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At least 19 records

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.

59 BASIC BIOLOGICAL SCIENCES↗

UFNet: Joint U-Net and Fully Connected Neural Network to Bias Correct Precipitation Predictions from

Paper information. Shuang Yu, Indrasis Chakraborty, Gemma J. Anderson, Donald D. Lucas, Yannic Lops, and Daniel Galea. UFNet: Joint U-Net and fully connected neural network to bias correct precipitation predictions from climate models. Artificial Intelligence for the Earth Systems, 2024. Overview. This work develops the UFNet methodology to correct E3SM historical precipitation projection bias. The UFNet deep learning framework consists of a two-part architecture: a U-Net convolutional network to capture the spatiotemporal distribution of precipitation and a fully connected network to capture the distribution of higher-order statistics. The joint network, termed UFNet, can simultaneously improve the spatial structure of the modeled precipitation and capture the distribution of extreme precipitation values. Below we provide guidance for applying UFNet to correct the Energy Exascale Earth System Model (E3SM; Golaz et al. 2019) daily precipitation projection over the contiguous United States (CONUS). Getting started 1. Obtain the historical climate simulation and observation data. The E3SM historical simulation data are available through https://aims2.llnl.gov/search/cmip6/. The CPC unified gauge-based analysis of daily precipitation can be found through https://psl.noaa.gov/data/gridded/data.cpc.globalprecip.html. The ECMWF atmospheric reanalysis of the 20th century (ERA-20C) data are available through https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era-20c. The spatial resolution of E3SM and observed datasets are both regridded to a common 1° resolution grid using conservative interpolation. The regridded E3SM, CPC and ERA-20C with 1° resolution can be found throught ./data/. 2. Train the fully connected network (DNN) Python train_dnn.py 3. Train the UFNet Python train_ufnet.py 4. Evaluation and compared with the baseline Python evaluation.py

Lucas, DonaldD↗

TANTE: Time-adaptive operator learning via neural Taylor expansion

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.

97 MATHEMATICS AND COMPUTING↗

Nanotubes Growth by Self-Assembly of DNA Strands at Room Temperature

Artificial biomolecular nanotubes are a promising approach to building materials mimicking the capacity of the cellular cytoskeleton to grow and self-organize dynamically. Nucleic acid nanotechnology has demonstrated a variety of self-assembling nanotubes with programmable, robust features and morphological similarities to actual cytoskeleton components. However, their production typically requires thermal annealing, which not only poses a general constraint on their potential applications but is also incompatible with physiological conditions. Here, we demonstrate that DNA nanotubes can self-assemble from a simple mixture of five short DNA strands at constant room temperature, growing for extended periods of time in bulk conditions as well as under confinement. Assembly is achieved using a monovalent salt buffer, which ensures a faithful nanoscale arrangement and avoids nanotube aggregation. We observe the formation of individual nanotubes up to 20 days with a diameter of 22 ± 4 nm and length of several tens of micrometers. We finally encapsulate the strands in microsized compartments, such as water-in-oil microdroplets and giant unilamellar vesicles serving as simple cell models. Notably, nanotubes not only isothermally self-assemble directly inside the microcompartments but also self-organize into dynamic higher-order structures resembling rings and dynamic networks. Our study provides an advantageous method for in situ assembly of programmable biomolecular scaffolds and materials using synthetic DNA strands without requirements of thermal treatment.

Chemistry↗

Improving ADAM through an implicit-explicit (IMEX) time-stepping approach

The ADAM optimizer, often used in machine learning for neural network training, corresponds to an underlying ordinary differential equation (ODE) in the limit of very small learning rates. Here, this work shows that the classical ADAM algorithm is a first-order implicit-explicit (IMEX) Euler discretization of the underlying ODE. Employing the time discretization point of view, we propose new extensions of the ADAM scheme obtained by using higher-order IMEX methods to solve the ODE. Based on this approach, we derive a new optimization algorithm for neural network training that performs better than classical ADAM on several regression and classification problems.

