arXiv subjects

Tekin Bicer

Publications and source records attributed to Tekin Bicer.

At least 19 recordsLinked to original sources

arXiv2026

StreamGuard: Low-Overhead Resilience for Real-time HPC Data Streams

Real-time scientific workflows operate on continuous data streams and must produce timely, high-quality results despite executing on complex, failure-prone infrastructure. Hardware faults, network disruptions, and performance anomalies caused by resource contention or system heterogeneity can severely degrade performance and violate real-time constraints. We focus on strengthening the resilience of the producer-consumer streaming pattern, a fundamental building block of scientific streaming workflows. We present two complementary techniques: (i) a dynamic, asynchronous, non-blocking checkpointing mechanism that preserves progress without interrupting computation, and (ii) a progress-aware load redistribution strategy that detects slow workers and proactively rebalances tasks. Together, these mechanisms maintain forward progress and balanced execution even in highly error-prone environments. Experimental results show that our approach reduces the impact of failures and performance anomalies by up to 6x, while introducing less than 1% overhead in failure-free execution.

cs.DC↗

arXiv2026

Training-Free Inference for High-Resolution Sinogram Completion

High-resolution sinogram completion is critical for computed tomography reconstruction, as missing projections can introduce severe artifacts. While diffusion models provide strong generative priors for this task, their inference cost grows prohibitively with resolution. We propose HRSino, a training-free and efficient diffusion inference approach for high-resolution sinogram completion. By explicitly accounting for spatial heterogeneity in signal characteristics, such as spectral sparsity and local complexity, HRSino allocates inference effort adaptively across spatial regions and resolutions, rather than applying uniform high-resolution diffusion steps. This enables global consistency to be captured at coarse scales while refining local details only where necessary. Experimental results show that HRSino reduces peak memory usage by up to 30.81% and inference time by up to 17.58% compared to the state-of-the-art framework, and maintains completion accuracy across datasets and resolutions.

cs.CV↗

arXiv2026

Beyond Fixed Budgets: Characterizing the Inelasticity and Limitations of Tree-of-Thought Reasoning Strategies

Tree of Thought (ToT) search has become a promising direction for improving the reasoning capabilities of large language models, but deploying these methods in practice raises a question that has received little systematic attention: how do different search strategies behave under varying compute budgets, model sizes, and problem difficulties? In this work, we evaluate two representative ToT methods; DPTS, a Monte Carlo tree search based approach, and SSDP, a semantic deduplication based approach, across two mathematical reasoning benchmarks (Math500 and GSM8K), two model scales (Llama-3B and Llama-8B), and four token budgets (3k--10k). Our analysis reveals that the two methods exhibit limitations that pull in opposite directions. DPTS suffers from a cold-start bottleneck at low budgets: it requires sufficient exploration before its value estimates become reliable, making it a poor fit for resource-constrained settings despite strong scaling behavior at higher budgets. SSDP, on the other hand, reaches candidate solutions efficiently but is prone to frontier depletion; its aggressive node merging permanently discards unexplored paths, leaving it unable to improve regardless of how much budget remains. Together, these findings suggest that neither a fixed exploration strategy nor a fixed pruning strategy is sufficient across compute continuum. We argue that effective search for scientific reasoning agents requires strategies that can adapt their behavior based on search progress and available resources.

cs.AI↗

arXiv2026

CoCoDiff: Optimizing Collective Communications for Distributed Diffusion Transformer Inference Under Ulysses Sequence Parallelism

Diffusion Transformers (DiTs) are increasingly adopted in scientific computing, yet growing model sizes and resolutions make distributed multi-GPU inference essential. Ulysses sequence parallelism scales DiT inference but introduces frequent all-to-all collectives that dominate latency. Overlapping these with computation is difficult due to tight data dependencies, large message volumes, and asymmetric interconnect bandwidths. We introduce CoCoDiff, a distributed DiT inference engine exploiting two observations: (1) V requires only linear projection while Q/K need additional normalization and RoPE, creating opportunities to overlap V's communication with Q/K computation; (2) adjacent denoising steps produce similar tensors, yielding temporal redundancy. CoCoDiff introduces three mechanisms: Tile-Aware Parallel All-to-all (TAPA) decomposes collectives into topology-aligned phases; V-First scheduling hides V's communication behind Q/K computation; and V-Major selective communication transmits only active projections on slow interconnects. On the Aurora supercomputer with four DiT models across 1-8 nodes (up to 96 Intel GPU tiles), CoCoDiff achieves an average speedup of 3.6x, peaking at 8.4x.

