Engineering topics

Karpatne, Anuj

Publications and source records attributed to Karpatne, Anuj.

4 records

DOE OSTI2024

Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution. (Model and code can be found at imageomics.github.io/phylo-diffusion)

Khurana, Mridul↗

DOE OSTI2024

Deep Image Prior Enabled Full Waveform Inversion (Final Technical Report)

MS Student Naveen Gupta worked on the problem of full waveform inversion (FWI) using neural networks as shown in Figure 1. Our goal was to learn a neural network to represent the subsurface velocity model, which when fed into the FWI module (implemented using a numerical forward model of wave equations) produces amplitude estimates that match with ground-truth observations of amplitude. We used neural networks to solve the inverse problem of estimating velocity distributions for a given seismic amplitude data such that, once trained, our neural network model can generate a distribution of velocity profiles for different random vectors fed as inputs to the neural network model.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Science-integrated Artificial-intelligence for Flooding and precipitation Extremes (SAFE)

A grand challenge in hydrologic science is to understand why signals of climate change and variability, which are often visible in precipitation extremes at aggregate scales, are not consistently observed in the case of extreme flooding. However, a solution to this challenge may prove elusive unless the water cycle is viewed in an integrative manner. Thus, for riverine flooding, while Hortonian (infiltration excess) runoff may have stronger correlation with precipitation extremes and hence perhaps to warming trends or climate oscillators, Dunne (saturation excess) runoff may have a more complex relationships with time series of precipitation and with evaporation and transpiration, but rain-on-snow and snowmelt events may depend on land-surface and atmospheric temperatures. Atmospheric rivers and tropical cyclones lead to precipitation or flooding and are impacted by climate. Flooding assessments need to consider long-term baselines, evolving risk factors, coupled natural-human systems, and novel adaptation such as nature-inspired design.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Predicting lake surface water phosphorus dynamics using process-guided machine learning

Phosphorus (P) loading to lakes is degrading the quality and usability of water globally. Accurate predictions of lake P dynamics are needed to understand whole-ecosystem P budgets, as well as the consequences of changing lake P concentrations for water quality. However, complex biophysical processes within lakes, along with limited observational data, challenge our capacity to reproduce short-term lake dynamics needed for water quality predictions, as well as long-term dynamics needed to understand broad scale controls over lake P. Here we use an emerging paradigm in modeling, process-guided machine learning (PGML), to produce a phosphorus budget for Lake Mendota (Wisconsin, USA) and to accurately predict epilimnetic phosphorus over a time range of days to decades. In our implementation of PGML, which we term a Process-Guided Recurrent Neural Network (PGRNN), we combine a process-based model for lake P with a recurrent neural network, and then constrain the predictions with ecological principles. We test independently the process-based model, the recurrent neural network, and the PGRNN to evaluate the overall approach. The process-based model accounted for most of the observed pattern in lake P; however it missed the long-term trend in lake P and had the worst performance in predicting winter and summer P in surface waters. The root mean square error (RMSE) for the process-based model, the recurrent neural network, and the PGRNN was 33.0 μg P L -1 , 22.7 μg P L -1 , and 20.7 μg P L -1 , respectively. All models performed better during summer, with RMSE values for the three models (same order) equal to 14.3 μg P L -1 , 10.9 μg P L -1 , and 10.7 μg P L -1 . Although the PGRNN had only marginally better RMSE during summer, it had lower bias and reproduced long-term decreases in lake P missed by the other two models. For all seasons and all years, the recurrent neural network had better predictions than process alone, with root mean square error (RMSE) of 23.8 μg P L -1 and 28.0 μg P L -1 , respectively. The output of PGRNN indicated that new processes related to water temperature, thermal stratification, and long term changes in external loads are needed to improve the process model. By using ecological knowledge, as well as the information content of complex data, PGML shows promise as a technique for accurate prediction in messy, real-world ecological dynamics, while providing valuable information that can improve our understanding of process.

54 ENVIRONMENTAL SCIENCES↗