Nanopore devices have emerged as powerful tools for single-molecule sensing, with potential for rapid, portable diagnostics. They detect changes in ionic current as analytes enter nanometer-scale pores, providing a means of identifying diverse biomarkers from their characteristic signal patterns. However, these signals are highly complex, and reliably assigning them to specific molecules remains a major challenge. Here, we address this by introducing a multi-modal deep learning architecture that jointly processes multiple signal representations, including raw time-series data, wavelet-based images, and static feature vectors. Our approach surpasses existing methods by more than 10 percentage points on a 42-peptide benchmark and transfers to a 20-amino-acid dataset with near-perfect accuracy. The model integrates complementary information from these representations, with attention analysis showing that the time-series and wavelet-image inputs emphasize different features of the same event. Together, these results demonstrate the potential of machine learning to enable robust, high-accuracy molecular identification with nanopore sensors.
Molecular property prediction from structure often uses a single representative conformation, even though many molecules exist as conformational ensembles in solution. We introduce EnsembleEGNN, a molecular ensemble foundation model that encodes an ensemble by first encoding each…
Bayesian Optimization (BO) is widely adopted for data-efficient optimization in scientific and engineering applications, yet its computational cost is rarely evaluated alongside optimization performance. Here we present a systematic, compute-aware study of BO that evaluates surro…
In this study, we introduce latent PDE mapping, a broadly applicable physics-informed learning technique designed to enable efficient geometric generalization with sparse training data. Latent PDE mapping pulls back geometry-specific PDE residuals and boundary conditions to a pre…
Unlike large language models (LLMs) that exhibit strong reasoning capabilities, vision-language models (VLMs) struggle with visual reasoning, even on geometry problems that admit equivalent text, diagram, and combined diagram+text views. We show that these views often elicit diff…
We study transcript management for fixed, finite-precision causal Transformers. A transcript is partitioned into channels of bounded blocks. Each transition consults a fixed visible suffix and may append one block, leaving the model, weights, and token protocol unchanged. The ope…
Talking-face (TF) deepfake generation synthesizes photore- alistic facial video from a static source image and an au- dio signal, producing forgeries that current image-based detectors consistently fail to identify. Unlike face-swap ma- nipulation, TF synthesis has no underlying…