Alan Williams

Sean R. Wilkinson, Johan Gustafsson, Finn Bacall et al.

Computational workflows represent major investments of effort and expertise. As first-class, publishable research objects of their own, they are key to sharing methodological know-how for reuse, reproducibility, and transparency. Thus, the application of the FAIR Principles to workflows is inevitable to enable them to be Findable, Accessible, Interoperable, and Reusable. Making workflows FAIR reduces duplication of effort, assists in the reuse of best practice approaches and community-supported standards, and ensures that workflows as digital objects can support reproducible, robust science. FAIR workflows draw from both FAIR data and software principles, and they help ensure and support data FAIRification. The FAIR Principles emphasize the association of persistent identifiers and machine-actionable metadata with workflows. Implementing the Principles requires a framework with appropriate programmatic protocols and an accompanying ecosystem of services, tools, policies, and best practices, as well the buy-in of existing workflow systems. The European EOSC-Life Workflow Collaboratory is an example of such a digital infrastructure for the Biosciences. It includes a metadata standards framework for describing workflows that is managed and used by dedicated new FAIR workflow services and programmatic APIs for interoperability and metadata access. It includes the WorkflowHub registry and LifeMonitor workflow testing service, and it incorporates existing workflow systems and packaging solutions. Here, we introduce the FAIR Principles for workflows and connect FAIR workflows with the FAIR ecosystems they inhabit with the EOSC-Life Collaboratory as a concrete example. We also introduce other community efforts that are easing the ways that workflows are shared and reused by others, and we discuss how the variations in different workflow settings impact their FAIR perspectives.

Xiaomin Lin, Vivek Mange, Arjun Suresh et al.

Oysters are a vital keystone species in coastal ecosystems, providing significant economic, environmental, and cultural benefits. As the importance of oysters grows, so does the relevance of autonomous systems for their detection and monitoring. However, current monitoring strategies often rely on destructive methods. While manual identification of oysters from video footage is non-destructive, it is time-consuming, requires expert input, and is further complicated by the challenges of the underwater environment. To address these challenges, we propose a novel pipeline using stable diffusion to augment a collected real dataset with realistic synthetic data. This method enhances the dataset used to train a YOLOv10-based vision model. The model is then deployed and tested on an edge platform in underwater robotics, achieving a state-of-the-art 0.657 mAP@50 for oyster detection on the Aqua2 platform.

Mahindra Rautela, Alan Williams, Alexander Scheinker

Charged particle dynamics under the influence of electromagnetic fields is a challenging spatiotemporal problem. Many high performance physics-based simulators for predicting behavior in a charged particle beam are computationally expensive, limiting their utility for solving inverse problems online. The problem of estimating upstream six-dimensional phase space given downstream measurements of charged particles in an accelerator is an inverse problem of growing importance. This paper introduces a reverse Latent Evolution Model (rLEM) designed for temporal inversion of forward beam dynamics. In this two-step self-supervised deep learning framework, we utilize a Conditional Variational Autoencoder (CVAE) to project 6D phase space projections of a charged particle beam into a lower-dimensional latent distribution. Subsequently, we autoregressively learn the inverse temporal dynamics in the latent space using a Long Short-Term Memory (LSTM) network. The coupled CVAE-LSTM framework can predict 6D phase space projections across all upstream accelerating sections based on single or multiple downstream phase space measurements as inputs. The proposed model also captures the aleatoric uncertainty of the high-dimensional input data within the latent space. This uncertainty, which reflects potential uncertain measurements at a given module, is propagated through the LSTM to estimate uncertainty bounds for all upstream predictions, demonstrating the robustness of the LSTM against in-distribution variations in the input data.

Yisheng Zhang, Michael Xu, Alan Williams et al.

Accurate seabed mapping is essential for habitat monitoring and infrastructure inspection. In turbid, shallow coastal waters, such as shellfish aquaculture farms, the effectiveness of traditional optical methods is limited. Autonomous surface vehicles (ASVs) equipped with forward-looking sonar (FLS) offer a promising alternative. However, existing sonar-based systems face challenges in achieving fine resolution mapping over long trajectories due to low-resolution positioning measurements and accumulated drift over long trajectories. In this paper, we present a drift-resilient seabed mapping framework that integrates local FLS frame alignment using the Fourier-Mellin transform (FMT) with global trajectory optimization based on an extended Kalman filter (EKF) that fuses global positioning system (GPS), inertial measurement unit (IMU), and compass data. A variance-based image blending strategy is used to further reduce visual artifacts in overlapping regions. Field trials on a structured oyster farm site show that our framework helps reduce drift in RMSE by 9.5% relative to the FMT-only baseline. This framework also enables sub-meter reconstruction accuracy and preservation of high-resolution textures needed for oyster inventory estimation within the mapped areas.

Brendan Campbell, Alan Williams, Kleio Baxevani et al.