cs.DC↗

arXiv2026

FCDM: A Physics-Guided Bidirectional Frequency Aware Convolution and Diffusion-Based Model for Sinogram Inpainting

Computed tomography (CT) is widely used in scientific imaging systems such as synchrotron and laboratory-based nano-CT, but acquiring full-view sinograms requires high radiation dose and long scan times. Sparse-view CT reduces this burden but produces incomplete sinograms with structured signal loss, degrading reconstruction quality. Unlike RGB images, sinograms encode globally coupled projections and exhibit directional spectral patterns, making conventional RGB-oriented inpainting methods, including diffusion models, ineffective because they ignore angular dependencies and physical constraints inherent to tomographic data. We propose FCDM, a diffusion-based framework for sinogram restoration that incorporates bidirectional frequency reasoning, angular-aware masking, and physics-guided regularization to preserve global structure and physical plausibility. Experiments on real-world datasets show that FCDM consistently outperforms existing baselines, achieving over 0.93 SSIM and 31 dB PSNR across diverse sparse-view settings.

eess.IV↗

arXiv2025

mLR: Scalable Laminography Reconstruction based on Memoization

ADMM-FFT is an iterative method with high reconstruction accuracy for laminography but suffers from excessive computation time and large memory consumption. We introduce mLR, which employs memoization to replace the time-consuming Fast Fourier Transform (FFT) operations based on an unique observation that similar FFT operations appear in iterations of ADMM-FFT. We introduce a series of techniques to make the application of memoization to ADMM-FFT performance-beneficial and scalable. We also introduce variable offloading to save CPU memory and scale ADMM-FFT across GPUs within and across nodes. Using mLR, we are able to scale ADMM-FFT on an input problem of 2Kx2Kx2K, which is the largest input problem laminography reconstruction has ever worked on with the ADMM-FFT solution on limited memory; mLR brings 52.8% performance improvement on average (up to 65.4%), compared to the original ADMM-FFT.

cs.DC↗

arXiv2025

RADAR-Radio Afterglow Detection and AI-driven Response: A Federated Framework for Gravitational Wave Event Follow-Up

The landmark detection of both gravitational waves (GWs) and electromagnetic (EM) radiation from the binary neutron star merger GW170817 has spurred efforts to streamline the follow-up of GW alerts in current and future observing runs of ground-based GW detectors. Within this context, the radio band of the EM spectrum presents unique challenges. Sensitive radio facilities capable of detecting the faint radio afterglow seen in GW170817, and with sufficient angular resolution, have small fields of view compared to typical GW localization areas. Additionally, theoretical models predict that the radio emission from binary neutron star mergers can evolve over weeks to years, necessitating long-term monitoring to probe the physics of the various post-merger ejecta components. These constraints, combined with limited radio observing resources, make the development of more coordinated follow-up strategies essential -- especially as the next generation of GW detectors promise a dramatic increase in detection rates. Here, we present RADAR, a framework designed to address these challenges by promoting community-driven information sharing, federated data analysis, and system resilience, while integrating AI methods for both GW signal identification and radio data aggregation. We show that it is possible to preserve data rights while sharing models that can help design and/or update follow-up strategies. We demonstrate our approach through a case study of GW170817, and discuss future directions for refinement and broader application.

