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 10363 publications
Heterogenous 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)
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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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Astute RAG: Overcoming Imperfect Retrieval Augmentation and Knowledge Conflicts for Large Language Models
Fei Wang
The Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (ACL 2025) (2025) (to appear)
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Retrieval-Augmented Generation (RAG), while effective in integrating external knowledge to address the limitations of large language models (LLMs), can be undermined by imperfect retrieval, which may introduce irrelevant, misleading, or even malicious information. Despite its importance, previous studies have rarely explored the behavior of RAG through joint analysis on how errors from imperfect retrieval attribute and propagate, and how potential conflicts arise between the LLMs' internal knowledge and external sources. We find that imperfect retrieval augmentation might be inevitable and quite harmful, through controlled analysis under realistic conditions. We identify the knowledge conflicts between LLM-internal and external knowledge from retrieval as a bottleneck to overcome in the post-retrieval stage of RAG. To render LLMs resilient to imperfect retrieval, we propose Astute RAG, a novel RAG approach that adaptively elicits essential information from LLMs' internal knowledge, iteratively consolidates internal and external knowledge with source-awareness, and finalizes the answer according to information reliability. Our experiments using Gemini and Claude demonstrate that Astute RAG significantly outperforms previous robustness-enhanced RAG methods. Notably, Astute RAG is the only approach that matches or exceeds the performance of LLMs without RAG under worst-case scenarios. Further analysis reveals that Astute RAG effectively resolves knowledge conflicts, improving the reliability and trustworthiness of RAG systems.
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Styled Handwritten Text Generation (HTG) has recently received attention from the computer vision and document analysis communities, which have developed several solutions, either GAN- or diffusion-based, that achieved promising results. Nonetheless, these strategies fail to generalize to novel styles and have technical constraints, particularly in terms of maximum output length and training efficiency. To overcome these limitations, in this work, we propose a novel framework for text image generation, dubbed Emuru. Our approach leverages a powerful text image representation model (a variational autoencoder) combined with an autoregressive Transformer. Our approach enables the generation of styled text images conditioned on textual content and style examples, such as specific fonts or handwriting styles. We train our model solely on a diverse, synthetic dataset of English text rendered in over 100,000 typewritten and calligraphy fonts, which gives it the capability to reproduce unseen styles (both fonts and users' handwriting) in zero-shot. To the best of our knowledge, Emuru is the first autoregressive model for HTG, and the first designed specifically for generalization to novel styles. Moreover, our model generates images without background artifacts, which are easier to use for downstream applications. Extensive evaluation on both typewritten and handwritten, any-length text image generation scenarios demonstrates the effectiveness of our approach.
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Zoom in, Zoom out, Reframe: Domain Experts’ Strategies for Addressing Non-Experts’ Complex Questions
Roma Ruparel
Proceedings of the 2025 CHI Conference on Human Factors in Computing Systems (CHI) (2025) (to appear)
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Consumers rely on the Internet for expert information in domains such as healthcare and law. Large Language Models (LLMs) have the potential to increase access to expert knowledge. However, past research has not addressed how to handle certain aspects of complex questions that commonly occur in expert-layperson interactions. We conducted in-depth interviews with 26 experts across multiple domains to understand how they experience and respond to challenges associated with non-experts’ questions. Results from a thematic analysis reveal three recurring strategies that experts across domains employ when fielding complex questions. Experts zoom in to clarify details of a broad information request, zoom out to address overly narrow questions or assumptions, and reframe when the underlying need is unstated or poorly represented. We discuss implications for the design of LLM-based experiences that facilitate access to expert information.
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SSDTrain: Faster Large Language Model Training Using SSD-Based Activation Offloading
Kun Wu
Jeongmin Brian Park
Mert Hidayetoğlu
Vikram Sharma Mailthody
Sitao Huang
Steven Lumetta
Wen-mei Hwu
Design Automation Conference (DAC) (2025)
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The scaling up of Large Language Models (LLMs) demands more memory than current GPUs can provide, hindering the training process. To address this challenge, we propose SSDTrain to efficiently offload activations, the intermediate tensors produced during LLM training, to SSDs. This approach reduces GPU memory usage without impacting performance by adaptively overlapping data transfers with computation. SSDTrain is compatible with popular deep learning frameworks like PyTorch, Megatron, and DeepSpeed, and it employs techniques such as tensor deduplication, forwarding, and adaptive offloading to further enhance efficiency. We conduct extensive experiments on Llama, BERT, and T5. Results demonstrate that SSDTrain effectively reduces 45% of the activation peak memory usage. It can perfectly overlap the IO with the computation without introducing performance penalty. SSDTrain can achieve a performance boost of up to 31% compared to the conventional training strategy using the same GPU systems.
