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Ilkay Altintas

Publications and source records attributed to Ilkay Altintas.

At least 19 recordsLinked to original sources

Physics-guided spatiotemporal neural models for fuel density prediction

This paper presents a physics-guided machine learning (PGML) framework for fuel density prediction, integrating physics constraints and domain knowledge into deep learning models to enhance model accuracy and stability. We explore three deep learning architectures -- ConvLSTM, Adaptive Fourier Neural Operator (AFNONet), and Video Vision Transformer (ViViT) -- to model the spatiotemporal evolution of fuel density. Our approach incorporates differentiable physics-informed terms in the loss function, including a mass-conserving fuel transport term and a rate-of-spread estimation. Experimental results, averaged across multiple independent trials, demonstrate that the proposed PGML framework outperforms purely data-driven baselines without physics constraints in both accuracy and stability. This framework enables computationally efficient, physically plausible fire forecasting to support adaptive prescribed burn management.

cs.LG

Natural Language to What? A Vision for Intermediate Representations in NL-to-X Querying

Natural-language-initiated querying is usually framed as translation into a predetermined backend language such as SQL, Cypher, or SPARQL. That framing is appropriate when the semantic target is known in advance, but it does not cover the full space of natural-language query workloads. In document-centric, mixed, and heterogeneous environments, the first semantic problem may be to determine what target should be constructed before backend-specific execution can begin. This paper proposes the $\textit{NLIQ}~$ lens for this broader space. It introduces target adequacy as the criterion for distinguishing settings in which the target is given, only partially specified, or must itself be constructed, and argues that intermediate representations in the latter regimes are not merely implementation devices but first-class semantic objects. The paper develops a compact framework of $\textit{NLIQ}~$ regimes, illustrates the distinction through representative examples, and identifies a new research terrain around semantic target formation, intermediate representation design, heterogeneous compilation, and answer formation in complex data environments.

cs.DB

National Data Platform's Education Hub

As demand for AI literacy and data science education grows, there is a critical need for infrastructure that bridges the gap between research data, computational resources, and educational experiences. To address this gap, we developed a first-of-its-kind Education Hub within the National Data Platform. This hub enables seamless connections between collaborative research workspaces, classroom environments, and data challenge settings. Early use cases demonstrate the effectiveness of the platform in supporting complex and resource-intensive educational activities. Ongoing efforts aim to enhance the user experience and expand adoption by educators and learners alike.

cs.CY

Bridging eResearch Infrastructure and Experimental Materials Science Process in the Quantum Data Hub

Experimental materials science is experiencing significant growth due to automated experimentation and AI techniques. Integrated autonomous platforms are emerging, combining generative models, robotics, simulations, and automated systems for material synthesis. However, two major challenges remain: democratizing access to these technologies and creating accessible infrastructure for under-resourced scientists. This paper introduces the Quantum Data Hub (QDH), a community-accessible research infrastructure aimed at researchers working with quantum materials. QDH integrates with the National Data Platform, adhering to FAIR principles while proposing additional UNIT principles for usability, navigability, interpretability, and timeliness. The QDH facilitates collaboration and extensibility, allowing seamless integration of new researchers, instruments, and data into the system.

cs.SE

Workflows Community Summit 2022: A Roadmap Revolution

Scientific workflows have become integral tools in broad scientific computing use cases. Science discovery is increasingly dependent on workflows to orchestrate large and complex scientific experiments that range from execution of a cloud-based data preprocessing pipeline to multi-facility instrument-to-edge-to-HPC computational workflows. Given the changing landscape of scientific computing and the evolving needs of emerging scientific applications, it is paramount that the development of novel scientific workflows and system functionalities seek to increase the efficiency, resilience, and pervasiveness of existing systems and applications. Specifically, the proliferation of machine learning/artificial intelligence (ML/AI) workflows, need for processing large scale datasets produced by instruments at the edge, intensification of near real-time data processing, support for long-term experiment campaigns, and emergence of quantum computing as an adjunct to HPC, have significantly changed the functional and operational requirements of workflow systems. Workflow systems now need to, for example, support data streams from the edge-to-cloud-to-HPC enable the management of many small-sized files, allow data reduction while ensuring high accuracy, orchestrate distributed services (workflows, instruments, data movement, provenance, publication, etc.) across computing and user facilities, among others. Further, to accelerate science, it is also necessary that these systems implement specifications/standards and APIs for seamless (horizontal and vertical) integration between systems and applications, as well as enabling the publication of workflows and their associated products according to the FAIR principles. This document reports on discussions and findings from the 2022 international edition of the Workflows Community Summit that took place on November 29 and 30, 2022.