astro-ph.HE↗

arXiv2025

ZenFlow: Enabling Stall-Free Offloading Training via Asynchronous Updates

Fine-tuning large language models (LLMs) often exceeds GPU memory limits, prompting systems to offload model states to CPU memory. However, existing offloaded training frameworks like ZeRO-Offload treat all parameters equally and update the full model on the CPU, causing severe GPU stalls, where fast, expensive GPUs sit idle waiting for slow CPU updates and limited-bandwidth PCIe transfers. We present ZenFlow, a new offloading framework that prioritizes important parameters and decouples updates between GPU and CPU. ZenFlow performs in-place updates of important gradients on GPU, while asynchronously offloading and accumulating less important ones on CPU, fully overlapping CPU work with GPU computation. To scale across GPUs, ZenFlow introduces a lightweight gradient selection method that exploits a novel spatial and temporal locality property of important gradients, avoiding costly global synchronization. ZenFlow achieves up to 5x end-to-end speedup, 2x lower PCIe traffic, and reduces GPU stalls by over 85 percent, all while preserving accuracy.

cs.DC↗

arXiv2025

Ptychographic Image Reconstruction from Limited Data via Score-Based Diffusion Models with Physics-Guidance

Ptychography is a data-intensive computational imaging technique that achieves high spatial resolution over large fields of view. The technique involves scanning a coherent beam across overlapping regions and recording diffraction patterns. Conventional reconstruction algorithms require substantial overlap, increasing data volume and experimental time, reaching PiB-scale experimental data and weeks to month-long data acquisition times. To address this, we propose a reconstruction method employing a physics-guided score-based diffusion model. Our approach trains a diffusion model on representative object images to learn an object distribution prior. During reconstruction, we modify the reverse diffusion process to enforce data consistency, guiding reverse diffusion toward a physically plausible solution. This method requires a single pretraining phase, allowing it to generalize across varying scan overlap ratios and positions. Our results demonstrate that the proposed method achieves high-fidelity reconstructions with only a 20% overlap, while the widely employed rPIE method requires a 62% overlap to achieve similar accuracy. This represents a significant reduction in data requirements, offering an alternative to conventional techniques.

eess.IV↗

arXiv2024

Integrating Generative and Physics-Based Models for Ptychographic Imaging with Uncertainty Quantification

Ptychography is a scanning coherent diffractive imaging technique that enables imaging nanometer-scale features in extended samples. One main challenge is that widely used iterative image reconstruction methods often require significant amount of overlap between adjacent scan locations, leading to large data volumes and prolonged acquisition times. To address this key limitation, this paper proposes a Bayesian inversion method for ptychography that performs effectively even with less overlap between neighboring scan locations. Furthermore, the proposed method can quantify the inherent uncertainty on the ptychographic object, which is created by the ill-posed nature of the ptychographic inverse problem. At a high level, the proposed method first utilizes a deep generative model to learn the prior distribution of the object and then generates samples from the posterior distribution of the object by using a Markov Chain Monte Carlo algorithm. Our results from simulated ptychography experiments show that the proposed framework can consistently outperform a widely used iterative reconstruction algorithm in cases of reduced overlap. Moreover, the proposed framework can provide uncertainty estimates that closely correlate with the true error, which is not available in practice. The project website is available here.

eess.IV↗

arXiv2024

Deep learning-based spatio-temporal fusion for high-fidelity ultra-high-speed x-ray radiography

Full-field ultra-high-speed (UHS) x-ray imaging experiments have been well established to characterize various processes and phenomena. However, the potential of UHS experiments through the joint acquisition of x-ray videos with distinct configurations has not been fully exploited. In this paper, we investigate the use of a deep learning-based spatio-temporal fusion (STF) framework to fuse two complementary sequences of x-ray images and reconstruct the target image sequence with high spatial resolution, high frame rate, and high fidelity. We applied a transfer learning strategy to train the model and compared the peak signal-to-noise ratio (PSNR), average absolute difference (AAD), and structural similarity (SSIM) of the proposed framework on two independent x-ray datasets with those obtained from a baseline deep learning model, a Bayesian fusion framework, and the bicubic interpolation method. The proposed framework outperformed the other methods with various configurations of the input frame separations and image noise levels. With 3 subsequent images from the low resolution (LR) sequence of a 4-time lower spatial resolution and another 2 images from the high resolution (HR) sequence of a 20-time lower frame rate, the proposed approach achieved an average PSNR of 37.57 dB and 35.15 dB, respectively. When coupled with the appropriate combination of high-speed cameras, the proposed approach will enhance the performance and therefore scientific value of the UHS x-ray imaging experiments.

