Publications

Combining intraoperative ultrasound brain shift correction and augmented reality visualizations: a pilot study of eight cases
Ian J. Gerard
Marta Kersten-Oertel
Simon Drouin
Jeffery A. Hall
Kevin Petrecca
Dante De Nigris
Daniel A. Di Giovanni
Tal Arbel
D. Louis Collins
Abstract. We present our work investigating the feasibility of combining intraoperative ultrasound for brain shift correction and augmented … (see more)reality (AR) visualization for intraoperative interpretation of patient-specific models in image-guided neurosurgery (IGNS) of brain tumors. We combine two imaging technologies for image-guided brain tumor neurosurgery. Throughout surgical interventions, AR was used to assess different surgical strategies using three-dimensional (3-D) patient-specific models of the patient’s cortex, vasculature, and lesion. Ultrasound imaging was acquired intraoperatively, and preoperative images and models were registered to the intraoperative data. The quality and reliability of the AR views were evaluated with both qualitative and quantitative metrics. A pilot study of eight patients demonstrates the feasible combination of these two technologies and their complementary features. In each case, the AR visualizations enabled the surgeon to accurately visualize the anatomy and pathology of interest for an extended period of the intervention. Inaccuracies associated with misregistration, brain shift, and AR were improved in all cases. These results demonstrate the potential of combining ultrasound-based registration with AR to become a useful tool for neurosurgeons to improve intraoperative patient-specific planning by improving the understanding of complex 3-D medical imaging data and prolonging the reliable use of IGNS.
2018-01-26
Journal of Medical Imaging (published)
doi.org
Modular Networks for Validating Community Detection Algorithms
Justin J Fagnan
Afra Abnar
Reihaneh Rabbany
Osmar R Zaiane
How can we accurately compare different community detection algorithms? These algorithms cluster nodes in a given network, and their perform… (see more)ance is often validated on benchmark networks with explicit ground-truth communities. Given the lack of cluster labels in real-world networks, a model that generates realistic networks is required for accurate evaluation of these algorithm. In this paper, we present a simple, intuitive, and flexible benchmark generator to generate intrinsically modular networks for community validation. We show how the generated networks closely comply with the characteristics observed for real networks; whereas their characteristics could be directly controlled to match wide range of real world networks. We further show how common community detection algorithms rank differently when being evaluated on these benchmarks compared to current available alternatives.
2018-01-04
ArXiv (preprint)
arxiv.org
arxiv.org
Accelerated Stochastic Power Iteration
Peng Xu
Bryan Dawei He
Christopher De Sa
Ioannis Mitliagkas
Christopher Re
Principal component analysis (PCA) is one of the most powerful tools in machine learning. The simplest method for PCA, the power iteration, … (see more)requires O ( 1 / Δ ) full-data passes to recover the principal component of a matrix with eigen-gap Δ. Lanczos, a significantly more complex method, achieves an accelerated rate of O ( 1 / Δ ) passes. Modern applications, however, motivate methods that only ingest a subset of available data, known as the stochastic setting. In the online stochastic setting, simple algorithms like Oja's iteration achieve the optimal sample complexity O ( σ 2 / Δ 2 ) . Unfortunately, they are fully sequential, and also require O ( σ 2 / Δ 2 ) iterations, far from the O ( 1 / Δ ) rate of Lanczos. We propose a simple variant of the power iteration with an added momentum term, that achieves both the optimal sample and iteration complexity. In the full-pass setting, standard analysis shows that momentum achieves the accelerated rate, O ( 1 / Δ ) . We demonstrate empirically that naively applying momentum to a stochastic method, does not result in acceleration. We perform a novel, tight variance analysis that reveals the "breaking-point variance" beyond which this acceleration does not occur. By combining this insight with modern variance reduction techniques, we construct stochastic PCA algorithms, for the online and offline setting, that achieve an accelerated iteration complexity O ( 1 / Δ ) . Due to the embarassingly parallel nature of our methods, this acceleration translates directly to wall-clock time if deployed in a parallel environment. Our approach is very general, and applies to many non-convex optimization problems that can now be accelerated using the same technique.
2018-01-01
AISTATS (published)
proceedings.mlr.press
arxiv.org
Advances in Artificial Intelligence
Ebrahim Bagheri
Jackie Cheung
2018-01-01
Lecture Notes in Computer Science (published)
doi.org
Advances in Artificial Intelligence
Ebrahim Bagheri
Jackie Cheung
2018-01-01
Lecture Notes in Computer Science (published)
doi.org
Automatic differentiation in ML: Where we are and where we should be going
Bart van Merriënboer
Olivier Breuleux
Arnaud Bergeron
Pascal Lamblin
We review the current state of automatic differentiation (AD) for array programming in machine learning (ML), including the different approa… (see more)ches such as operator overloading (OO) and source transformation (ST) used for AD, graph-based intermediate representations for programs, and source languages. Based on these insights, we introduce a new graph-based intermediate representation (IR) which specifically aims to efficiently support fully-general AD for array programming. Unlike existing dataflow programming representations in ML frameworks, our IR naturally supports function calls, higher-order functions and recursion, making ML models easier to implement. The ability to represent closures allows us to perform AD using ST without a tape, making the resulting derivative (adjoint) program amenable to ahead-of-time optimization using tools from functional language compilers, and enabling higher-order derivatives. Lastly, we introduce a proof of concept compiler toolchain called Myia which uses a subset of Python as a front end.
