3,380 results on '"Ergen A"'
Search Results
2. Investigation of RASSF4 gene in head and neck cancers
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Karagedik Emine H., Pamuk Saim, Ataş Merve N., Ulusan Murat, Aydemir Levent, and Ergen Arzu
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elisa ,gene expression ,head and neck ,polymorphism ,rassf4 ,gen anlatımı ,baş boyun ,polimorfizm ,Biochemistry ,QD415-436 - Abstract
RASSF gene family can inhibit the growth of RAS oncogene. This gene family is suggested to have a role in cell cycle control, apoptosis, cell migration, and mitosis control. This study evaluated RASSF4 gene expression levels, SNPs and serum levels in tissues dissected from both healthy individuals and patients diagnosed with head, and neck cancer.
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- 2021
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3. SPRIG: Improving Large Language Model Performance by System Prompt Optimization
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Zhang, Lechen, Ergen, Tolga, Logeswaran, Lajanugen, Lee, Moontae, and Jurgens, David
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Human-Computer Interaction ,Computer Science - Machine Learning - Abstract
Large Language Models (LLMs) have shown impressive capabilities in many scenarios, but their performance depends, in part, on the choice of prompt. Past research has focused on optimizing prompts specific to a task. However, much less attention has been given to optimizing the general instructions included in a prompt, known as a system prompt. To address this gap, we propose SPRIG, an edit-based genetic algorithm that iteratively constructs prompts from prespecified components to maximize the model's performance in general scenarios. We evaluate the performance of system prompts on a collection of 47 different types of tasks to ensure generalizability. Our study finds that a single optimized system prompt performs on par with task prompts optimized for each individual task. Moreover, combining system and task-level optimizations leads to further improvement, which showcases their complementary nature. Experiments also reveal that the optimized system prompts generalize effectively across model families, parameter sizes, and languages. This study provides insights into the role of system-level instructions in maximizing LLM potential.
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- 2024
4. A Generally Covariant Model of Spacetime as a 4-Brane in 4+1 Flat Dimensions
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Ergen, Mert and Arık, Metin
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General Relativity and Quantum Cosmology ,High Energy Physics - Theory - Abstract
We construct a simple model of a closed FLRW spacetime by starting from a flat five dimensional scalar field space with a quartic potential. The action contains no curvature terms. The spacetime metric is uniquely determined from the dynamical equations of the metric tensor. An SO(4) invariant ansatz for the scalar fields is shown to lead to a linearly expanding universe provided that the cosmological constant is negative.
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- 2024
5. Hearing Your Blood Sugar: Non-Invasive Glucose Measurement Through Simple Vocal Signals, Transforming any Speech into a Sensor with Machine Learning
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Ahmadli, Nihat, Sarsil, Mehmet Ali, and Ergen, Onur
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Computer Science - Machine Learning ,Computer Science - Sound ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
Effective diabetes management relies heavily on the continuous monitoring of blood glucose levels, traditionally achieved through invasive and uncomfortable methods. While various non-invasive techniques have been explored, such as optical, microwave, and electrochemical approaches, none have effectively supplanted these invasive technologies due to issues related to complexity, accuracy, and cost. In this study, we present a transformative and straightforward method that utilizes voice analysis to predict blood glucose levels. Our research investigates the relationship between fluctuations in blood glucose and vocal characteristics, highlighting the influence of blood vessel dynamics during voice production. By applying advanced machine learning algorithms, we analyzed vocal signal variations and established a significant correlation with blood glucose levels. We developed a predictive model using artificial intelligence, based on voice recordings and corresponding glucose measurements from participants, utilizing logistic regression and Ridge regularization. Our findings indicate that voice analysis may serve as a viable non-invasive alternative for glucose monitoring. This innovative approach not only has the potential to streamline and reduce the costs associated with diabetes management but also aims to enhance the quality of life for individuals living with diabetes by providing a painless and user-friendly method for monitoring blood sugar levels., Comment: 5 figure and 5 tables. This manuscript is a pre-print to be submitted to a journal or/and a conference. arXiv admin note: substantial text overlap with arXiv:2402.13812
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- 2024
6. MASSW: A New Dataset and Benchmark Tasks for AI-Assisted Scientific Workflows
