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Data and code for reproducing the deep learning framerwork described in CatPred: a comprehensive framework for deep learning in vitro enzyme kinetic parameters
With the rapid digitization of the world, an increasing number of real-world applications are turning to nonEuclidean data, modeled as graphs. Due to their intrinsic high complexity and irregularity, learning from graph data demands tremendous computational power. Recently, CMOS-compatible Ising machines, i.e., dynamic systems composed of CMOS components, have emerged as a new approach that harnesses the inherent power of natural annealing within dynamic systems to efficiently resolve binary optimization problems and have been adopted for traditional graph computation, such as max-cut. However, when performing complex Graph Learning (GL) tasks, Ising machines face significant hurdles: (i) they are inherently binary and thus ill-suited for real-valued problems; (ii) their expensive all-to-all coupling network that guarantees effective natural annealing poses daunting scalability concerns. To address these challenges, this paper proposes a nature-powered graph learning framework dubbed DS-GL, which is the first effort to transform the process of solving graph learning problems into the natural annealing process within a parameterized dynamic system embodied as a CMOS chip. To tackle the two major hurdles, DS-GL first augments the Ising machine architecture to modify the self-reaction term of its Hamiltonian function from linear to quadratic, effectively serving as an energy regulator. This adjustment maintains the system’s original physical interpretation while enabling it to process continuous, real-valued data. Second, to address the scaling issue, DS-GL further upgrades the real-valued dense Ising machine by decomposing it into a mesh-based multi-PE dynamic system that supports efficient distributed spatial-temporal co-annealing across different PEs through sparse interconnects. By exploiting the inherent sparsity and component structures in real-world graphs, DS-GL is able to map complex graph learning tasks onto the scalable dynamic system while maintaining high accuracy. Evaluations with three diverse GL applications across six real-world datasets, including traffic flow and COVID-19 prediction, show that DS-GL can deliver from 102× to 106× speedups and 500× energy reduction over Graph Neural Networks on GPUs, with 5% - 20% accuracy enhancement.
Metal halide perovskite (MHP) solar cells exhibit a metastable response to bias governed by coupled ionic–electronic processes, complicating the conventional reciprocity relation between luminescence intensity and device open-circuit voltage (V oc ). This limits the use of luminescence as a diagnostic for device screening or accelerated stress testing, motivating new approaches that can interpret photoluminescence (PL) signals under nonequilibrium conditions. From the artificial intelligence perspective, we develop an explainable deep learning framework that integrates convolutional neural networks (CNN), long short-term memory (LSTM) layers, and an attention mechanism to learn spatiotemporal features from operando photoluminescence PL image sequences. The model achieves a mean absolute error of ±0.027 V in predicting open-circuit voltage transients and reduces extreme-tail errors by up to 78% compared to physics-based reciprocity calculations. Gradient-weighted Class Activation Mapping (Grad-CAM) provides interpretability by highlighting physically meaningful regions such as electrode edges and emergent defect features. From the engineering application perspective, this framework enables accurate, contactless prediction of device V oc and identification of degradation-relevant features during accelerated aging of perovskite solar cells. This approach demonstrates how explainable AI can enhance operando diagnostics and reliability analysis in photovoltaic devices under nonequilibrium conditions.
Electrochemistry workflows utilize various instruments and computing systems to execute workflows consisting of electrocatalyst synthesis, testing and evaluation tasks. The heterogeneity of the software and hardware of these ecosystems makes it challenging to orchestrate a complete workflow from production to characterization by automating its tasks. We propose an autonomous electrochemistry computing platform for a multi-site ecosystem that provides the services for remote experiment steering, real-time measurement transfer, and AI/ML-driven analytics. We describe the integration of a mobile robot and synthesis workstation into the ecosystem by developing custom hub-networks and software modules to support remote operations over the ecosystem’s wireless and wired networks. We describe a workflow task for generating I-V voltammetry measurements using a potentiostat, and a machine learning framework to ensure their normality by detecting abnormal conditions such as disconnected electrodes. We study a number of machine learning methods for the underlying detection problem, including smooth, non-smooth, structural and statistical methods, and their fusers. We present experimental results to illustrate the effectiveness of this platform, and also validate the proposed ML method by deriving its rigorous generalization equations.