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Despite the advent of legislation such as the General Data Protection Regulation (GDPR) with its associated "Right to be Forgotten" (RTBF), few, if any, studies have measured user reactions to realistic edge cases with public-interest content. Surveying both users covered by and excluded from RTBF, this vignette-based survey experiment sought to better understand how users think of delisting content from search engine results and what factors influence user perceptions. While leaving information accessible in search engine results generally leads to warmer feelings towards those search engines than delisting it, we find that users do prefer different outcomes
depending on contextual elements specific to given cases. We also find that whether a country has active RTBF legislation does seem to be associated with both knowledge and attitudes about RTBF, but is unlikely to explain all of it. These results indicate a complex context around removing public-interest content from search engines’ results; it is essential that experts sensitive to local context perform the review in order to ensure that removal requests are handled in a way that meets users’ expectations.
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This paper explores the integration of model-based and data-driven approaches within the realm of neural speech and audio coding systems. It highlights the challenges posed by the subjective evaluation processes of speech and audio codecs and discusses the limitations of purely data-driven approaches, which often require inefficiently large architectures to match the performance of model-based methods. The study presents hybrid systems as a viable solution, offering significant improvements to the performance of conventional codecs through meticulously chosen design enhancements. Specifically, it introduces a neural network-based signal enhancer designed to post-process existing codecs’ output, along with the autoencoder-based end-to-end models and LPCNet—hybrid systems that combine linear predictive coding (LPC) with neural networks. Furthermore, the paper delves into predictive models operating within custom feature spaces (TF-Codec) or predefined transform domains (MDCTNet) and examines the use of psychoacoustically calibrated loss functions to train end-to-end neural audio codecs. Through these investigations, the paper demonstrates the potential of hybrid systems to advance the field of speech and audio coding by bridging the gap between traditional model-based approaches and modern data-driven techniques.
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Delay monitoring is a commonly arising problem in applications such as queue management systems, scheduling, and traffic monitoring. Motivated by such applications, we formulate a queue monitoring problem, where there is a FIFO queue with arbitrary arrivals and departures, and a server needs to monitor the length of a queue by using (decentralized) pings from packets in the queue. Packets can send pings informing the server about the number of packets ahead of them in the queue. Via novel online algorithms and lower bounds, we tightly characterize the trade-off between the number of pings sent and the accuracy of the server's real time estimates. Further, our approximate estimates can be made to be accurate to an arbitrary precision.
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This invited OFC 2025 tutorial will review recent progress and scaling limitations of IM-DD-based low-cost optical interconnects. It will examine how datacenter-reach optimized coherent optics can address these challenges
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Mitigating Clinician Information Overload: Generative AI for Integrated EHR and RPM Data Analysis
Ankit Shetgaonkar
Shashank Kapoor
Aman Raj
2025
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Generative AI (GenAI), particularly Large Language Models (LLMs), offer powerful capabilities for interpreting the complex data landscape in healthcare. In this paper, we present a comprehensive overview of the capabilities, requirements and applications of GenAI for deriving clinical insights and improving clinical efficiency. We first provide some background on the forms and sources of patient data, namely real-time Remote Patient Monitoring (RPM) streams and traditional Electronic Health Records (EHR). The sheer volume and heterogeneity of this combined data present significant challenges to clinicians and contribute to information overload.
In addition, we explore the potential of LLM-powered applications for improving clinical efficiency. These applications can enhance navigation of longitudinal patient data and provide actionable clinical decision support through natural language dialogue. We discuss the opportunities this presents for streamlining clinician workflows and personalizing care, alongside critical challenges such as data integration complexity, ensuring data quality and RPM data reliability, maintaining patient privacy, validating AI outputs for clinical safety, mitigating bias, and ensuring clinical acceptance. We believe this work represents the first summarization of GenAI techniques for managing clinician data overload due to combined RPM / EHR data complexities.