cs.DC

Multimodal Wildland Fire Smoke Detection

Research has shown that climate change creates warmer temperatures and drier conditions, leading to longer wildfire seasons and increased wildfire risks in the United States. These factors have in turn led to increases in the frequency, extent, and severity of wildfires in recent years. Given the danger posed by wildland fires to people, property, wildlife, and the environment, there is an urgency to provide tools for effective wildfire management. Early detection of wildfires is essential to minimizing potentially catastrophic destruction. In this paper, we present our work on integrating multiple data sources in SmokeyNet, a deep learning model using spatio-temporal information to detect smoke from wildland fires. Camera image data is integrated with weather sensor measurements and processed by SmokeyNet to create a multimodal wildland fire smoke detection system. We present our results comparing performance in terms of both accuracy and time-to-detection for multimodal data vs. a single data source. With a time-to-detection of only a few minutes, SmokeyNet can serve as an automated early notification system, providing a useful tool in the fight against destructive wildfires.

cs.CV

Towards a Dynamic Composability Approach for using Heterogeneous Systems in Remote Sensing

Influenced by the advances in data and computing, the scientific practice increasingly involves machine learning and artificial intelligence driven methods which requires specialized capabilities at the system-, science- and service-level in addition to the conventional large-capacity supercomputing approaches. The latest distributed architectures built around the composability of data-centric applications led to the emergence of a new ecosystem for container coordination and integration. However, there is still a divide between the application development pipelines of existing supercomputing environments, and these new dynamic environments that disaggregate fluid resource pools through accessible, portable and re-programmable interfaces. New approaches for dynamic composability of heterogeneous systems are needed to further advance the data-driven scientific practice for the purpose of more efficient computing and usable tools for specific scientific domains. In this paper, we present a novel approach for using composable systems in the intersection between scientific computing, artificial intelligence (AI), and remote sensing domain. We describe the architecture of a first working example of a composable infrastructure that federates Expanse, an NSF-funded supercomputer, with Nautilus, a Kubernetes-based GPU geo-distributed cluster. We also summarize a case study in wildfire modeling, that demonstrates the application of this new infrastructure in scientific workflows: a composed system that bridges the insights from edge sensing, AI and computing capabilities with a physics-driven simulation.

cs.DC

FIgLib & SmokeyNet: Dataset and Deep Learning Model for Real-Time Wildland Fire Smoke Detection

The size and frequency of wildland fires in the western United States have dramatically increased in recent years. On high-fire-risk days, a small fire ignition can rapidly grow and become out of control. Early detection of fire ignitions from initial smoke can assist the response to such fires before they become difficult to manage. Past deep learning approaches for wildfire smoke detection have suffered from small or unreliable datasets that make it difficult to extrapolate performance to real-world scenarios. In this work, we present the Fire Ignition Library (FIgLib), a publicly available dataset of nearly 25,000 labeled wildfire smoke images as seen from fixed-view cameras deployed in Southern California. We also introduce SmokeyNet, a novel deep learning architecture using spatiotemporal information from camera imagery for real-time wildfire smoke detection. When trained on the FIgLib dataset, SmokeyNet outperforms comparable baselines and rivals human performance. We hope that the availability of the FIgLib dataset and the SmokeyNet architecture will inspire further research into deep learning methods for wildfire smoke detection, leading to automated notification systems that reduce the time to wildfire response.

cs.CV

A Community Roadmap for Scientific Workflows Research and Development

The landscape of workflow systems for scientific applications is notoriously convoluted with hundreds of seemingly equivalent workflow systems, many isolated research claims, and a steep learning curve. To address some of these challenges and lay the groundwork for transforming workflows research and development, the WorkflowsRI and ExaWorks projects partnered to bring the international workflows community together. This paper reports on discussions and findings from two virtual "Workflows Community Summits" (January and April, 2021). The overarching goals of these workshops were to develop a view of the state of the art, identify crucial research challenges in the workflows community, articulate a vision for potential community efforts, and discuss technical approaches for realizing this vision. To this end, participants identified six broad themes: FAIR computational workflows; AI workflows; exascale challenges; APIs, interoperability, reuse, and standards; training and education; and building a workflows community. We summarize discussions and recommendations for each of these themes.

