Engineering topics

Auerbach, Scott

Publications and source records attributed to Auerbach, Scott.

3 records

DOE OSTI2025

TransPlatformer

We propose TransPlatformer for translating toxicogenomics from one platform to another. Transcriptomic profiling has evolved through multiple generations of technology, from microarrays (e.g., Affymetrix, CodeLink) to more recent high-throughput sequencing and targeted panels such as S1500+. Microarrays, which dominated gene expression studies in the early 2000s, provided affordable and high-throughput transcript quantification but suffered from cross-hybridization issues and limited dynamic range . RNA-Seq, introduced in the late 2000s, revolutionized transcriptomics by enabling unbiased and comprehensive gene expression analysis, albeit at higher costs and computational demands . Despite advances, many studies rely on historical microarray data, necessitating the translation of legacy data into modern platforms to ensure continuity and comparability. This translation is complicated by factors such as platform-specific probe design, differences in transcript coverage, and batch effects . Existing methods for cross-platform mapping include statistical normalization, machine learning models, and biological anchoring approaches. The ability to translate transcriptomic data between platforms has broad implications, including enhanced meta-analyses, improved toxicological modeling, and better integration of historical datasets with contemporary research. TransPlatformer seeks to contribute to this effort by evaluating translation methodologies and proposing novel strategies to improve cross-platform gene expression harmonization. In this repository there are code examples for TransPlatformer implementation

Cong, Guojing↗

DOE OSTI2023

Clustering High-dimensional Toxicogenomics Data with Rare Signals

Toxicogenomics studies the gene and protein activities to drug treatments or toxic exposures. As the drugs and genes are numerous, toxicogenomics data are naturally high dimensional, with dimension sizes up to millions. In addition, the distribution of toxicogenomics data is oftentimes skewed, and they contain rare but important signals representing a cell or organism’s response to toxicity. The combination of high dimension and extremely skewed distribution of toxicogenomics data makes clustering analysis extremely challenging.We present our study of clustering toxicogenomics data using classical approaches such as principal component analysis as well as deep learning approaches such as auto-encoders. Our experiments show that these approaches fail to preserve rare signals and produce high-quality clusters. We then explore augmenting matrix factorization with deep learning techniques such as attention mechanism to produce latent representations for clustering. Our technique is able to better preserve rare signals after dimensionality reduction than prior approaches. Furthermore, we combine our augmented matrix factorization with a mechanism similar to autoencoder to balance separable clusters and low regeneration errors. Our experiments demonstrate better clustering with our proposed approach.

Cong, Guojing↗

DOE OSTI2017

Modeling the self-assembly of ordered nanoporous materials

This report describes progress on a collaborative project on the multiscale modeling of the assembly processes in the synthesis of nanoporous materials. Such materials are of enormous importance in modern technology with application in the chemical process industries, biomedicine and biotechnology as well as microelectronics. The project focuses on two important classes of materials: i) microporous crystalline materials, such as zeolites, and ii) ordered mesoporous materials. In the first case the pores are part of the crystalline structure, while in the second the structures are amorphous on the atomistic length scale but where surfactant templating gives rise to order on the length scale of 2 - 20 nm. We have developed a modeling framework that encompasses both these kinds of materials. Our models focus on the assembly of corner sharing silica tetrahedra in the presence of structure directing agents. We emphasize a balance between sufficient realism in the models and computational tractibility given the complex many-body phenomena. We use both on-lattice and off-lattice models and the primary computational tools are Monte Carlo simulations with sampling techniques and ensembles appropriate to specific situations. Our modeling approach is the first to capture silica polymerization, nanopore crystallization, and mesopore formation through computer-simulated self assembly.

36 MATERIALS SCIENCE↗