97 MATHEMATICS AND COMPUTING↗

Evidential Deep Learning: Enhancing Predictive Uncertainty Estimation for Earth System Science Applications

Abstract Robust quantification of predictive uncertainty is a critical addition needed for machine learning applied to weather and climate problems to improve the understanding of what is driving prediction sensitivity. Ensembles of machine learning models provide predictive uncertainty estimates in a conceptually simple way but require multiple models for training and prediction, increasing computational cost and latency. Parametric deep learning can estimate uncertainty with one model by predicting the parameters of a probability distribution but does not account for epistemic uncertainty. Evidential deep learning, a technique that extends parametric deep learning to higher-order distributions, can account for both aleatoric and epistemic uncertainties with one model. This study compares the uncertainty derived from evidential neural networks to that obtained from ensembles. Through applications of the classification of winter precipitation type and regression of surface-layer fluxes, we show evidential deep learning models attaining predictive accuracy rivaling standard methods while robustly quantifying both sources of uncertainty. We evaluate the uncertainty in terms of how well the predictions are calibrated and how well the uncertainty correlates with prediction error. Analyses of uncertainty in the context of the inputs reveal sensitivities to underlying meteorological processes, facilitating interpretation of the models. The conceptual simplicity, interpretability, and computational efficiency of evidential neural networks make them highly extensible, offering a promising approach for reliable and practical uncertainty quantification in Earth system science modeling. To encourage broader adoption of evidential deep learning, we have developed a new Python package, Machine Integration and Learning for Earth Systems (MILES) group Generalized Uncertainty for Earth System Science (GUESS) (MILES-GUESS) ( https://github.com/ai2es/miles-guess ), that enables users to train and evaluate both evidential and ensemble deep learning. Significance Statement This study demonstrates a new technique, evidential deep learning, for robust and computationally efficient uncertainty quantification in modeling the Earth system. The method integrates probabilistic principles into deep neural networks, enabling the estimation of both aleatoric uncertainty from noisy data and epistemic uncertainty from model limitations using a single model. Our analyses reveal how decomposing these uncertainties provides valuable insights into reliability, accuracy, and model shortcomings. We show that the approach can rival standard methods in classification and regression tasks within atmospheric science while offering practical advantages such as computational efficiency. With further advances, evidential networks have the potential to enhance risk assessment and decision-making across meteorology by improving uncertainty quantification, a longstanding challenge. This work establishes a strong foundation and motivation for the broader adoption of evidential learning, where properly quantifying uncertainties is critical yet lacking.

Schreck, John S.↗

Direct observation of key aluminum hydroxide prenucleation oligomers for gibbsite nucleation and crystallization in sodium aluminate solution by liquid ToF-SIMS

The mechanism of gibbsite (aluminum hydroxide) crystallization from highly alkaline solutions such as Bayer liquors remains poorly understood, where aluminum (Al) transforms from largely tetrahedrally coordinated aluminate monomers in sodium aluminate solutions into a network of octahedra in gibbsite crystals. A variety of traditional analytical approaches applied to this system do not readily reveal the presence of higher-order oligomeric intermediates. To overcome this limitation, we employed in-situ liquid Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) to examine the Al species present in concentrated sodium aluminate solutions favoring crystallization of gibbsite or sodium aluminate. A complex mixture of Al oligomers was found. By comparing the change in the relative concentration of Al oligomers with +1 and -1 charge, we were able to identify three major Al oligomer candidates, iso-tetramers, iso-pentamers, and cyclic-hexamers, for the nucleation and crystallization of gibbsite. The concentrations of iso-tetramers and iso-pentamers significantly surpass those of cyclic-hexamers. Time-dependent in-situ Raman spectroscopy analysis indicated that the appearance of gibbsite coincided with the peak concentration of these oligomers. The Density-functional theory (DFT) calculation suggests that the formation of iso-oligomers is more favorable than that of cyclic-hexamers. The combined results suggest that iso-tetramers and iso-pentamers play the most substantial role in the nucleation and growth of gibbsite in the sodium aluminate solutions. Our findings also suggest that the oligomers that promote gibbsite crystallization are more stable in dilute sodium aluminate solutions, making these solutions particularly suitable for efficient gibbsite crystallization. In conclusion, our study fills a major knowledge gap in understanding Al speciation that leads to the nucleation and crystallization of gibbsite in concentrated sodium aluminate solutions.

