Models, code, and papers for "Sanja L. Antic":

Deep Multi-task Prediction of Lung Cancer and Cancer-free Progression from Censored Heterogenous Clinical Imaging

Nov 12, 2019
Riqiang Gao, Lingfeng Li, Yucheng Tang, Sanja L. Antic, Alexis B. Paulson, Yuankai Huo, Kim L. Sandler, Pierre P. Massion, Bennett A. Landman

Annual low dose computed tomography (CT) lung screening is currently advised for individuals at high risk of lung cancer (e.g., heavy smokers between 55 and 80 years old). The recommended screening practice significantly reduces all-cause mortality, but the vast majority of screening results are negative for cancer. If patients at very low risk could be identified based on individualized, image-based biomarkers, the health care resources could be more efficiently allocated to higher risk patients and reduce overall exposure to ionizing radiation. In this work, we propose a multi-task (diagnosis and prognosis) deep convolutional neural network to improve the diagnostic accuracy over a baseline model while simultaneously estimating a personalized cancer-free progression time (CFPT). A novel Censored Regression Loss (CRL) is proposed to perform weakly supervised regression so that even single negative screening scans can provide small incremental value. Herein, we study 2287 scans from 1433 de-identified patients from the Vanderbilt Lung Screening Program (VLSP) and Molecular Characterization Laboratories (MCL) cohorts. Using five-fold cross-validation, we train a 3D attention-based network under two scenarios: (1) single-task learning with only classification, and (2) multi-task learning with both classification and regression. The single-task learning leads to a higher AUC compared with the Kaggle challenge winner pre-trained model (0.878 v. 0.856), and multi-task learning significantly improves the single-task one (AUC 0.895, p<0.01, McNemar test). In summary, the image-based predicted CFPT can be used in follow-up year lung cancer prediction and data assessment.

* 8 pages, 5 figures, SPIE 2020 Medical Imaging, oral presentation 

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Lung Cancer Detection using Co-learning from Chest CT Images and Clinical Demographics

Feb 21, 2019
Jiachen Wang, Riqiang Gao, Yuankai Huo, Shunxing Bao, Yunxi Xiong, Sanja L. Antic, Travis J. Osterman, Pierre P. Massion, Bennett A. Landman

Early detection of lung cancer is essential in reducing mortality. Recent studies have demonstrated the clinical utility of low-dose computed tomography (CT) to detect lung cancer among individuals selected based on very limited clinical information. However, this strategy yields high false positive rates, which can lead to unnecessary and potentially harmful procedures. To address such challenges, we established a pipeline that co-learns from detailed clinical demographics and 3D CT images. Toward this end, we leveraged data from the Consortium for Molecular and Cellular Characterization of Screen-Detected Lesions (MCL), which focuses on early detection of lung cancer. A 3D attention-based deep convolutional neural net (DCNN) is proposed to identify lung cancer from the chest CT scan without prior anatomical location of the suspicious nodule. To improve upon the non-invasive discrimination between benign and malignant, we applied a random forest classifier to a dataset integrating clinical information to imaging data. The results show that the AUC obtained from clinical demographics alone was 0.635 while the attention network alone reached an accuracy of 0.687. In contrast when applying our proposed pipeline integrating clinical and imaging variables, we reached an AUC of 0.787 on the testing dataset. The proposed network both efficiently captures anatomical information for classification and also generates attention maps that explain the features that drive performance.

* SPIE Medical Image, oral presentation 

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Distanced LSTM: Time-Distanced Gates in Long Short-Term Memory Models for Lung Cancer Detection

Sep 11, 2019
Riqiang Gao, Yuankai Huo, Shunxing Bao, Yucheng Tang, Sanja L. Antic, Emily S. Epstein, Aneri B. Balar, Steve Deppen, Alexis B. Paulson, Kim L. Sandler, Pierre P. Massion, Bennett A. Landman

The field of lung nodule detection and cancer prediction has been rapidly developing with the support of large public data archives. Previous studies have largely focused on cross-sectional (single) CT data. Herein, we consider longitudinal data. The Long Short-Term Memory (LSTM) model addresses learning with regularly spaced time points (i.e., equal temporal intervals). However, clinical imaging follows patient needs with often heterogeneous, irregular acquisitions. To model both regular and irregular longitudinal samples, we generalize the LSTM model with the Distanced LSTM (DLSTM) for temporally varied acquisitions. The DLSTM includes a Temporal Emphasis Model (TEM) that enables learning across regularly and irregularly sampled intervals. Briefly, (1) the time intervals between longitudinal scans are modeled explicitly, (2) temporally adjustable forget and input gates are introduced for irregular temporal sampling; and (3) the latest longitudinal scan has an additional emphasis term. We evaluate the DLSTM framework in three datasets including simulated data, 1794 National Lung Screening Trial (NLST) scans, and 1420 clinically acquired data with heterogeneous and irregular temporal accession. The experiments on the first two datasets demonstrate that our method achieves competitive performance on both simulated and regularly sampled datasets (e.g. improve LSTM from 0.6785 to 0.7085 on F1 score in NLST). In external validation of clinically and irregularly acquired data, the benchmarks achieved 0.8350 (CNN feature) and 0.8380 (LSTM) on the area under the ROC curve (AUC) score, while the proposed DLSTM achieves 0.8905.

* This paper is accepted by MLMI (oral), MICCAI workshop 

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Order-Embeddings of Images and Language

Mar 01, 2016
Ivan Vendrov, Ryan Kiros, Sanja Fidler, Raquel Urtasun

Hypernymy, textual entailment, and image captioning can be seen as special cases of a single visual-semantic hierarchy over words, sentences, and images. In this paper we advocate for explicitly modeling the partial order structure of this hierarchy. Towards this goal, we introduce a general method for learning ordered representations, and show how it can be applied to a variety of tasks involving images and language. We show that the resulting representations improve performance over current approaches for hypernym prediction and image-caption retrieval.

* ICLR camera-ready version 

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VSE++: Improving Visual-Semantic Embeddings with Hard Negatives

Jul 29, 2018
Fartash Faghri, David J. Fleet, Jamie Ryan Kiros, Sanja Fidler

We present a new technique for learning visual-semantic embeddings for cross-modal retrieval. Inspired by hard negative mining, the use of hard negatives in structured prediction, and ranking loss functions, we introduce a simple change to common loss functions used for multi-modal embeddings. That, combined with fine-tuning and use of augmented data, yields significant gains in retrieval performance. We showcase our approach, VSE++, on MS-COCO and Flickr30K datasets, using ablation studies and comparisons with existing methods. On MS-COCO our approach outperforms state-of-the-art methods by 8.8% in caption retrieval and 11.3% in image retrieval (at R@1).

* Accepted as spotlight presentation at British Machine Vision Conference (BMVC) 2018. Code: https://github.com/fartashf/vsepp 

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Human-Machine CRFs for Identifying Bottlenecks in Holistic Scene Understanding

Jun 16, 2014
Roozbeh Mottaghi, Sanja Fidler, Alan Yuille, Raquel Urtasun, Devi Parikh

Recent trends in image understanding have pushed for holistic scene understanding models that jointly reason about various tasks such as object detection, scene recognition, shape analysis, contextual reasoning, and local appearance based classifiers. In this work, we are interested in understanding the roles of these different tasks in improved scene understanding, in particular semantic segmentation, object detection and scene recognition. Towards this goal, we "plug-in" human subjects for each of the various components in a state-of-the-art conditional random field model. Comparisons among various hybrid human-machine CRFs give us indications of how much "head room" there is to improve scene understanding by focusing research efforts on various individual tasks.


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