arXiv subjects

Sully F. Chen

Publications and source records attributed to Sully F. Chen.

4 recordsLinked to original sources

arXiv2026

Large-Scale Multi-omic Biosequence Transformers for Modeling Protein-Nucleic Acid Interactions

The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. To date, most biosequence transformers have been trained on single-omic data - either proteins or nucleic acids - and have seen incredible success in downstream tasks in each domain, with particularly noteworthy breakthroughs in protein structural modeling. However, single-omic pretraining limits the ability of these models to capture cross-modal interactions. Here we present OmniBioTE, the largest open-source multi-omic model trained on over 250 billion tokens of mixed protein and nucleic acid data. We show that despite only being trained on unlabeled sequence data, OmniBioTE learns joint representations mapping genes to their corresponding protein sequences. We further demonstrate that OmniBioTE achieves state-of-the-art results predicting the change in Gibbs free energy ({ΔG}) of the binding interaction between a given nucleic acid and protein. Remarkably, we show that multi-omic biosequence transformers emergently learn useful structural information without any a priori structural training, allowing us to predict which protein residues are most involved in the protein-nucleic acid binding interaction. Compared to single-omic controls trained with identical compute, OmniBioTE also demonstrates superior performance-per-FLOP across both multi-omic and single-omic benchmarks. Together, these results highlight the power of a unified modeling approach for biological sequences and establish OmniBioTE as a foundation model for multi-omic discovery.

cs.LG↗

arXiv2024

Sparse learned kernels for interpretable and efficient medical time series processing

Rapid, reliable, and accurate interpretation of medical time-series signals is crucial for high-stakes clinical decision-making. Deep learning methods offered unprecedented performance in medical signal processing but at a cost: they were compute-intensive and lacked interpretability. We propose Sparse Mixture of Learned Kernels (SMoLK), an interpretable architecture for medical time series processing. SMoLK learns a set of lightweight flexible kernels that form a single-layer sparse neural network, providing not only interpretability, but also efficiency, robustness, and generalization to unseen data distributions. We introduce a parameter reduction techniques to reduce the size of SMoLK's networks while maintaining performance. We test SMoLK on two important tasks common to many consumer wearables: photoplethysmography (PPG) artifact detection and atrial fibrillation detection from single-lead electrocardiograms (ECGs). We find that SMoLK matches the performance of models orders of magnitude larger. It is particularly suited for real-time applications using low-power devices, and its interpretability benefits high-stakes situations.

eess.SP↗

arXiv2024

Computer Vision for Increased Operative Efficiency via Identification of Instruments in the Neurosurgical Operating Room: A Proof-of-Concept Study

Objectives Computer vision (CV) is a field of artificial intelligence that enables machines to interpret and understand images and videos. CV has the potential to be of assistance in the operating room (OR) to track surgical instruments. We built a CV algorithm for identifying surgical instruments in the neurosurgical operating room as a potential solution for surgical instrument tracking and management to decrease surgical waste and opening of unnecessary tools. Methods We collected 1660 images of 27 commonly used neurosurgical instruments. Images were labeled using the VGG Image Annotator and split into 80% training and 20% testing sets in order to train a U-Net Convolutional Neural Network using 5-fold cross validation. Results Our U-Net achieved a tool identification accuracy of 80-100% when distinguishing 25 classes of instruments, with 19/25 classes having accuracy over 90%. The model performance was not adequate for sub classifying Adson, Gerald, and Debakey forceps, which had accuracies of 60-80%. Conclusions We demonstrated the viability of using machine learning to accurately identify surgical instruments. Instrument identification could help optimize surgical tray packing, decrease tool usage and waste, decrease incidence of instrument misplacement events, and assist in timing of routine instrument maintenance. More training data will be needed to increase accuracy across all surgical instruments that would appear in a neurosurgical operating room. Such technology has the potential to be used as a method to be used for proving what tools are truly needed in each type of operation allowing surgeons across the world to do more with less.

eess.IV↗

arXiv2019

The irrationality measure of $π$ as seen through the eyes of $\cos(n)$

For different values of $γ\geq 0$, analysis of the end behavior of the sequence $a_n = \cos (n)^{n^γ}$ yields a strong connection to the irrationality measure of $π$. We show that if $\limsup |\cos n|^{n^2} \neq 1$, then the irrationality measure of $π$ is exactly 2. We also give some numerical evidence to support the conjecture that $μ(π)=2$, based on the appearance of some startling subsequences of $\cos(n)^n$.

math.NT↗