Bayer liquor↗

Gradient flow based phase-field modeling using separable neural networks

Allen–Cahn equation is a reaction–diffusion equation and is widely used for modeling phase separation. Machine learning methods for solving the Allen–Cahn equation in its strong form suffer from inaccuracies in collocation techniques, errors in computing higher-order spatial derivatives, and the large system size required by the space–time approach. To overcome these challenges, we propose solving the gradient flow of the Ginzburg–Landau free energy functional, which is equivalent to the Allen–Cahn equation, thereby avoiding the second-order spatial derivatives associated with the Allen–Cahn equation. A minimizing movement scheme is employed to solve the gradient flow problem, eliminating the complexities of a space–time approach. We utilize a separable neural network that efficiently represents the phase field through low-rank tensor decomposition. As we use the minimizing movement scheme to numerically solve the gradient flow problem, we thus, refer to the proposed method as the Separable Deep Minimizing Movement (SDMM) method. The evaluation of the functional in the minimizing movement scheme using the Gauss quadrature technique bypasses the inaccuracies associated with collocation techniques traditionally used to solve partial differential equations. A hyperbolic tangent transformation is introduced on the phase field prior to the evaluation of the functional to ensure that it remains strictly bounded within the values of the two phases. For this transformation, theoretical guarantee for energy stability of the minimizing movement scheme is established. Our results suggest that this transformation helps to improve the accuracy and efficiency significantly. The proposed method resolves the challenges faced by state-of-the-art machine learning techniques, outperforming them in both accuracy and efficiency. It is also the first machine learning method to achieve an order of magnitude speed improvement over the finite element method. In addition to its formulation and computational implementation, several case studies illustrate the applicability of the proposed method.

42 ENGINEERING↗

Ginsparg-Wilson Hamiltonians with Improved Chiral Symmetry

We construct a family of Ginsparg-Wilson Hamiltonians with improved chiral properties, starting from a construction of Creutz-Horvath-Neuberger that provides a doubler-free Hamiltonian lattice regularization for Dirac fermions in even spacetime dimensions. We use a higher-order generalization of the Ginsparg-Wilson relation due to Fujikawa, which yields an order-$k$ Hamiltonian overlap operator for each integer $k \geq 0$, with an exactly conserved but nonquantized chiral charge that becomes quantized as $k \to \infty$. Our construction provides physical insight into how Fujikawa's higher-order Ginsparg-Wilson relation improves chiral symmetry while reproducing the anomaly, highlighting the trade-offs inherent in any Hamiltonian lattice realization of an anomalous chiral symmetry. This class of Hamiltonian lattice regularizations, with their tunable chiral symmetry properties, offers potential advantages for quantum and tensor-network simulations.

Singh, Hersh [Fermilab]↗

Graph characterization of higher-order structure in atmospheric chemical reaction mechanisms

Atmospheric chemical reactions play an important role in air quality and climate change. While the structure and dynamics of individual chemical reactions are fairly well understood, the emergent properties of the entire atmospheric chemical system, which can involve many different species that participate in many different reactions, are not well described. In this work, we leverage graph-theoretic techniques to characterize patterns of interaction (“motifs”) in three different representations of gas-phase atmospheric chemistry, termed “chemical mechanisms.” These widely used mechanisms, the master chemical mechanism, the GEOS-Chem mechanism, and the Super-Fast mechanism, vary dramatically in scale and application, but they all generally aim to simulate the abundance and variability of chemical species in the atmosphere. This motif analysis quantifies the fundamental patterns of interaction within the mechanisms, which are directly related to their construction. For example, the gas-phase chemistry in the very small Super-Fast mechanism is entirely composed of bimolecular reactions, and its motif distribution matches that of an individual bimolecular reaction well. The larger and more complex mechanisms show emergent motif distributions that differ strongly from any specific reaction type, consistent with their complexity. The proposed motif analysis demonstrates that while these mechanisms all have a similar design goal, their higher-order structure of interactions differs strongly and thus provides a novel set of tools for exploring differences across chemical mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analyzing LF/VLF Lightning Waveforms to Estimate D-region Electron Density Profiles