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Zhang, Xingjian, Xie, Yutong, Huang, Jin, Ma, Jinge, Pan, Zhaoying, Liu, Qijia, Xiong, Ziyang, Ergen, Tolga, Shim, Dongsub, Lee, Honglak, and Mei, Qiaozhu
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
Scientific innovation relies on detailed workflows, which include critical steps such as analyzing literature, generating ideas, validating these ideas, interpreting results, and inspiring follow-up research. However, scientific publications that document these workflows are extensive and unstructured. This makes it difficult for both human researchers and AI systems to effectively navigate and explore the space of scientific innovation. To address this issue, we introduce MASSW, a comprehensive text dataset on Multi-Aspect Summarization of Scientific Workflows. MASSW includes more than 152,000 peer-reviewed publications from 17 leading computer science conferences spanning the past 50 years. Using Large Language Models (LLMs), we automatically extract five core aspects from these publications -- context, key idea, method, outcome, and projected impact -- which correspond to five key steps in the research workflow. These structured summaries facilitate a variety of downstream tasks and analyses. The quality of the LLM-extracted summaries is validated by comparing them with human annotations. We demonstrate the utility of MASSW through multiple novel machine-learning tasks that can be benchmarked using this new dataset, which make various types of predictions and recommendations along the scientific workflow. MASSW holds significant potential for researchers to create and benchmark new AI methods for optimizing scientific workflows and fostering scientific innovation in the field. Our dataset is openly available at \url{https://github.com/xingjian-zhang/massw}., Comment: arXiv admin note: text overlap with arXiv:1706.03762 by other authors
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- 2024
7. A Library of Mirrors: Deep Neural Nets in Low Dimensions are Convex Lasso Models with Reflection Features
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Zeger, Emi, Wang, Yifei, Mishkin, Aaron, Ergen, Tolga, Candès, Emmanuel, and Pilanci, Mert
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Computer Science - Neural and Evolutionary Computing ,Mathematics - Optimization and Control ,Statistics - Machine Learning - Abstract
We prove that training neural networks on 1-D data is equivalent to solving convex Lasso problems with discrete, explicitly defined dictionary matrices. We consider neural networks with piecewise linear activations and depths ranging from 2 to an arbitrary but finite number of layers. We first show that two-layer networks with piecewise linear activations are equivalent to Lasso models using a discrete dictionary of ramp functions, with breakpoints corresponding to the training data points. In certain general architectures with absolute value or ReLU activations, a third layer surprisingly creates features that reflect the training data about themselves. Additional layers progressively generate reflections of these reflections. The Lasso representation provides valuable insights into the analysis of globally optimal networks, elucidating their solution landscapes and enabling closed-form solutions in certain special cases. Numerical results show that reflections also occur when optimizing standard deep networks using standard non-convex optimizers. Additionally, we demonstrate our theory with autoregressive time series models.
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- 2024
8. Successful Management of a Pediatric Patient with Humeral Lateral Condyle Non-union, Elbow Valgus Deformity and Ulnar Neuropathy
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Çoban, İdris, Karakaplan, Mustafa, Ergen, Emre, Aslantürk, Okan, Köroğlu, Muhammed, and Ertem, Kadir
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- 2024
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9. Total Completion Time Scheduling Under Scenarios
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Bosman, Thomas, van Ee, Martijn, Ergen, Ekin, Imreh, Csanad, Marchetti-Spaccamela, Alberto, Skutella, Martin, and Stougie, Leen
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Computer Science - Data Structures and Algorithms - Abstract
Scheduling jobs with given processing times on identical parallel machines so as to minimize their total completion time is one of the most basic scheduling problems. We study interesting generalizations of this classical problem involving scenarios. In our model, a scenario is defined as a subset of a predefined and fully specified set of jobs. The aim is to find an assignment of the whole set of jobs to identical parallel machines such that the schedule, obtained for the given scenarios by simply skipping the jobs not in the scenario, optimizes a function of the total completion times over all scenarios. While the underlying scheduling problem without scenarios can be solved efficiently by a simple greedy procedure (SPT rule), scenarios, in general, make the problem NP-hard. We paint an almost complete picture of the evolving complexity landscape, drawing the line between easy and hard. One of our main algorithmic contributions relies on a deep structural result on the maximum imbalance of an optimal schedule, based on a subtle connection to Hilbert bases of a related convex cone.
