Deniz Erdogmus

Bio: Deniz Erdogmus is an academic researcher from Northeastern University. The author has contributed to research in topics: Mutual information & Entropy (information theory). The author has an hindex of 51, co-authored 499 publications receiving 9753 citations. Previous affiliations of Deniz Erdogmus include Oregon Health & Science University & University of Florida.

Tversky loss function for image segmentation using 3D fully convolutional deep networks

Abstract: Fully convolutional deep neural networks carry out excellent potential for fast and accurate image segmentation. One of the main challenges in training these networks is data imbalance, which is particularly problematic in medical imaging applications such as lesion segmentation where the number of lesion voxels is often much lower than the number of non-lesion voxels. Training with unbalanced data can lead to predictions that are severely biased towards high precision but low recall (sensitivity), which is undesired especially in medical applications where false negatives are much less tolerable than false positives. Several methods have been proposed to deal with this problem including balanced sampling, two step training, sample re-weighting, and similarity loss functions. In this paper, we propose a generalized loss function based on the Tversky index to address the issue of data imbalance and achieve much better trade-off between precision and recall in training 3D fully convolutional deep neural networks. Experimental results in multiple sclerosis lesion segmentation on magnetic resonance images show improved \(F_2\) score, Dice coefficient, and the area under the precision-recall curve in test data. Based on these results we suggest Tversky loss function as a generalized framework to effectively train deep neural networks.

Automated Diagnosis of Plus Disease in Retinopathy of Prematurity Using Deep Convolutional Neural Networks

Abstract: Importance Retinopathy of prematurity (ROP) is a leading cause of childhood blindness worldwide. The decision to treat is primarily based on the presence of plus disease, defined as dilation and tortuosity of retinal vessels. However, clinical diagnosis of plus disease is highly subjective and variable. Objective To implement and validate an algorithm based on deep learning to automatically diagnose plus disease from retinal photographs. Design, Setting, and Participants A deep convolutional neural network was trained using a data set of 5511 retinal photographs. Each image was previously assigned a reference standard diagnosis (RSD) based on consensus of image grading by 3 experts and clinical diagnosis by 1 expert (ie, normal, pre–plus disease, or plus disease). The algorithm was evaluated by 5-fold cross-validation and tested on an independent set of 100 images. Images were collected from 8 academic institutions participating in the Imaging and Informatics in ROP (i-ROP) cohort study. The deep learning algorithm was tested against 8 ROP experts, each of whom had more than 10 years of clinical experience and more than 5 peer-reviewed publications about ROP. Data were collected from July 2011 to December 2016. Data were analyzed from December 2016 to September 2017. Exposures A deep learning algorithm trained on retinal photographs. Main Outcomes and Measures Receiver operating characteristic analysis was performed to evaluate performance of the algorithm against the RSD. Quadratic-weighted κ coefficients were calculated for ternary classification (ie, normal, pre–plus disease, and plus disease) to measure agreement with the RSD and 8 independent experts. Results Of the 5511 included retinal photographs, 4535 (82.3%) were graded as normal, 805 (14.6%) as pre–plus disease, and 172 (3.1%) as plus disease, based on the RSD. Mean (SD) area under the receiver operating characteristic curve statistics were 0.94 (0.01) for the diagnosis of normal (vs pre–plus disease or plus disease) and 0.98 (0.01) for the diagnosis of plus disease (vs normal or pre–plus disease). For diagnosis of plus disease in an independent test set of 100 retinal images, the algorithm achieved a sensitivity of 93% with 94% specificity. For detection of pre–plus disease or worse, the sensitivity and specificity were 100% and 94%, respectively. On the same test set, the algorithm achieved a quadratic-weighted κ coefficient of 0.92 compared with the RSD, outperforming 6 of 8 ROP experts. Conclusions and Relevance This fully automated algorithm diagnosed plus disease in ROP with comparable or better accuracy than human experts. This has potential applications in disease detection, monitoring, and prognosis in infants at risk of ROP.

An error-entropy minimization algorithm for supervised training of nonlinear adaptive systems

Abstract: The paper investigates error-entropy-minimization in adaptive systems training. We prove the equivalence between minimization of error's Renyi (1970) entropy of order /spl alpha/ and minimization of a Csiszar (1981) distance measure between the densities of desired and system outputs. A nonparametric estimator for Renyi's entropy is presented, and it is shown that the global minimum of this estimator is the same as the actual entropy. The performance of the error-entropy-minimization criterion is compared with mean-square-error-minimization in the short-term prediction of a chaotic time series and in nonlinear system identification.

The Future of Human-in-the-Loop Cyber-Physical Systems

Abstract: A prototyping platform and a design framework for rapid exploration of a novel human-in-the-loop application serves as an accelerator for new research into a broad class of systems that augment human interaction with the physical world.

Generalized information potential criterion for adaptive system training

Abstract: We have previously proposed the quadratic Renyi's error entropy as an alternative cost function for supervised adaptive system training. An entropy criterion instructs the minimization of the average information content of the error signal rather than merely trying to minimize its energy. In this paper, we propose a generalization of the error entropy criterion that enables the use of any order of Renyi's entropy and any suitable kernel function in density estimation. It is shown that the proposed entropy estimator preserves the global minimum of actual entropy. The equivalence between global optimization by convolution smoothing and the convolution by the kernel in Parzen windowing is also discussed. Simulation results are presented for time-series prediction and classification where experimental demonstration of all the theoretical concepts is presented.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

Machine learning

Abstract: Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Pattern Recognition and Machine Learning

Abstract: Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.