In silico methods for predicting the effects of multi-gene perturbations hold great promise for advancing functional genomics, computational drug discovery, and disease modeling. However, the development of these predictive algorithms for mammalian systems has been hampered by limited datasets and high experimental costs. In this study, we present a Bayesian active learning framework designed to discover pairwise host gene knockdowns that effectively inhibit viral proliferation in an in vitro HIV-1 infection model. Our method leverages a biological knowledge graph as side information and employs a computationally efficient batch diversification approach. We evaluated this framework using a dataset of viral load measurements obtained from multi-day dual-gene depletion experiments, encompassing all possible pairwise knockdowns of over 350 host genes associated with HIV infection. We demonstrate that our framework rapidly identifies the most effective gene knockdown pairs for reducing viral load. Furthermore, we show that incorporating side information enhances performance during the early stages of active learning (low data regime), while our batch diversification strategy significantly boosts performance in later stages (high data regime). This framework is general and can be adapted to explore gene interactions in other contexts, such as synthetic lethality prediction and mapping epistatic effects across quantitative trait loci.
High-resolution historical wind data was developed for the entirety of South America using the innovative Super-Resolution for Renewable Resource Data (sup3r) machine learning framework. The publicly available Sup3rWind South America dataset represents a significant advancement in wind resource data generation, leveraging generative machine learning conditioned on near-surface observations from the Meteorological Assimilation Data Ingest System (MADIS) to efficiently and accurately downscale coarse reanalysis data from the European Centre for Medium-Range Weather Forecasts (ERA5). This approach produces fine-scale, spatially and temporally coherent wind and meteorological fields hundreds of times more computationally efficient than traditional numerical weather modeling methods, enabling access to high-fidelity wind information across both continental and offshore regions. Sup3rWind South America builds on the earlier Sup3rWind Ukraine dataset through improvements in model architecture and outputs conditioned on near-surface observation inputs. As with the Ukraine data release, this dataset includes wind speed, wind direction, temperature, relative humidity, and pressure at a horizontal resolution of ~2 km, representing a 15x spatial enhancement relative to the 31 km ERA5 grid. Wind speed and direction are provided at 5-minute resolution, a 12x temporal refinement compared to the hourly ERA5 data, while temperature, relative humidity, and pressure remain at hourly resolution. The data covers all years from 2005 to 2024. Before downscaling, ERA5 inputs were bias-corrected using long-term monthly means and a limited number of quality-controlled observations to align large-scale statistics with regional conditions. The resulting dataset is the first publicly available high-resolution timeseries wind record that provides full spatial coverage of South America. Model validation demonstrates strong agreement with observations across several statistical metrics, consistent with other state-of-the-art high-resolution wind resource datasets. The potential applications of Sup3rWind South America span renewable energy resource assessment, energy system modeling, and grid resilience analysis. The 20-year record and high spatial and temporal resolution support accurate estimation of long-term energy yield and the economic feasibility of potential wind development sites. Continuous coverage across both continental and offshore regions enables comprehensive site prospecting within exclusive economic zones. The 2 km, 5-minute resolution data provide the spatial and temporal variability required for power system simulation, operational planning, and regional risk assessments.
Accurately predicting stream temperature in ungauged basins remains a critical challenge for water resource management, thermoelectric power plant cooling, and ecosystem conservation. Large-sample machine learning models trained on hundreds of well-monitored river basins have shown remarkable performance; however, such models have yet to be developed solely using forcing data that can be readily extracted to simulate stream temperatures anywhere in the contiguous United States (CONUS). In this study, we present a scalable, large-sample deep learning framework using Long Short-Term Memory (LSTM) networks to simulate daily stream temperatures in ungauged basins across the CONUS. The framework leverages both modeled reanalysis of meteorological and streamflow inputs as well as static attributes available for all 2.7 million CONUS river reaches in the National Hydrography Dataset Plus (NHDPlusV2). By generating dynamical inputs from predefined thermally relevant upstream contributing areas, rather than the entire upstream basin, the model also offers improvements in very large basins where full-basin averaging can dilute the most important influences on stream temperature. Evaluated across 300 basins, the model achieves a median Mean Absolute Error (MAE) of 1.1 °C and a Nash-Sutcliffe Efficiency (NSE) of 0.95 on temporally and spatially distinct test folds—comparable to models trained exclusively using meteorological and streamflow observational data. The flexible, high-performing framework generalizes to any unmonitored river reach without significant regulation or unnatural thermal input immediately upstream, substantially expanding predictive capabilities in data-scarce regions.