eess.IV↗

arXiv2024

Steering a Fleet: Adaptation for Large-Scale, Workflow-Based Experiments

Experimental science is increasingly driven by instruments that produce vast volumes of data and thus a need to manage, compute, describe, and index this data. High performance and distributed computing provide the means of addressing the computing needs; however, in practice, the variety of actions required and the distributed set of resources involved, requires sophisticated "flows" defining the steps to be performed on data. As each scan or measurement is performed by an instrument, a new instance of the flow is initiated resulting in a "fleet" of concurrently running flows, with the overall goal to process all the data collected during a potentially long-running experiment. During the course of the experiment, each flow may need to adapt its execution due to changes in the environment, such as computational or storage resource availability, or based on the progress of the fleet as a whole such as completion or discovery of an intermediate result leading to a change in subsequent flow's behavior. We introduce a cloud-based decision engine, Braid, which flows consult during execution to query their run-time environment and coordinate with other flows within their fleet. Braid accepts streams of measurements taken from the run-time environment or from within flow runs which can then be statistically aggregated and compared to other streams to determine a strategy to guide flow execution. For example, queue lengths in execution environments can be used to direct a flow to run computations in one environment or another, or experiment progress as measured by individual flows can be aggregated to determine the progress and subsequent direction of the flows within a fleet. We describe Braid, its interface, implementation and performance characteristics. We further show through examples and experience modifying an existing scientific flow how Braid is used to make adaptable flows.

cs.DC↗

arXiv2023

AI-assisted Automated Workflow for Real-time X-ray Ptychography Data Analysis via Federated Resources

We present an end-to-end automated workflow that uses large-scale remote compute resources and an embedded GPU platform at the edge to enable AI/ML-accelerated real-time analysis of data collected for x-ray ptychography. Ptychography is a lensless method that is being used to image samples through a simultaneous numerical inversion of a large number of diffraction patterns from adjacent overlapping scan positions. This acquisition method can enable nanoscale imaging with x-rays and electrons, but this often requires very large experimental datasets and commensurately high turnaround times, which can limit experimental capabilities such as real-time experimental steering and low-latency monitoring. In this work, we introduce a software system that can automate ptychography data analysis tasks. We accelerate the data analysis pipeline by using a modified version of PtychoNN -- an ML-based approach to solve phase retrieval problem that shows two orders of magnitude speedup compared to traditional iterative methods. Further, our system coordinates and overlaps different data analysis tasks to minimize synchronization overhead between different stages of the workflow. We evaluate our workflow system with real-world experimental workloads from the 26ID beamline at Advanced Photon Source and ThetaGPU cluster at Argonne Leadership Computing Resources.

cs.CV↗

arXiv2022

SOLAR: A Highly Optimized Data Loading Framework for Distributed Training of CNN-based Scientific Surrogates

CNN-based surrogates have become prevalent in scientific applications to replace conventional time-consuming physical approaches. Although these surrogates can yield satisfactory results with significantly lower computation costs over small training datasets, our benchmarking results show that data-loading overhead becomes the major performance bottleneck when training surrogates with large datasets. In practice, surrogates are usually trained with high-resolution scientific data, which can easily reach the terabyte scale. Several state-of-the-art data loaders are proposed to improve the loading throughput in general CNN training; however, they are sub-optimal when applied to the surrogate training. In this work, we propose SOLAR, a surrogate data loader, that can ultimately increase loading throughput during the training. It leverages our three key observations during the benchmarking and contains three novel designs. Specifically, SOLAR first generates a pre-determined shuffled index list and accordingly optimizes the global access order and the buffer eviction scheme to maximize the data reuse and the buffer hit rate. It then proposes a tradeoff between lightweight computational imbalance and heavyweight loading workload imbalance to speed up the overall training. It finally optimizes its data access pattern with HDF5 to achieve a better parallel I/O throughput. Our evaluation with three scientific surrogates and 32 GPUs illustrates that SOLAR can achieve up to 24.4X speedup over PyTorch Data Loader and 3.52X speedup over state-of-the-art data loaders.

