Advait Balaji

Advait Balaji, Trevor Teolis, S. David Mis et al.

Surrogate modeling of wave propagation and scattering (i.e. the wave speed and source to wave field map) in heterogeneous media has significant potential in applications such as seismic imaging and inversion. High-contrast settings, such as subsurface models with salt bodies, exhibit strong scattering and phase sensitivity that challenge existing neural operators. We propose a hybrid architecture that decomposes the scattering operator into two separate contributions: a smooth background propagation and a high-contrast scattering correction. The smooth component is learned with a Fourier Neural Operator (FNO), which produces globally coupled feature tokens encoding background wave propagation; these tokens are then passed to a vision transformer, where attention is used to model the high-contrast scattering correction dominated by strong, spatial interactions. Evaluated on high-frequency Helmholtz problems with strong contrasts, the hybrid model achieves substantially improved phase and amplitude accuracy compared to standalone FNOs or transformers, with favorable accuracy-parameter scaling.

Ali Azizpour, Advait Balaji, Todd J. Treangen et al.

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and non-repetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudo-labels for a small proportion of the nodes. We then use those pseudo-labels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with pre-defined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic datasets. The results on the simulated data highlight our GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, our experiments with synthetic metagenomic datasets reveal that incorporating the graph structure and the GNN enhances our detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.