Ultrahigh field (UHF) Magnetic Resonance Imaging (MRI) provides a higher signal-to-noise ratio and, thereby, higher spatial resolution. However, UHF MRI introduces challenges such as transmit radiofrequency (RF) field (B+1) inhomogeneities, leading to uneven flip angles and image intensity anomalies. These issues can significantly degrade imaging quality and its medical applications. This study addresses B+1 field homogeneity through a novel deep learning-based strategy. Traditional methods like Magnitude Least Squares (MLS) optimization have been effective but are time-consuming and dependent on the patient’s presence. Recent machine learning approaches, such as RF Shim Prediction by Iteratively Projected Ridge Regression and deep learning frameworks, have shown promise but face limitations like extensive training times and oversimplified architectures. We propose a two-step deep learning strategy. First, we obtain the desired reference RF shimming weights from multi-channel B+1 fields using random-initialized Adaptive Moment Estimation. Then, we employ Residual Networks (ResNets) to train a model that maps B+1 fields to target RF shimming outputs. Our approach does not rely on pre-calculated reference optimizations for the testing process and efficiently learns residual functions. Comparative studies with traditional MLS optimization demonstrate our method’s advantages in terms of speed and accuracy. The proposed strategy achieves a faster and more efficient RF shimming design, significantly improving imaging quality at UHF. This advancement holds potential for broader applications in medical imaging and diagnostics.
Observations of atmospheric 3D winds are critical for improving short-range and long-range forecasting. Such advancement in forecasting directly applies to research in a number of areas including convective processes, wildfire plumes and tornado prediction. Atmospheric Motion Vectors (AMVs) provide a passively sensed approach to quantifying horizontal motion and cloud heights, which are typically sourced from geostationary sensors due to the availability of high frequency observations. Recent work has shown that estimating AMVs by tracking individual pixels with dense optical flow is a promising new direction. In this work, we compare state-of-the-art convolutional neural networks for optical flow in a physics-guided deep learning framework for predicting AMVs. The approach is semi-supervised and uses physically informed wind vectors from high-resolution numerical simulations for supervised learning followed by fine-tuning though warping and reconstruction of full-disk geostationary images (GOES-16). In the vertical direction, we use labels from the CALIPSO low-earth orbit satellite to predict cloud height from 16-band geostationary images with a neural network. We present results for both tasks on held-out time periods and secondary datasets.
In the context of managing distributed energy resources (DERs) within distribution networks (DNs), this work focuses on the task of developing local controllers. We propose an unsupervised learning framework to train functions that can closely approximate optimal power flow (OPF) solutions. The primary aim is to establish specific conditions under which these learned functions can collectively guide the network towards desired configurations asymptotically, leveraging an incremental control approach. The flexibility of the proposed methodology allows to integrate fairness-driven components into the cost function associated with the OPF problem. This addition seeks to mitigate power curtailment disparities among DERs, thereby promoting equitable power injections across the network. To demonstrate the effectiveness of the proposed approach, power flow simulations are conducted using the IEEE 37-bus feeder. The findings not only showcase the guaranteed system stability but also underscore its improved overall performance.
In this work we explore the capability of physics-informed neural networks (PINNs) to discover multiple solutions. Many real-world phenomena governed by nonlinear differential equations (DEs), such as fluid flow, exhibit multiple solutions under the same conditions, yet capturing this solution multiplicity remains a significant challenge. A key difficulty lies in providing appropriate initial conditions or guesses, as widely used time-marching schemes and Newton’s method are highly sensitive to these choices when solving complex computational problems. While machine learning models, particularly PINNs, have shown promise in solving DEs, their ability to capture multiple solutions remains underexplored. In this work, we propose a simple and practical approach using PINNs to learn and discover multiple solutions. We first demonstrate that PINNs, when combined with random initialization and deep ensemble method—originally developed for uncertainty quantification—can effectively uncover multiple solutions to nonlinear ordinary and partial DEs. Although training large ensembles of PINNs may appear computationally demanding, this can be done efficiently using vectorization techniques supported by modern deep learning frameworks, allowing many networks to be trained simultaneously. Our approach highlights the critical role of initialization in shaping solution diversity, addressing an often-overlooked aspect of machine learning for scientific computing. Furthermore, we propose utilizing PINN-generated solutions as initial conditions or initial guesses for conventional numerical solvers to enhance accuracy and efficiency in capturing multiple solutions. Extensive numerical experiments, including the Allen–Cahn equation and cavity flow, where our approach successfully identifies both stable and unstable solutions, validate the effectiveness of our method. These findings establish a general and efficient framework for addressing solution multiplicity in nonlinear DEs.
High Entropy Alloys (HEAs) have drawn great interest due to their exceptional properties compared to conventional materials. The configuration of HEA system is considered a key to their superior properties, but exhausting all possible configurations of atom coordinates and species to find the ground energy state is extremely challenging. In this work, we proposed a quantum annealing-assisted lattice optimization (QALO) algorithm, which is an active learning framework that integrates the Field-aware Factorization Machine (FFM) as the surrogate model for lattice energy prediction, Quantum Annealing (QA) as an optimizer and Machine Learning Potential (MLP) for ground truth energy calculation. By applying our algorithm to the NbMoTaW alloy, we reproduced the Nb depletion and W enrichment observed in bulk HEA. We found our optimized HEAs to have superior mechanical properties compared to the randomly generated alloy configurations. Our algorithm highlights the potential of quantum computing in materials design and discovery, laying a foundation for further exploring and optimizing structure-property relationships.