cs.DC

Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development

Scientific workflows are a cornerstone of modern scientific computing, and they have underpinned some of the most significant discoveries of the last decade. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale HPC platforms. Workflows will play a crucial role in the data-oriented and post-Moore's computing landscape as they democratize the application of cutting-edge research techniques, computationally intensive methods, and use of new computing platforms. As workflows continue to be adopted by scientific projects and user communities, they are becoming more complex. Workflows are increasingly composed of tasks that perform computations such as short machine learning inference, multi-node simulations, long-running machine learning model training, amongst others, and thus increasingly rely on heterogeneous architectures that include CPUs but also GPUs and accelerators. The workflow management system (WMS) technology landscape is currently segmented and presents significant barriers to entry due to the hundreds of seemingly comparable, yet incompatible, systems that exist. Another fundamental problem is that there are conflicting theoretical bases and abstractions for a WMS. Systems that use the same underlying abstractions can likely be translated between, which is not the case for systems that use different abstractions. More information: https://workflowsri.org/summits/technical

cs.DC

Workflows Community Summit: Bringing the Scientific Workflows Community Together

Scientific workflows have been used almost universally across scientific domains, and have underpinned some of the most significant discoveries of the past several decades. Many of these workflows have high computational, storage, and/or communication demands, and thus must execute on a wide range of large-scale platforms, from large clouds to upcoming exascale high-performance computing (HPC) platforms. These executions must be managed using some software infrastructure. Due to the popularity of workflows, workflow management systems (WMSs) have been developed to provide abstractions for creating and executing workflows conveniently, efficiently, and portably. While these efforts are all worthwhile, there are now hundreds of independent WMSs, many of which are moribund. As a result, the WMS landscape is segmented and presents significant barriers to entry due to the hundreds of seemingly comparable, yet incompatible, systems that exist. As a result, many teams, small and large, still elect to build their own custom workflow solution rather than adopt, or build upon, existing WMSs. This current state of the WMS landscape negatively impacts workflow users, developers, and researchers. The "Workflows Community Summit" was held online on January 13, 2021. The overarching goal of the summit was to develop a view of the state of the art and identify crucial research challenges in the workflow community. Prior to the summit, a survey sent to stakeholders in the workflow community (including both developers of WMSs and users of workflows) helped to identify key challenges in this community that were translated into 6 broad themes for the summit, each of them being the object of a focused discussion led by a volunteer member of the community. This report documents and organizes the wealth of information provided by the participants before, during, and after the summit.

cs.DC

Cardiac MRI Image Segmentation for Left Ventricle and Right Ventricle using Deep Learning

The goal of this project is to use magnetic resonance imaging (MRI) data to provide an end-to-end analytics pipeline for left and right ventricle (LV and RV) segmentation. Another aim of the project is to find a model that would be generalizable across medical imaging datasets. We utilized a variety of models, datasets, and tests to determine which one is well suited to this purpose. Specifically, we implemented three models (2-D U-Net, 3-D U-Net, and DenseNet), and evaluated them on four datasets (Automated Cardiac Diagnosis Challenge, MICCAI 2009 LV, Sunnybrook Cardiac Data, MICCAI 2012 RV). While maintaining a consistent preprocessing strategy, we tested the performance of each model when trained on data from the same dataset as the test data, and when trained on data from a different dataset than the test dataset. Data augmentation was also used to increase the adaptability of the models. The results were compared to determine performance and generalizability.

eess.IV

Workflow-Driven Distributed Machine Learning in CHASE-CI: A Cognitive Hardware and Software Ecosystem Community Infrastructure

The advances in data, computing and networking over the last two decades led to a shift in many application domains that includes machine learning on big data as a part of the scientific process, requiring new capabilities for integrated and distributed hardware and software infrastructure. This paper contributes a workflow-driven approach for dynamic data-driven application development on top of a new kind of networked Cyberinfrastructure called CHASE-CI. In particular, we present: 1) The architecture for CHASE-CI, a network of distributed fast GPU appliances for machine learning and storage managed through Kubernetes on the high-speed (10-100Gbps) Pacific Research Platform (PRP); 2) A machine learning software containerization approach and libraries required for turning such a network into a distributed computer for big data analysis; 3) An atmospheric science case study that can only be made scalable with an infrastructure like CHASE-CI; 4) Capabilities for virtual cluster management for data communication and analysis in a dynamically scalable fashion, and visualization across the network in specialized visualization facilities in near real-time; and, 5) A step-by-step workflow and performance measurement approach that enables taking advantage of the dynamic architecture of the CHASE-CI network and container management infrastructure.

