• AI for medical education
• Medical AI
  • Accurate and adversarially robust classification of medical images and ECG time-series with gradient-free trained sign activation neural networks (2020)
  • Two-stage and dual-decoder convolutional U-Net ensembles for reliable vessel and plaque segmentation in carotid ultrasound images (2020)
  • Classifying histopathology images with random depthwise convolutional neural networks (2020)
  • An Ensemble-Based Confidence Score to Increase Accuracy of Carotid Ultrasound Vessel Lumen Segmentation by Convolutional Neural Networks (2020)
  • Deep Learning Neural Networks To Automate The Identification Of Vessel Lumen In B- Mode Carotid Ultrasound Images (2020)
  • CPM-RadPath2019: Brain tumor classification with tumor segmentations and a dual path residual convolutional neural network from MRI and pathology images (2019)
  • BraTS2019: A multi-path decoder network for brain tumor segmentation (2019)
  • Vessel lumen segmentation in internal carotid artery ultrasounds with deep convolutional neural networks (2019)
  • 2.5D convolutional neural network system for identifying stroke lesions in brain MRI images (2019)
  • A fully 3D multi-path convolutional neural network with feature fusion and feature weighting for automatic lesion identification in brain MRI images (2019)
• Robust machine learning
  • Towards adversarial robustness with 01 loss neural networks (2020) - See GitHub site for source code and data
  • On the transferability of adversarial examples between convex and 01 loss models (2020)
  • Stochastic coordinate descent for 01 loss and its sensitivity to adversarial attacks (2019)
• Machine learning and representation learning
  • Random depthwise signed convolutional neural networks (2019)
  • K-means-based feature learning for protein sequence classification (2018)
  • Weighted maximum variance dimensionality reduction (2014)
• Sequence alignment:
  • Anchor selection for pairwise whole genome sequence alignment with the maximum scoring subsequence and GPUs (2018)
  • MaxSSmap: fast and accurate mapping of divergent short reads to genomes (suitable for cross-species mapping and unmapped reads) (2014)
  • PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences (2010)
  • Identifying distantly related RNAs in genomic sequences (2008)
  • eProbalign: web server and source code for Probalign multiple sequence alignment program (2007)
    Also available at the CIPRES portal
• Genomics
  • Chi8: a GPU program for detecting significant interacting SNPs with the chi-square 8-df test (2015)
  • Ranking causal SNPs and disease associated regions in genome wide association studies by the support vector machine and random forest (2011)
  • Semi-supervised feature extraction for population structure identification using the Laplacian linear discriminant
• Large-scale phylogeny reconstruction:
  • Recursive-Iterative-DCM3: divide-and-conquer booster for large-scale phylogeny reconstruction (2004)
• Gene expression clustering:
  • Diametrical clustering for identifying anti-correlated gene clusters (2003)