Operator learning for time-dependent partial differential equations (PDEs) has seen rapid progress in recent years, enabling efficient approximation of complex spatiotemporal dynamics. However, most existing methods rely on fixed time step sizes during rollout, which limits their ability to adapt to varying temporal complexity and often leads to error accumulation. In this work, we propose the Time-Adaptive Transformer with Neural Taylor Expansion (TANTE), a novel operator-learning framework that produces continuous-time predictions with adaptive step sizes. TANTE predicts future states by performing a Taylor expansion at the current state, where neural networks learn both the higher-order temporal derivatives and the local radius of convergence. This allows the model to dynamically adjust its rollout based on the local behavior of the solution, thereby reducing cumulative error and improving computational efficiency. We demonstrate the effectiveness of TANTE across a wide range of PDE benchmarks, achieving superior accuracy and adaptability compared to fixed-step baselines, delivering accuracy gains of 60-80 % and speed-ups of 30-40 % at inference time.
Abstract Expressing plant metabolic pathways in microbial platforms is an efficient, cost‐effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour‐intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost‐effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data‐driven machine learning framework designed to extract ‘yeastizing’ rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design‐build‐test cycle.
Yeasts in the subphylum Saccharomycotina are found across the globe in disparate ecosystems. A major aim of yeast research is to understand the diversity and evolution of ecological traits, such as carbon metabolic breadth, insect association, and cactophily. This includes studying aspects of ecological traits like genetic architecture or association with other phenotypic traits. Genomic resources in the Saccharomycotina have grown rapidly. Ecological data, however, are still limited for many species, especially those only known from species descriptions where usually only a limited number of strains are studied. Moreover, ecological information is recorded in natural language format limiting high throughput computational analysis. To address these limitations, we developed an ontological framework for the analysis of yeast ecology. A total of 1,088 yeast strains were added to the Ontology of Yeast Environments (OYE) and analyzed in a machine-learning framework to connect genotype to ecology. This framework is flexible and can be extended to additional isolates, species, or environmental sequencing data. Widespread adoption of OYE would greatly aid the study of macroecology in the Saccharomycotina subphylum.
Atmospheric 3D winds in the horizontal and vertical directions are critical for improving short-range and long-range forecasting. Such advancement in forecasting directly applies to research in a number of areas including convective processes, wildfire plumes and tornado prediction. Atmospheric Motion Vectors (AMVs) provide a passively sensed approach to quantifying horizontal motion and cloud heights, which are typically sourced from geostationary sensors due to the availability of high frequency observations. Recent work has shown that estimating AMVs by tracking individual pixels with dense optical flow is a promising new direction. In this work, we use a state-of-the-art convolutional neural network for optical flow (FlowNetS) in a physics-guided deep learning framework for predicting AMVs in the horizontal direction. The approach is semi-supervised and uses physically informed wind vectors from high-resolution numerical simulations (DYAMOND) for supervised learning followed by fine-tuning though warping and reconstruction of full-disk geostationary images (GOES-16). In the vertical direction, we use labels from the CALIPSO low-earth orbit satellite to predict cloud height from 16-band geostationary images with a neural network. We present results for both tasks on held-out time periods and secondary datasets.
Kinases are a family of proteins that function as molecular switches, regulating several essential cellular activities such as cell proliferation. Dysfunctional kinases are implicated in several types of cancers and hence they are actively pursued as drug targets. Given the vast number of complex kinase structures that are available in the protein data bank (PDB), there is a necessity to develop methodologies that can identify structurally important moieties of the kinases in an automated fashion, for such techniques can be instrumental in identifying novel drug targets. In this work, we develop a graph neural network (GNN) based deep learning framework for classifying the functionally active and inactive states of a large set of eukaryotic protein kinases, making use of their 3D structure from the PDB. We show that GNN based machine learning models can classify protein states with an accuracy greater than 97%. We further use the GNN models to automatically identify regions of the kinases that are important for its function. For this purpose, Gradient-weighted Class Activation Mapping (Grad-CAM) was implemented on the protein graphs. Remarkably, Grad-CAM consistently identifies the highly conserved DFG motif as the most important part of the protein across the entire kinome, without any prior input. Other regions of the hydrophobic core such as the HRD motif were also identified by the interpretable GNN framework, consistent with the literature. We discuss the significance of each of these regions in detail.