2018-01-01
NeurIPS (published)
arxiv.org
arxiv.org
Challenging Conventional Segmentation Evaluation Metrics Focal Pathology ( Lesion and Tumour ) Segmentation from Patient Images
Tal Arbel
2018-01-01
(published)
www.semanticscholar.org
Frank-Wolfe Splitting via Augmented Lagrangian Method
Gauthier Gidel
Fabian Pedregosa
Simon Lacoste-Julien
Minimizing a function over an intersection of convex sets is an important task in optimization that is often much more challenging than mini… (see more)mizing it over each individual constraint set. While traditional methods such as Frank-Wolfe (FW) or proximal gradient descent assume access to a linear or quadratic oracle on the intersection, splitting techniques take advantage of the structure of each sets, and only require access to the oracle on the individual constraints. In this work, we develop and analyze the Frank-Wolfe Augmented Lagrangian (FW-AL) algorithm, a method for minimizing a smooth function over convex compact sets related by a "linear consistency" constraint that only requires access to a linear minimization oracle over the individual constraints. It is based on the Augmented Lagrangian Method (ALM), also known as Method of Multipliers, but unlike most existing splitting methods, it only requires access to linear (instead of quadratic) minimization oracles. We use recent advances in the analysis of Frank-Wolfe and the alternating direction method of multipliers algorithms to prove a sublinear convergence rate for FW-AL over general convex compact sets and a linear convergence rate for polytopes.
2018-01-01
AISTATS (published)
proceedings.mlr.press
arxiv.org
A Hierarchical Neural Attention-based Text Classifier
Koustuv Sinha
Yue Dong
Jackie Cheung
Derek Ruths
Deep neural networks have been displaying superior performance over traditional supervised classifiers in text classification. They learn to… (see more) extract useful features automatically when sufficient amount of data is presented. However, along with the growth in the number of documents comes the increase in the number of categories, which often results in poor performance of the multiclass classifiers. In this work, we use external knowledge in the form of topic category taxonomies to aide the classification by introducing a deep hierarchical neural attention-based classifier. Our model performs better than or comparable to state-of-the-art hierarchical models at significantly lower computational cost while maintaining high interpretability.
2018-01-01
Conference on Empirical Methods in Natural Language Processing (published)
doi.org
How can we do better ? Pitfalls in biomedical challenge design and how to address them
Annika Reinke
Matthias Eisenmann
Sinan Onogur
Marko Stankovic
Patrick Scholz
Tal Arbel
Hrvoje Bogunovic
Andrew P. Bradley
Aaron
Carass
Carolin Feldmann
Alejandro F. Frangi
Peter M. Full
Bram Ginneken Van
Ginneken
Allan Hanbury
Katrin Honauer
Michal Kozubek
Adam Bennett
Landman … (see 22 more)
Keno März
Oskar Maier
Klaus Maier-Hein
Bjoern Menze
Henning Müller
Peter F. Neher
Wiro Niessen
Nasir Rajpoot
Catherine Gregory
Sharp
Korsuk Sirinukunwattana
Stefanie Speidel
Christian Stock
Danail
Stoyanov
Abdel Aziz Taha
F. V. D. Sommen
Ching-Wei Wang
Marc-André Weber
Guoyan Zheng
Pierre Jannin
Lena Maier-Hein
Since the first MICCAI grand challenge was organized in 2007 [1], the impact of biomedical image analysis challenges on both the research fi… (see more)eld as well as on individual careers has been steadily growing. For example, the acceptance of a journal article today often depends on the performance of a new algorithm being assessed against the state-ofthe-art work on publicly available challenge datasets. Furthermore, the results are also important for the individuals scientific careers as well as the potential that algorithms can be translated into clinical practice. Yet, while the publication of papers in scientific journals and prestigious conferences, such as MICCAI, undergoes strict quality control, the design and organization of challenges do not. To investigate the effect of common practice, we have formed an international initiative dedicated to analyzing and improving a variety of aspects related to biomedical challenge design, execution and reporting [2]. In the first part of our abstract presentation at LABELS workshop, we are going to present some of the major pitfalls related to biomedical image analysis challenges today. Specifically, we will look at the following research questions: RQ1: How robust are challenge rankings? What is the effect of – the specific test cases used? – the specific metric variant(s) applied? – the rank aggregation method chosen (e.g. aggregation of metric values with the mean vs median)? ? Shared first/senior authors.
2018-01-01
(published)
www.semanticscholar.org
Learning Graph Weighted Models on Pictures
Philip Amortila
Guillaume Rabusseau
Graph Weighted Models (GWMs) have recently been proposed as a natural generalization of weighted automata over strings and trees to arbitrar… (see more)y families of labeled graphs (and hypergraphs). A GWM generically associates a labeled graph with a tensor network and computes a value by successive contractions directed by its edges. In this paper, we consider the problem of learning GWMs defined over the graph family of pictures (or 2-dimensional words). As a proof of concept, we consider regression and classification tasks over the simple Bars & Stripes and Shifting Bits picture languages and provide an experimental study investigating whether these languages can be learned in the form of a GWM from positive and negative examples using gradient-based methods. Our results suggest that this is indeed possible and that investigating the use of gradient-based methods to learn picture series and functions computed by GWMs over other families of graphs could be a fruitful direction.
2018-01-01
ICGI (published)
proceedings.mlr.press
arxiv.org
Nash equilibria for integer programming games
Margarida Carvalho
Andrea Lodi
João Pedro Pedroso
In this paper, we develop algorithmic approaches for a recently defined class of games, the integer programming games. Two general methods t… (see more)o approximate an equilibrium are presented and enhanced in order to improve their practical efficiency. Their performance is analysed through computational experiments in a knapsack game and a competitive lot-sizing game. To the best of our knowledge, this is the first time that equilibria computation methods for general integer programming games are build and computationally tested.
2018-01-01
(published)
www.semanticscholar.org