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Context is Key for Agent Security
Lillian Tsai
Eugene Bagdasaryan
arXiv (2025)
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Judging the safety of an action, whether taken by a human or a system, must take into account the context in which the action takes place. For example, deleting an email from a user's mailbox may or may not be appropriate depending on the email's content, the user's goals, or even available space. Systems today that make these judgements---providing security against harmful or inappropriate actions---rely on manually-crafted policies or user confirmation for each relevant context. With the upcoming deployment of systems like generalist agents, we argue that we must rethink security designs to adapt to the scale of contexts and capabilities of these systems. As a first step, this paper explores contextual security in the domain of agents and proposes contextual security for agents (Conseca), a framework to generate just-in-time, contextual, and human-verifiable security policies.
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Adversarial Attacks in Multimodal Systems: A Practitioner's Survey
Shashank Kapoor
Ankit Shetgaonkar
Aman Raj
2025
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Multimodal models represent a significant advancement in Artificial Intelligence. A single model is trained to understand unstructured modalities: text, image, video, and audio. Open-source variants of multimodal models have made these breakthroughs further accessible. ML practitioners adopt, finetune, and deploy open-source models in real-world applications. However, considering the vast landscape of adversarial attacks across these modalities, these models also inherit vulnerabilities of all the modalities, and eventually, the adversarial threat amplifies. While broad research is available on possible attacks within or across these modalities, a practitioner-focused view of outlining attack types remains absent in the multimodal world. This paper addresses the gap by surveying adversarial attacks targeting all four modalities: text, image, video, and audio. This survey provides a view of the adversarial attack landscape and presents how multimodal adversarial threats have evolved. To the best of our knowledge, this survey is the first comprehensive summarization of the threat landscape in the multimodal world.
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Shadow Hamiltonian Simulation
Rolando Somma
Robbie King
Tom O'Brien
Nature Communications, 16 (2025), pp. 2690
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Simulating quantum dynamics is one of the most important applications of quantum computers. Traditional approaches for quantum simulation involve preparing the full evolved state of the system and then measuring some physical quantity. Here, we present a different and novel approach to quantum simulation that uses a compressed quantum state that we call the "shadow state". The amplitudes of this shadow state are proportional to the time-dependent expectations of a specific set of operators of interest, and it evolves according to its own Schrödinger equation. This evolution can be simulated on a quantum computer efficiently under broad conditions. Applications of this approach to quantum simulation problems include simulating the dynamics of exponentially large systems of free fermions or free bosons, the latter example recovering a recent algorithm for simulating exponentially many classical harmonic oscillators. These simulations are hard for classical methods and also for traditional quantum approaches, as preparing the full states would require exponential resources. Shadow Hamiltonian simulation can also be extended to simulate expectations of more complex operators such as two-time correlators or Green's functions, and to study the evolution of operators themselves in the Heisenberg picture.
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Explainable Artificial Intelligence Techniques for Software Development Lifecycle: A phase-specific survey
Shashank Kapoor
Aman Raj
Ankit Shetgaonkar
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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Project and task scheduling under uncertainty remains a fundamental challenge in program and project management, where accurate estimation of task durations and dependencies is critical for delivering complex, multi project systems. The Program Evaluation and Review Technique provides a probabilistic framework to model task variability and critical paths. In this paper, the author presents a novel formulation of PERT scheduling as an energy minimization problem within a Hopfield neural network architecture. By mapping task start times and precedence constraints into a neural computation framework, the networks inherent optimization dynamics is exploited to approximate globally consistent schedules. The author addresses key theoretical issues related to energy function differentiability, constraint encoding, and convergence, and extends the Hopfield model for structured precedence graphs. Numerical simulations on synthetic project networks comprising up to 1000 tasks demonstrate the viability of this approach, achieving near optimal makespans with minimal constraint violations. The findings suggest that neural optimization models offer a promising direction for scalable and adaptive project tasks scheduling under uncertainty in areas such as the agentic AI workflows, microservice based applications that the modern AI systems are being built upon.
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