Lightning waveforms in the low frequency (LF; 30-300 kHz) and the very low frequency (VLF; 3-30 kHz) bands can be exploited to produce data-driven ionospheric D-region electron density profile (EDP) estimates with significantly higher spatial and temporal coverage than previously available. The lightning waveforms used in this paper are signals detected in the LF/VLF of negative cloud-to-ground lightning by the Earth Networks Total Lightning Detection Network. Each waveform contains a ground wave and a time-delayed ionospheric reflection. The time delay between the ground wave and ionospheric reflection has previously been used to estimate a single specular reflection altitude, where LF/VLF emissions are reflected by the ionosphere. Here, we expand upon previous methods to include filtering and spectral analysis, and account for oblique propagation to produce higher-order estimates for reflection altitudes and corresponding electron densities. Once estimated, reflection altitudes and corresponding electron densities can be used to derive parameters β and h’, which define an EDP for the D-region. In this study, the lightning waveform (LW) analysis is demonstrated using a single representative 24-hour dataset over the Southeast United States, and then extended to a total of 10 separate datasets with varying locations and ionospheric conditions. The LW-derived D-region EDPs are in agreement with predictions made by the Faraday International Reference Ionosphere model, and the LW EDPs β and h’ values are consistent with previous LF/VLF-derived estimates.

D-region ionosphere↗

Deriving cloud droplet number concentration from surface-based remote sensors with an emphasis on lidar measurements

Abstract. Given the importance of constraining cloud droplet number concentrations (Nd) in low-level clouds, we explore two methods for retrieving Nd from surface-based remote sensing that emphasize the information content in lidar measurements. Because Nd is the zeroth moment of the droplet size distribution (DSD), and all remote sensing approaches respond to DSD moments that are at least 2 orders of magnitude greater than the zeroth moment, deriving Nd from remote sensing measurements has significant uncertainty. At minimum, such algorithms require the extrapolation of information from two other measurements that respond to different moments of the DSD. Lidar, for instance, is sensitive to the second moment (cross-sectional area) of the DSD, while other measures from microwave sensors respond to higher-order moments. We develop methods using a simple lidar forward model that demonstrates that the depth to the maximum in lidar-attenuated backscatter (Rmax⁡) is strongly sensitive to Nd when some measure of the liquid water content vertical profile is given or assumed. Knowledge of Rmax⁡ to within 5 m can constrain Nd to within several tens of percent. However, operational lidar networks provide vertical resolutions of > 15 m, making a direct calculation of Nd from Rmax⁡ very uncertain. Therefore, we develop a Bayesian optimal estimation algorithm that brings additional information to the inversion such as lidar-derived extinction and radar reflectivity near the cloud top. This statistical approach provides reasonable characterizations of Nd and effective radius (re) to within approximately a factor of 2 and 30 %, respectively. By comparing surface-derived cloud properties with MODIS satellite and aircraft data collected during the MARCUS and CAPRICORN II campaigns, we demonstrate the utility of the methodology.

54 ENVIRONMENTAL SCIENCES↗

Neural chaos: A spectral stochastic neural operator

Building surrogate models for operators with uncertainty quantification capabilities is essential for many engineering applications where randomness–such as variability in material properties, boundary conditions, and initial conditions–is unavoidable. Polynomial Chaos Expansion (PCE) is widely recognized as a go-to method for constructing stochastic surrogates in both intrusive and non-intrusive ways, and it has recently been used in the context of operator learning. However, its application becomes challenging for complex or high-dimensional processes, as achieving accuracy requires higher-order polynomials, which can increase computational demand and/or the risk of overfitting. Furthermore, PCE requires specialized treatments to manage random variables that are not independent, and these treatments may be problem-dependent or may fail with increasing complexity. Here, in this work, we adopt the same formalism as the spectral expansion used in PCE; however, we replace the classical polynomial basis functions with neural network (NN) basis functions to leverage their expressivity. To achieve this, we propose an algorithm that identifies NN-parameterized basis functions in a purely data-driven manner, without any prior assumptions about the joint distribution of the random variables involved, whether independent or dependent, or about their marginal distributions. The proposed algorithm identifies each NN-parameterized basis function sequentially, ensuring they are orthogonal with respect to the data distribution. The basis functions are constructed directly on the joint stochastic variables without requiring a tensor product structure or assuming independence of the random variables. This approach may offer greater flexibility for complex stochastic models, while simplifying implementation compared to the tensor product structures typically used in PCE to handle random vectors. This is particularly advantageous given the current state of open-source packages, where building and training neural networks can be done with just a few lines of code and extensive community support. We demonstrate the effectiveness of the proposed scheme through several numerical examples of varying complexity and provide comparisons with classical PCE.