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- 2024
10. Voice-Driven Mortality Prediction in Hospitalized Heart Failure Patients: A Machine Learning Approach Enhanced with Diagnostic Biomarkers
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Ahmadli, Nihat, Sarsil, Mehmet Ali, Mizrak, Berk, Karauzum, Kurtulus, Shaker, Ata, Tulumen, Erol, Mirzamidinov, Didar, Ural, Dilek, and Ergen, Onur
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Computer Science - Machine Learning ,Computer Science - Sound ,Electrical Engineering and Systems Science - Audio and Speech Processing - Abstract
Addressing heart failure (HF) as a prevalent global health concern poses difficulties in implementing innovative approaches for enhanced patient care. Predicting mortality rates in HF patients, in particular, is difficult yet critical, necessitating individualized care, proactive management, and enabling educated decision-making to enhance outcomes. Recently, the significance of voice biomarkers coupled with Machine Learning (ML) has surged, demonstrating remarkable efficacy, particularly in predicting heart failure. The synergy of voice analysis and ML algorithms provides a non-invasive and easily accessible means to evaluate patients' health. However, there is a lack of voice biomarkers for predicting mortality rates among heart failure patients with standardized speech protocols. Here, we demonstrate a powerful and effective ML model for predicting mortality rates in hospitalized HF patients through the utilization of voice biomarkers. By seamlessly integrating voice biomarkers into routine patient monitoring, this strategy has the potential to improve patient outcomes, optimize resource allocation, and advance patient-centered HF management. In this study, a Machine Learning system, specifically a logistic regression model, is trained to predict patients' 5-year mortality rates using their speech as input. The model performs admirably and consistently, as demonstrated by cross-validation and statistical approaches (p-value < 0.001). Furthermore, integrating NT-proBNP, a diagnostic biomarker in HF, improves the model's predictive accuracy substantially., Comment: 11 pages, 6 figures, 5 tables. The first 2 authors have contributed equally
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- 2024
11. The Convex Landscape of Neural Networks: Characterizing Global Optima and Stationary Points via Lasso Models
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Ergen, Tolga and Pilanci, Mert
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Mathematics - Optimization and Control ,Statistics - Machine Learning - Abstract
Due to the non-convex nature of training Deep Neural Network (DNN) models, their effectiveness relies on the use of non-convex optimization heuristics. Traditional methods for training DNNs often require costly empirical methods to produce successful models and do not have a clear theoretical foundation. In this study, we examine the use of convex optimization theory and sparse recovery models to refine the training process of neural networks and provide a better interpretation of their optimal weights. We focus on training two-layer neural networks with piecewise linear activations and demonstrate that they can be formulated as a finite-dimensional convex program. These programs include a regularization term that promotes sparsity, which constitutes a variant of group Lasso. We first utilize semi-infinite programming theory to prove strong duality for finite width neural networks and then we express these architectures equivalently as high dimensional convex sparse recovery models. Remarkably, the worst-case complexity to solve the convex program is polynomial in the number of samples and number of neurons when the rank of the data matrix is bounded, which is the case in convolutional networks. To extend our method to training data of arbitrary rank, we develop a novel polynomial-time approximation scheme based on zonotope subsampling that comes with a guaranteed approximation ratio. We also show that all the stationary of the nonconvex training objective can be characterized as the global optimum of a subsampled convex program. Our convex models can be trained using standard convex solvers without resorting to heuristics or extensive hyper-parameter tuning unlike non-convex methods. Through extensive numerical experiments, we show that convex models can outperform traditional non-convex methods and are not sensitive to optimizer hyperparameters., Comment: A preliminary version of part of this work was published at ICML 2020 with the title "Neural Networks are Convex Regularizers: Exact Polynomial-time Convex Optimization Formulations for Two-layer Networks"
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- 2023
12. The Energy Prediction Smart-Meter Dataset: Analysis of Previous Competitions and Beyond
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Pekaslan, Direnc, Alonso-Moral, Jose Maria, Bandara, Kasun, Bergmeir, Christoph, Bernabe-Moreno, Juan, Eigenmann, Robert, Einecke, Nils, Ergen, Selvi, Godahewa, Rakshitha, Hewamalage, Hansika, Lago, Jesus, Limmer, Steffen, Rebhan, Sven, Rabinovich, Boris, Rajapasksha, Dilini, Song, Heda, Wagner, Christian, Wu, Wenlong, Magdalena, Luis, and Triguero, Isaac
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence - Abstract
This paper presents the real-world smart-meter dataset and offers an analysis of solutions derived from the Energy Prediction Technical Challenges, focusing primarily on two key competitions: the IEEE Computational Intelligence Society (IEEE-CIS) Technical Challenge on Energy Prediction from Smart Meter data in 2020 (named EP) and its follow-up challenge at the IEEE International Conference on Fuzzy Systems (FUZZ-IEEE) in 2021 (named as XEP). These competitions focus on accurate energy consumption forecasting and the importance of interpretability in understanding the underlying factors. The challenge aims to predict monthly and yearly estimated consumption for households, addressing the accurate billing problem with limited historical smart meter data. The dataset comprises 3,248 smart meters, with varying data availability ranging from a minimum of one month to a year. This paper delves into the challenges, solutions and analysing issues related to the provided real-world smart meter data, developing accurate predictions at the household level, and introducing evaluation criteria for assessing interpretability. Additionally, this paper discusses aspects beyond the competitions: opportunities for energy disaggregation and pattern detection applications at the household level, significance of communicating energy-driven factors for optimised billing, and emphasising the importance of responsible AI and data privacy considerations. These aspects provide insights into the broader implications and potential advancements in energy consumption prediction. Overall, these competitions provide a dataset for residential energy research and serve as a catalyst for exploring accurate forecasting, enhancing interpretability, and driving progress towards the discussion of various aspects such as energy disaggregation, demand response programs or behavioural interventions.