cs.DC

Towards A Methodology and Framework for Workflow-Driven Team Science

Scientific workflows are powerful tools for management of scalable experiments, often composed of complex tasks running on distributed resources. Existing cyberinfrastructure provides components that can be utilized within repeatable workflows. However, data and computing advances continuously change the way scientific workflows get developed and executed, pushing the scientific activity to be more data-driven, heterogeneous and collaborative. Workflow development today depends on the effective collaboration and communication of a cross-disciplinary team, not only with humans but also with analytical systems and infrastructure. This paper presents a collaboration-centered reference architecture to extend workflow systems with dynamic, predictable and programmable interfaces to systems and infrastructure while bridging the exploratory and scalable activities in the scientific process. We also present a conceptual design towards the development of methodologies and tools for effective workflow-driven collaborations, namely the PPoDS methodology and the SmartFlows Toolkit for smart utilization of workflows in a rapidly evolving cyberinfrastructure ecosystem.

cs.CY

Left Ventricle Segmentation and Volume Estimation on Cardiac MRI using Deep Learning

In the United States, heart disease is the leading cause of death for both men and women, accounting for 610,000 deaths each year [1]. Physicians use Magnetic Resonance Imaging (MRI) scans to take images of the heart in order to non-invasively estimate its structural and functional parameters for cardiovascular diagnosis and disease management. The end-systolic volume (ESV) and end-diastolic volume (EDV) of the left ventricle (LV), and the ejection fraction (EF) are indicators of heart disease. These measures can be derived from the segmented contours of the LV; thus, consistent and accurate segmentation of the LV from MRI images are critical to the accuracy of the ESV, EDV, and EF, and to non-invasive cardiac disease detection. In this work, various image preprocessing techniques, model configurations using the U-Net deep learning architecture, postprocessing methods, and approaches for volume estimation are investigated. An end-to-end analytics pipeline with multiple stages is provided for automated LV segmentation and volume estimation. First, image data are reformatted and processed from DICOM and NIfTI formats to raw images in array format. Secondly, raw images are processed with multiple image preprocessing methods and cropped to include only the Region of Interest (ROI). Thirdly, preprocessed images are segmented using U-Net models. Lastly, post processing of segmented images to remove extra contours along with intelligent slice and frame selection are applied, followed by calculation of the ESV, EDV, and EF. This analytics pipeline is implemented and runs on a distributed computing environment with a GPU cluster at the San Diego Supercomputer Center at UCSD.

cs.CV

Ten Simple Rules for Reproducible Research in Jupyter Notebooks

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses.

cs.OH

Enabling FAIR Research in Earth Science through Research Objects

Data-intensive science communities are progressively adopting FAIR practices that enhance the visibility of scientific breakthroughs and enable reuse. At the core of this movement, research objects contain and describe scientific information and resources in a way compliant with the FAIR principles and sustain the development of key infrastructure and tools. This paper provides an account of the challenges, experiences and solutions involved in the adoption of FAIR around research objects over several Earth Science disciplines. During this journey, our work has been comprehensive, with outcomes including: an extended research object model adapted to the needs of earth scientists; the provisioning of digital object identifiers (DOI) to enable persistent identification and to give due credit to authors; the generation of content-based, semantically rich, research object metadata through natural language processing, enhancing visibility and reuse through recommendation systems and third-party search engines; and various types of checklists that provide a compact representation of research object quality as a key enabler of scientific reuse. All these results have been integrated in ROHub, a platform that provides research object management functionality to a wealth of applications and interfaces across different scientific communities. To monitor and quantify the community uptake of research objects, we have defined indicators and obtained measures via ROHub that are also discussed herein.

cs.CL

Deep Learning on Operational Facility Data Related to Large-Scale Distributed Area Scientific Workflows

Distributed computing platforms provide a robust mechanism to perform large-scale computations by splitting the task and data among multiple locations, possibly located thousands of miles apart geographically. Although such distribution of resources can lead to benefits, it also comes with its associated problems such as rampant duplication of file transfers increasing congestion, long job completion times, unexpected site crashing, suboptimal data transfer rates, unpredictable reliability in a time range, and suboptimal usage of storage elements. In addition, each sub-system becomes a potential failure node that can trigger system wide disruptions. In this vision paper, we outline our approach to leveraging Deep Learning algorithms to discover solutions to unique problems that arise in a system with computational infrastructure that is spread over a wide area. The presented vision, motivated by a real scientific use case from Belle II experiments, is to develop multilayer neural networks to tackle forecasting, anomaly detection and optimization challenges in a complex and distributed data movement environment. Through this vision based on Deep Learning principles, we aim to achieve reduced congestion events, faster file transfer rates, and enhanced site reliability.

cs.DC