Riya Gupta

Christopher Benka, Judah Goldfeder, Carl Gross et al.

Intelligent robots must be able to perform safe and efficient motion planning in their environments. Central to modern motion planning is the configuration space. Configuration spaces define the set of configurations of a robot that result in collisions with obstacles in the workspace, $\text{C}_{\text{clsn}}$, and the set of configurations that do not, $\text{C}_{\text{free}}$. Modern approaches to motion planning first compute the configuration space and then perform motion planning using the calculated configuration space. Real-time motion planning requires accurate and efficient construction of configuration spaces. We are the first to apply a convolutional encoder-decoder framework for calculating highly accurate approximations to configuration spaces, essentially learning how the robot and physical world interact. Our model achieves an average 97.5% F1-score for predicting $\text{C}_{\text{free}}$ and $\text{C}_{\text{clsn}}$ for 2-D robotic workspaces with a dual-arm robot. Our method limits undetected collisions to less than 2.5% on robotic workspaces that involve translation, rotation, and removal of obstacles. Our model learns highly transferable features between robotic workspaces, requiring little to no fine-tuning to adapt to new transformations of obstacles in the workspace.

Riya Gupta, Alexander Chowdhury, Sahil Nalawade

Federated Learning (FL) has emerged as a transformative paradigm in medical AI, enabling collaborative model training across institutions without direct data sharing. This study benchmarks three prominent FL frameworks NVIDIA FLARE, Flower, and Owkin Substra to evaluate their suitability for medical imaging applications in real-world settings. Using the PathMNIST dataset, we assess model performance, convergence efficiency, communication overhead, scalability, and developer experience. Results indicate that NVIDIA FLARE offers superior production scalability, Flower provides flexibility for prototyping and academic research, and Owkin Substra demonstrates exceptional privacy and compliance features. Each framework exhibits strengths optimized for distinct use cases, emphasizing their relevance to practical deployment in healthcare environments.

Riya Gupta, Yiwei Zong, Dennis H. Murphree

The rapid generation of whole-slide images (WSIs) in dermatopathology necessitates automated methods for efficient processing and accurate classification. This study evaluates the performance of two foundation models, UNI and Virchow2, as feature extractors for classifying WSIs into three diagnostic categories: melanocytic, basaloid, and squamous lesions. Patch-level embeddings were aggregated into slide-level features using a mean-aggregation strategy and subsequently used to train multiple machine learning classifiers, including logistic regression, gradient-boosted trees, and random forest models. Performance was assessed using precision, recall, true positive rate, false positive rate, and the area under the receiver operating characteristic curve (AUROC) on the test set. Results demonstrate that patch-level features extracted using Virchow2 outperformed those extracted via UNI across most slide-level classifiers, with logistic regression achieving the highest accuracy (90%) for Virchow2, though the difference was not statistically significant. The study also explored data augmentation techniques and image normalization to enhance model robustness and generalizability. The mean-aggregation approach provided reliable slide-level feature representations. All experimental results and metrics were tracked and visualized using WandB.ai, facilitating reproducibility and interpretability. This research highlights the potential of foundation models for automated WSI classification, providing a scalable and effective approach for dermatopathological diagnosis while paving the way for future advancements in slide-level representation learning.

Rakesh Thakur, Riya Gupta

Comprehending the long-timescale dynamics of protein-ligand complexes is very important for drug discovery and structural biology, but it continues to be computationally challenging for large biomolecular systems. We introduce HemePLM-Diffuse, an innovative generative transformer model that is designed for accurate simulation of protein-ligand trajectories, inpaints the missing ligand fragments, and sample transition paths in systems with more than 10,000 atoms. HemePLM-Diffuse has features of SE(3)-Invariant tokenization approach for proteins and ligands, that utilizes time-aware cross-attentional diffusion to effectively capture atomic motion. We also demonstrate its capabilities using the 3CQV HEME system, showing enhanced accuracy and scalability compared to leading models such as TorchMD-Net, MDGEN, and Uni-Mol.