Oysters are ecologically and commercially important species that require frequent monitoring to track population demographics (e.g. abundance, growth, mortality). Current methods of monitoring oyster reefs often require destructive sampling methods and extensive manual effort. Therefore, they are suboptimal for small-scale or sensitive environments. A recent alternative, the ODYSSEE model, was developed to use deep learning techniques to identify live oysters using video or images taken in the field of oyster reefs to assess abundance. The validity of this model in identifying live oysters on a reef was compared to expert and non-expert annotators. In addition, we identified potential sources of prediction error. Although the model can make inferences significantly faster than expert and non-expert annotators (39.6 s, $2.34 \pm 0.61$ h, $4.50 \pm 1.46$ h, respectively), the model overpredicted the number of live oysters, achieving lower accuracy (63\%) in identifying live oysters compared to experts (74\%) and non-experts (75\%) alike. Image quality was an important factor in determining the accuracy of the model and the annotators. Better quality images improved human accuracy and worsened model accuracy. Although ODYSSEE was not sufficiently accurate, we anticipate that future training on higher-quality images, utilizing additional live imagery, and incorporating additional annotation training classes will greatly improve the model's predictive power based on the results of this analysis. Future research should address methods that improve the detection of living vs. dead oysters.

Shaifalee Saxena, Alan Williams, Rafael Fierro et al.

In this paper, we study the use of robust model independent bounded extremum seeking (ES) feedback control to improve the robustness of deep reinforcement learning (DRL) controllers for a class of nonlinear time-varying systems. DRL has the potential to learn from large datasets to quickly control or optimize the outputs of many-parameter systems, but its performance degrades catastrophically when the system model changes rapidly over time. Bounded ES can handle time-varying systems with unknown control directions, but its convergence speed slows down as the number of tuned parameters increases and, like all local adaptive methods, it can get stuck in local minima. We demonstrate that together, DRL and bounded ES result in a hybrid controller whose performance exceeds the sum of its parts with DRL taking advantage of historical data to learn how to quickly control a many-parameter system to a desired setpoint while bounded ES ensures its robustness to time variations. We present a numerical study of a general time-varying system and a combined ES-DRL controller for automatic tuning of the Low Energy Beam Transport section at the Los Alamos Neutron Science Center linear particle accelerator.

Alexander Scheinker, Alan Williams

Beam loss (BLM) and beam current monitors (BCM) are ubiquitous at particle accelerator around the world. These simple devices provide non-invasive high level beam measurements, but give no insight into the detailed 6D (x,y,z,px,py,pz) beam phase space distributions or dynamics. We show that generative conditional latent diffusion models can learn intricate patterns to map waveforms of tens of BLMs or BCMs along an accelerator to detailed 2D projections of a charged particle beam's 6D phase space density. This transformational method can be used at any particle accelerator to transform simple non-invasive devices into detailed beam phase space diagnostics. We demonstrate this concept via multi-particle simulations of the high intensity beam in the kilometer-long LANSCE linear proton accelerator.

Mahindra Rautela, Alan Williams, Alexander Scheinker

Complex dynamical systems, such as particle accelerators, often require complicated and time-consuming tuning procedures for optimal performance. It may also be required that these procedures estimate the optimal system parameters, which govern the dynamics of a spatiotemporal beam -- this can be a high-dimensional optimization problem. To address this, we propose a Classifier-pruned Bayesian Optimization-based Latent space Tuner (CBOL-Tuner), a framework for efficient exploration within a temporally-structured latent space. The CBOL-Tuner integrates a convolutional variational autoencoder (CVAE) for latent space representation, a long short-term memory (LSTM) network for temporal dynamics, a dense neural network (DNN) for parameter estimation, and a classifier-pruned Bayesian optimizer (C-BO) to adaptively search and filter the latent space for optimal solutions. CBOL-Tuner demonstrates superior performance in identifying multiple optimal settings and outperforms alternative global optimization methods.

Mahindra Rautela, Alan Williams, Alexander Scheinker

Particle accelerators are complex systems that focus, guide, and accelerate intense charged particle beams to high energy. Beam diagnostics present a challenging problem due to limited non-destructive measurements, computationally demanding simulations, and inherent uncertainties in the system. We propose a two-step unsupervised deep learning framework named as Conditional Latent Autoregressive Recurrent Model (CLARM) for learning the spatiotemporal dynamics of charged particles in accelerators. CLARM consists of a Conditional Variational Autoencoder (CVAE) transforming six-dimensional phase space into a lower-dimensional latent distribution and a Long Short-Term Memory (LSTM) network capturing temporal dynamics in an autoregressive manner. The CLARM can generate projections at various accelerator modules by sampling and decoding the latent space representation. The model also forecasts future states (downstream locations) of charged particles from past states (upstream locations). The results demonstrate that the generative and forecasting ability of the proposed approach is promising when tested against a variety of evaluation metrics.