Models, code, and papers for "A N Vaishnavi":

##### Multimodal fusion of imaging and genomics for lung cancer recurrence prediction

Feb 05, 2020
Vaishnavi Subramanian, Minh N. Do, Tanveer Syeda-Mahmood

Lung cancer has a high rate of recurrence in early-stage patients. Predicting the post-surgical recurrence in lung cancer patients has traditionally been approached using single modality information of genomics or radiology images. We investigate the potential of multimodal fusion for this task. By combining computed tomography (CT) images and genomics, we demonstrate improved prediction of recurrence using linear Cox proportional hazards models with elastic net regularization. We work on a recent non-small cell lung cancer (NSCLC) radiogenomics dataset of 130 patients and observe an increase in concordance-index values of up to 10%. Employing non-linear methods from the neural network literature, such as multi-layer perceptrons and visual-question answering fusion modules, did not improve performance consistently. This indicates the need for larger multimodal datasets and fusion techniques better adapted to this biological setting.

* Accepted for presentation at International Symposium on Biomedical Imaging (ISBI) 2020 (Iowa City). 5 pages, last page references
##### Attentional networks for music generation

Realistic music generation has always remained as a challenging problem as it may lack structure or rationality. In this work, we propose a deep learning based music generation method in order to produce old style music particularly JAZZ with rehashed melodic structures utilizing a Bi-directional Long Short Term Memory (Bi-LSTM) Neural Network with Attention. Owing to the success in modelling long-term temporal dependencies in sequential data and its success in case of videos, Bi-LSTMs with attention serve as the natural choice and early utilization in music generation. We validate in our experiments that Bi-LSTMs with attention are able to preserve the richness and technical nuances of the music performed.

Sep 12, 2019
Pratik Vaishnavi, Kevin Eykholt, Atul Prakash, Amir Rahmati

Dec 21, 2019
Pratik Vaishnavi, Tianji Cong, Kevin Eykholt, Atul Prakash, Amir Rahmati

Deep Neural Networks (DNNs) are known to be susceptible to adversarial examples. Adversarial examples are maliciously crafted inputs that are designed to fool a model, but appear normal to human beings. Recent work has shown that pixel discretization can be used to make classifiers for MNIST highly robust to adversarial examples. However, pixel discretization fails to provide significant protection on more complex datasets. In this paper, we take the first step towards reconciling these contrary findings. Focusing on the observation that discrete pixelization in MNIST makes the background completely black and foreground completely white, we hypothesize that the important property for increasing robustness is the elimination of image background using attention masks before classifying an object. To examine this hypothesis, we create foreground attention masks for two different datasets, GTSRB and MS-COCO. Our initial results suggest that using attention mask leads to improved robustness. On the adversarially trained classifiers, we see an adversarial robustness increase of over 20% on MS-COCO.

* Version presented at AAAI-20 workshop on Engineering Dependable and Secure Machine Learning Systems (EDSMLS)
##### Automated Detection and Type Classification of Central Venous Catheters in Chest X-Rays

Central venous catheters (CVCs) are commonly used in critical care settings for monitoring body functions and administering medications. They are often described in radiology reports by referring to their presence, identity and placement. In this paper, we address the problem of automatic detection of their presence and identity through automated segmentation using deep learning networks and classification based on their intersection with previously learned shape priors from clinician annotations of CVCs. The results not only outperform existing methods of catheter detection achieving 85.2% accuracy at 91.6% precision, but also enable high precision (95.2%) classification of catheter types on a large dataset of over 10,000 chest X-rays, presenting a robust and practical solution to this problem.

* Accepted to Medical Image Computing and Computer Assisted Intervention (MICCAI) 2019; Data available: ML-CDS Challenge, MICCAI2019 (http://www.mcbr-cds.org/challenge/challenge-description.html)
##### Machine Learning for Classification of Protein Helix Capping Motifs

The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the sequence, defines a protein). Given the costs (time, money, human resources) of determining protein structures via experimental means such as X-ray crystallography, can we better describe and compare protein 3D structures in a robust and efficient manner, so as to gain meaningful biological insights? We begin by considering a relatively simple problem, limiting ourselves to just protein secondary structural elements. Historically, many computational methods have been devised to classify amino acid residues in a protein chain into one of several discrete secondary structures, of which the most well-characterized are the geometrically regular $\alpha$-helix and $\beta$-sheet; irregular structural patterns, such as 'turns' and 'loops', are less understood. Here, we present a study of Deep Learning techniques to classify the loop-like end cap structures which delimit $\alpha$-helices. Previous work used highly empirical and heuristic methods to manually classify helix capping motifs. Instead, we use structural data directly--including (i) backbone torsion angles computed from 3D structures, (ii) macromolecular feature sets (e.g., physicochemical properties), and (iii) helix cap classification data (from CAPS-DB)--as the ground truth to train a bidirectional long short-term memory (BiLSTM) model to classify helix cap residues. We tried different network architectures and scanned hyperparameters in order to train and assess several models; we also trained a Support Vector Classifier (SVC) to use as a baseline. Ultimately, we achieved 85% class-balanced accuracy with a deep BiLSTM model.

* 6 pages, 3 figures, 4 tables