Huu Phong Nguyen

Jake Y. Chen, Huu Phong Nguyen, Fuad Al Abir et al.

This work examines perturbation generalization in spatial foundation-model embeddings derived from fluorescence microscopy images. Although these models can discriminate drug conditions accurately, it remains unclear whether the learned representations reflect patterns consistent with expected perturbation axes that transfer across drugs. We introduce SVC-Probe, a perturbation-aware framework that combines Subcellular Embedding Atlas Stability, Mondrian Neighborhood Graphs, and a Foundation Model Perturbation Probe to assess embedding stability, neighborhood rewiring, and centroid prediction under drug treatment. Applied to the CM4AI MDA-MB-468 chemical-perturbation atlas comprising 462 antibody labels and SubCell 1536-dimensional embeddings, SVC-Probe demonstrates that 98.6% three-way condition accuracy does not correlate with reliable cross-drug prediction, with cosine similarity diminishing from 0.944 in-domain to 0.30 under leave-one-drug-out evaluation, constituting a two-drug stress test rather than a general benchmark. Null calibration indicates that raw residual-turnover coupling is largely influenced by generic embedding structure, whereas a drug-specific signal emerges under vorinostat and is consistent with chromatin-related reorganization. In contrast, the paclitaxel axis is not robustly reconstructed, likely due to sparse coverage of microtubule-associated proteins. Together, these results introduce and demonstrate a reusable diagnostic framework for stress-testing spatial virtual-cell representations and indicate that perturbation generalization may serve as a stricter and more informative benchmark than baseline condition discrimination.

Shekhar Madhav Khairnar, Huu Phong Nguyen, Alexis Desir et al.

Automated assessment of surgical skills using artificial intelligence (AI) provides trainees with instantaneous feedback. After bimanual tool motions are captured, derived kinematic metrics are reliable predictors of performance in laparoscopic tasks. Implementing automated tool tracking requires time-intensive human annotation. We developed AI-based tool tracking using the Segment Anything Model (SAM) to eliminate the need for human annotators. Here, we describe a study evaluating the usefulness of our tool tracking model in automated assessment during a laparoscopic suturing task in the fundoplication procedure. An automated tool tracking model was applied to recorded videos of Nissen fundoplication on porcine bowel. Surgeons were grouped as novices (PGY1-2) and experts (PGY3-5, attendings). The beginning and end of each suturing step were segmented, and motions of the left and right tools were extracted. A low-pass filter with a 24 Hz cut-off frequency removed noise. Performance was assessed using supervised and unsupervised models, and an ablation study compared results. Kinematic features--RMS velocity, RMS acceleration, RMS jerk, total path length, and Bimanual Dexterity--were extracted and analyzed using Logistic Regression, Random Forest, Support Vector Classifier, and XGBoost. PCA was performed for feature reduction. For unsupervised learning, a Denoising Autoencoder (DAE) model with classifiers, such as a 1-D CNN and traditional models, was trained. Data were extracted for 28 participants (9 novices, 19 experts). Supervised learning with PCA and Random Forest achieved an accuracy of 0.795 and an F1 score of 0.778. The unsupervised 1-D CNN achieved superior results with an accuracy of 0.817 and an F1 score of 0.806, eliminating the need for kinematic feature computation. We demonstrated an AI model capable of automated performance classification, independent of human annotation.