improves the fractions of problems solved by any attempt, namely the coverage. In this work, we suggest that inference scaling gains should be compared with proper baselines, as some datasets become degenerate when allowing a large number of attempts. We focus on two domains - mathematical reasoning and factual knowledge, showing that for the MATH and Entity Questions datasets, informed answer enumeration obtains similar or even better results than repeated model sampling, with a much lower sample budget. While we believe that inference scaling is a promising approach for unlocking the potential of language models, we recommend carefully selecting models and datasets when applying this method. Otherwise, the results of inference scaling should be interpreted with caution.
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The Cost of Consistency: Submodular Maximization with Constant Recourse
Paul Duetting
Federico Fusco
Ashkan Norouzi Fard
Ola Svensson
Proceedings of the 57th Annual ACM Symposium on Theory of Computing (2025), 1406–1417
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In this work, we study online submodular maximization and how the requirement of maintaining a stable solution impacts the approximation. In particular, we seek bounds on the best-possible
approximation ratio that is attainable when the algorithm is allowed to make, at most, a constant number of updates per step. We show a tight information-theoretic bound of $2/3$ for general monotone submodular functions and an improved (also tight) bound of $3/4$ for coverage functions. Since both these bounds are attained by non poly-time algorithms, we also give a poly-time randomized algorithm that achieves a $0.51$-approximation. Combined with an
information-theoretic hardness of $1/2$ for deterministic algorithms from prior work, our work thus shows a separation between deterministic and randomized algorithms, both information theoretically and for poly-time algorithms.
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AfriMed-QA: A Pan-African Multi-Specialty Medical Question-Answering Benchmark Dataset
Tobi Olatunji
Abraham Toluwase Owodunni
Charles Nimo
Jennifer Orisakwe
Henok Biadglign Ademtew
Chris Fourie
Foutse Yuehgoh
Stephen Moore
Mardhiyah Sanni
Emmanuel Ayodele
Timothy Faniran
Bonaventure F. P. Dossou
Fola Omofoye
Wendy Kinara
Tassallah Abdullahi
Michael Best
2025
Preview abstract
Recent advancements in large language model (LLM) performance on medical multiple-choice question (MCQ) benchmarks have stimulated significant interest from patients and healthcare providers globally. Particularly in low- and middle-income countries (LMICs) facing acute physician shortages and lack of specialists, LLMs offer a potentially scalable pathway to enhance healthcare access and reduce costs. However, LLM training data is sourced from predominantly Western text, existing benchmarks are predominantly Western-centric, limited to MCQs, and focused on a narrow range of clinical specialties, raising concerns about their applicability in the Global South, particularly across Africa where localized medical knowledge and linguistic diversity are often underrepresented. In this work, we introduce AfriMed-QA, the first large-scale multi-specialty Pan-African medical Question-Answer (QA) dataset designed to evaluate and develop equitable and effective LLMs for African healthcare. It contains 3,000 multiple-choice professional medical exam questions with answers and rationale, 1,500 short answer questions (SAQ) with long-from answers, and 5,500 consumer queries, sourced from over 60 medical schools across 15 countries, covering 32 medical specialties. We further rigorously evaluate multiple open, closed, general, and biomedical LLMs across multiple axes including accuracy, consistency, factuality, bias, potential for harm, local geographic relevance, medical reasoning, and recall. We believe this dataset provides a valuable resource for practical application of large language models in African healthcare and enhances the geographical diversity of health-LLM benchmark datasets.
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Study of Arterials in the City of Rio de Janeiro for Traffic Coordination
Ori Rottenstreich
Eliav Buchnik
Danny Veikherman
Dan Karliner
Tom Kalvari
Shai Ferster
Ron Tsibulsky
Jack Haddad
2025
Preview abstract
Urban traffic congestion is a growing challenge, and optimizing signal timing strategies is crucial for improving traffic flow and reducing emissions. The coordination of signalized intersections improves both traffic operations and environmental aspects. Coordination is particularly important along arterials, sequences of signalized intersections that serve as the primary routes and carry a high volume of traffic. In this paper we analyze real data from the city of Rio de Janeiro to study properties of arterials. We refer to their length, the distance between intersections and to the properties of the traffic light plans such as cycle time. We then study their in practice level of coordination in terms of number of stops and their common locations along the arterials. We dive into particular arterials and provide insights that can be useful for efficient design of arterials in additional cities. Based on the analysis, we show how simple traffic properties can indicate the potential upon coordinating two adjacent intersections as part of an arterial in improving traffic performance.
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Quartic Quantum Speedups for Planted Inference Problems
Alexander Schmidhuber
Ryan O'Donnell
Physical Review X, 15 (2025), pp. 021077
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We describe a quantum algorithm for the Planted Noisy kXOR problem (also known as sparse Learning Parity with Noise) that achieves a nearly quartic (4th power) speedup over the best known classical algorithm while also only using logarithmically many qubits. Our work generalizes and simplifies prior work of Hastings, by building on his quantum algorithm for the Tensor Principal Component Analysis (PCA) problem. We achieve our quantum speedup using a general framework based on the Kikuchi Method (recovering the quartic speedup for Tensor PCA), and we anticipate it will yield similar speedups for further planted inference problems. These speedups rely on the fact that planted inference problems naturally instantiate the Guided Sparse Hamiltonian problem. Since the Planted Noisy kXOR problem has been used as a component of certain cryptographic constructions, our work suggests that some of these are susceptible to super-quadratic quantum attacks.
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Automated loss of pulse detection on a commercial smartwatch
Kamal Shah
Anran Wang
Yiwen Chen
Anthony Stange
Lawrence Cai
Matt Wimmer
Pramod Rudrapatna
Shelten Yuen
Anupam Pathak
Shwetak Patel
Mark Malhotra
Marc Stogaitis
Jeanie Phan
Ali Connell
Jim Taylor
Jacqueline Shreibati
Daniel McDuff
Tajinder Gadh
Jake Sunshine
Nature, 642 (2025), pp. 174-181
Preview abstract
Out-of-hospital cardiac arrest is a time-sensitive emergency that requires prompt identification and intervention: sudden, unwitnessed cardiac arrest is nearly unsurvivable. A cardinal sign of cardiac arrest is sudden loss of pulse. Automated biosensor detection of unwitnessed cardiac arrest, and dispatch of medical assistance, may improve survivability given the substantial prognostic role of time, but only if the false-positive burden on public emergency medical systems is minimized. Here we show that a multimodal, machine learning-based algorithm on a smartwatch can reach performance thresholds making it deployable at a societal scale. First, using photoplethysmography, we show that wearable photoplethysmography measurements of peripheral pulselessness (induced through an arterial occlusion model) manifest similarly to pulselessness caused by a common cardiac arrest arrhythmia, ventricular fibrillation. On the basis of the similarity of the photoplethysmography signal (from ventricular fibrillation or arterial occlusion), we developed and validated a loss of pulse detection algorithm using data from peripheral pulselessness and free-living conditions. Following its development, we evaluated the end-to-end algorithm prospectively: there was 1 unintentional emergency call per 21.67 user-years across two prospective studies; the sensitivity was 67.23% (95% confidence interval of 64.32% to 70.05%) in a prospective arterial occlusion cardiac arrest simulation model. These results indicate an opportunity, deployable at scale, for wearable-based detection of sudden loss of pulse while minimizing societal costs of excess false detections.
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