cs.DC↗

arXiv2022

Deep learning at the edge enables real-time streaming ptychographic imaging

Coherent microscopy techniques provide an unparalleled multi-scale view of materials across scientific and technological fields, from structural materials to quantum devices, from integrated circuits to biological cells. Driven by the construction of brighter sources and high-rate detectors, coherent X-ray microscopy methods like ptychography are poised to revolutionize nanoscale materials characterization. However, associated significant increases in data and compute needs mean that conventional approaches no longer suffice for recovering sample images in real-time from high-speed coherent imaging experiments. Here, we demonstrate a workflow that leverages artificial intelligence at the edge and high-performance computing to enable real-time inversion on X-ray ptychography data streamed directly from a detector at up to 2 kHz. The proposed AI-enabled workflow eliminates the sampling constraints imposed by traditional ptychography, allowing low dose imaging using orders of magnitude less data than required by traditional methods.

cs.LG↗

arXiv2022

Linking Scientific Instruments and HPC: Patterns, Technologies, Experiences

Powerful detectors at modern experimental facilities routinely collect data at multiple GB/s. Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly discarding some data elements or by directing instruments to relevant areas of experimental space. Such online analyses require methods for configuring and running high-performance distributed computing pipelines--what we call flows--linking instruments, HPC (e.g., for analysis, simulation, AI model training), edge computing (for analysis), data stores, metadata catalogs, and high-speed networks. In this article, we review common patterns associated with such flows and describe methods for instantiating those patterns. We also present experiences with the application of these methods to the processing of data from five different scientific instruments, each of which engages HPC resources for data inversion, machine learning model training, or other purposes. We also discuss implications of these new methods for operators and users of scientific facilities.

cs.DC↗

arXiv2021

High-Performance Ptychographic Reconstruction with Federated Facilities

Beamlines at synchrotron light source facilities are powerful scientific instruments used to image samples and observe phenomena at high spatial and temporal resolutions. Typically, these facilities are equipped only with modest compute resources for the analysis of generated experimental datasets. However, high data rate experiments can easily generate data in volumes that take days (or even weeks) to process on those local resources. To address this challenge, we present a system that unifies leadership computing and experimental facilities by enabling the automated establishment of data analysis pipelines that extend from edge data acquisition systems at synchrotron beamlines to remote computing facilities; under the covers, our system uses Globus Auth authentication to minimize user interaction, funcX to run user-defined functions on supercomputers, and Globus Flows to define and execute workflows. We describe the application of this system to ptychography, an ultra-high-resolution coherent diffraction imaging technique that can produce 100s of gigabytes to terabytes in a single experiment. When deployed on the DGX A100 ThetaGPU cluster at the Argonne Leadership Computing Facility and a microscopy beamline at the Advanced Photon Source, our system performs analysis as an experiment progresses to provide timely feedback.

cs.DC↗

arXiv2021

Joint ptycho-tomography with deep generative priors

Joint ptycho-tomography is a powerful computational imaging framework to recover the refractive properties of a 3D object while relaxing the requirements for probe overlap that is common in conventional phase retrieval. We use an augmented Lagrangian scheme for formulating the constrained optimization problem and employ an alternating direction method of multipliers (ADMM) for the joint solution. ADMM allows the problem to be split into smaller and computationally more efficient subproblems: ptychographic phase retrieval, tomographic reconstruction, and regularization of the solution. We extend our ADMM framework with plug-and-play (PnP) denoisers by replacing the regularization subproblem with a general denoising operator based on machine learning. While the PnP framework enables integrating such learned priors as denoising operators, tuning of the denoiser prior remains challenging. To overcome this challenge, we propose a denoiser parameter to control the effect of the denoiser and to accelerate the solution. In our simulations, we demonstrate that our proposed framework with parameter tuning and learned priors generates high-quality reconstructions under limited and noisy measurement data.

eess.IV↗