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DOE OSTI2021

A reproducibility study of "Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space"

Nigam et al. reported a genetic algorithm (GA) utilizing the SELFIES representation and also propose an adaptive, neural network-based penalty that is supposed to improve the diversity of the generated molecules. The main claims of the paper are that this GA outperforms other generative techniques (as measured by the penalized logP) and that a neural network-based adaptive penalty increases the diversity of the generated molecules. In this work, we investigated the reproducibility of their claims. Overall, we were able to reproduce comparable results using the SELFIES-based GA, but mostly by exploiting deficiencies of the (easily optimizable) fitness function (i.e., generating long, sulfur containing chains). In addition, we reproduce results showing that the discriminator can be used to bias the generation of molecules to ones that are similar to the reference set. Lastly, we attempted to quantify the evolution of the diversity, understand the influence of some hyperparameters, and propose improvements to the adaptive penalty.

Jablonka, Kevin Maik↗
DOE OSTI2022

Discriminative Dimensionality Reduction using Deep Neural Networks for Clustering of LIGO Data

In this paper, leveraging the capabilities of neural networks for modeling the non-linearities that exist in the data, we propose several models that can project data into a low dimensional, discriminative, and smooth manifold. The proposed models can transfer knowledge from the domain of known classes to a new domain where the classes are unknown. A clustering algorithm is further applied in the new domain to find potentially new classes from the pool of unlabeled data. The research problem and data for this paper originated from the Gravity Spy project which is a side project of Advanced Laser Interferometer Gravitational-wave Observatory (LIGO). The LIGO project aims at detecting cosmic gravitational waves using huge detectors. However non-cosmic, non-Gaussian disturbances known as "glitches", show up in gravitational-wave data of LIGO. This is undesirable as it creates problems for the gravitational wave detection process. Gravity Spy aids in glitch identification with the purpose of understanding their origin. Since new types of glitches appear over time, one of the objective of Gravity Spy is to create new glitch classes. Towards this task, we offer a methodology in this paper to accomplish this.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Systems and methods for customizing kernel machines with deep neural networks

A method including receiving an input data set. The input data set can include one of a feature domain set or a kernel matrix. The method also can include constructing dense embeddings using: (i) Nyström approximations on the input data set when the input data set comprises the kernel matrix, and (ii) clustered Nyström approximations on the input data set when the input data set comprises the feature domain set. The method additionally can include performing representation learning on each of the dense embeddings using a multi-layer fully-connected network for each of the dense embeddings to generate latent representations corresponding to each of the dense embeddings. The method further can include applying a fusion layer to the latent representations corresponding to the dense embeddings to generate a combined representation. The method additionally can include performing classification on the combined representation. Other embodiments of related systems and methods are also disclosed.

Song, Huan↗
DOE OSTI2023

Few-view computed tomography reconstruction using deep neural network inference

A system for generating 2D slices of a 3D image of a target volume is provided. The system receives a target sinogram collected during a computed tomography scan of the target volume. The system inputs the target sinogram to a convolutional neural network (CNN) to generate predicted 2D slices of the 3D image. The CNN is trained using training 2D slices of training 3D images. The system initializes 2D slices to the predicted 2D slices. The system reconstructs 2D slices of the 3D image from the target sinogram and the initialized 2D slices.

Kim, Hyojin↗