Polynomial chaos expansion↗

Evaluating Probabilistic Deep Learning Methods for Uncertainty Quantification of Precipitation Bias Correction

Climate models often exhibit biases in their precipitation predictions, particularly underestimating high-intensity events and overestimating low precipitation. Deep learning approaches offer promising solutions, but their epistemic uncertainty associated with a deep learning–based bias correction method has not previously been quantified for reliable downstream climate impact studies. While methods for capturing the epistemic uncertainty in deep learning frameworks exist, there is currently no consensus on the best method. In this work, we compare three uncertainty quantification (UQ) methods—Deep Ensembles (DEns), Monte Carlo Dropout (MCD), and Flipout—by assessing the reliability of their uncertainty estimates using standard measures such as sharpness and calibration. These UQ methods are applied to an existing deep learning precipitation bias correction model known as UFNet: a coupled U-Net and fully connected neural network. The methods utilized to assess the models’ uncertainties are 1) calibration, which ensures that the expected probabilities of the model align with reality and 2) sharpness, which is a measure of the precision of the model’s probabilistic predictions. Of the three UQ methods evaluated, the DEns and MCD methods demonstrated the best-calibrated performance (expected calibration error of 0.36 and 0.35, respectively), compared to Flipout (0.58). In contrast, Flipout had the sharpest predictions and the highest metric performance in bias correcting precipitation—especially for higher-order moments such as kurtosis with a spatial correlation of 72% compared to 32% and 55% spatial correlation for DEns and MCD, respectively. Of the three UQ methods, MCD was found to be the most suitable method for UQ purposes based on its calibration, sharpness, and computational requirements.

Bayesian methods↗

Learning interpretable surface elasticity properties from bulk properties via neural network equation learners

Surface elasticity is central to understanding the mechanics and stability of surfaces and interfaces. It is characterized by quantities such as surface tension, residual surface stress, and surface stiffness. However their analytical expressions are typically difficult to derive from atomistic data, and depend strongly on modeling choices. This work presents a neural network-based equation learner which combines customized activation functions and connection-based pruning to discover parsimonious, closed-form equations for surface elasticity from atomistic simulations. Applying the method to seven face-centered cubic (FCC) metals, our equation learner uncovers interpretable equations that describe both low-Miller index and high-Miller index surface properties, capturing long-tail property distributions accurately. The discovered expressions are decoupled into two components: a universal, geometry-driven orientation function, and material-specific baseline coefficients. We find that lower-order properties such as surface tension are fundamentally geometry dependent, while higher-order properties such as surface stress and elasticity show more complex geometry and material dependence. We also relate material dependent coefficients to bulk properties, forming a clear map from bulk material properties to surface elasticity. Overall, this approach demonstrates that interpretable neurosymbolic machine learning can bridge the gap between atomistic simulations and physical laws, enabling the discovery of generalizable structure–property relationships for materials science phenomena such as surface elasticity.

Equation learning↗

Quantum real-time evolution using tensor renormalization group methods

We introduce an approach for approximate real-time evolution of quantum systems using tensor renormalization group (TRG) methods originally developed for imaginary time. We use higher-order TRG to generate a coarse-grained time evolution operator for a 1+1⁢D transverse Ising model with a longitudinal field. We show that the standard tensor norm used for the singular value decomposition-based truncation is degenerate and propose an alternate method to discriminate. We show that it is effective and efficient in evolving Gaussian wave packets for one and two particles in the disordered phase, while ordered phase behavior is more challenging to capture. We compare our algorithm with local simulators for universal quantum computers and discuss possible benchmarking in the near future.

lattice gauge theory↗