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- 2023
13. Topological Expressivity of ReLU Neural Networks
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Ergen, Ekin and Grillo, Moritz
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Computer Science - Machine Learning ,Computer Science - Discrete Mathematics ,Mathematics - Algebraic Topology - Abstract
We study the expressivity of ReLU neural networks in the setting of a binary classification problem from a topological perspective. Recently, empirical studies showed that neural networks operate by changing topology, transforming a topologically complicated data set into a topologically simpler one as it passes through the layers. This topological simplification has been measured by Betti numbers, which are algebraic invariants of a topological space. We use the same measure to establish lower and upper bounds on the topological simplification a ReLU neural network can achieve with a given architecture. We therefore contribute to a better understanding of the expressivity of ReLU neural networks in the context of binary classification problems by shedding light on their ability to capture the underlying topological structure of the data. In particular the results show that deep ReLU neural networks are exponentially more powerful than shallow ones in terms of topological simplification. This provides a mathematically rigorous explanation why deeper networks are better equipped to handle complex and topologically rich data sets., Comment: 44 pages, to appear in COLT 2024
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- 2023
14. Fixing the NTK: From Neural Network Linearizations to Exact Convex Programs
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Dwaraknath, Rajat Vadiraj, Ergen, Tolga, and Pilanci, Mert
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
Recently, theoretical analyses of deep neural networks have broadly focused on two directions: 1) Providing insight into neural network training by SGD in the limit of infinite hidden-layer width and infinitesimally small learning rate (also known as gradient flow) via the Neural Tangent Kernel (NTK), and 2) Globally optimizing the regularized training objective via cone-constrained convex reformulations of ReLU networks. The latter research direction also yielded an alternative formulation of the ReLU network, called a gated ReLU network, that is globally optimizable via efficient unconstrained convex programs. In this work, we interpret the convex program for this gated ReLU network as a Multiple Kernel Learning (MKL) model with a weighted data masking feature map and establish a connection to the NTK. Specifically, we show that for a particular choice of mask weights that do not depend on the learning targets, this kernel is equivalent to the NTK of the gated ReLU network on the training data. A consequence of this lack of dependence on the targets is that the NTK cannot perform better than the optimal MKL kernel on the training set. By using iterative reweighting, we improve the weights induced by the NTK to obtain the optimal MKL kernel which is equivalent to the solution of the exact convex reformulation of the gated ReLU network. We also provide several numerical simulations corroborating our theory. Additionally, we provide an analysis of the prediction error of the resulting optimal kernel via consistency results for the group lasso., Comment: Accepted to Neurips 2023
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- 2023
15. CalibFPA: A Focal Plane Array Imaging System based on Online Deep-Learning Calibration
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Güngör, Alper, Bahceci, M. Umut, Ergen, Yasin, Sözak, Ahmet, Ekiz, O. Oner, Yelboga, Tolga, and Çukur, Tolga
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Compressive focal plane arrays (FPA) enable cost-effective high-resolution (HR) imaging by acquisition of several multiplexed measurements on a low-resolution (LR) sensor. Multiplexed encoding of the visual scene is typically performed via electronically controllable spatial light modulators (SLM). An HR image is then reconstructed from the encoded measurements by solving an inverse problem that involves the forward model of the imaging system. To capture system non-idealities such as optical aberrations, a mainstream approach is to conduct an offline calibration scan to measure the system response for a point source at each spatial location on the imaging grid. However, it is challenging to run calibration scans when using structured SLMs as they cannot encode individual grid locations. In this study, we propose a novel compressive FPA system based on online deep-learning calibration of multiplexed LR measurements (CalibFPA). We introduce a piezo-stage that locomotes a pre-printed fixed coded aperture. A deep neural network is then leveraged to correct for the influences of system non-idealities in multiplexed measurements without the need for offline calibration scans. Finally, a deep plug-and-play algorithm is used to reconstruct images from corrected measurements. On simulated and experimental datasets, we demonstrate that CalibFPA outperforms state-of-the-art compressive FPA methods. We also report analyses to validate the design elements in CalibFPA and assess computational complexity.
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- 2023
16. Single-cell multiomic analysis of thymocyte development reveals drivers of CD4+ T cell and CD8+ T cell lineage commitment.
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Steier, Zoë, Aylard, Dominik, McIntyre, Laura, Baldwin, Isabel, Kim, Esther, Lutes, Lydia, Ergen, Can, Huang, Tse-Shun, Yosef, Nir, Robey, Ellen, and Streets, Aaron
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Mice ,Animals ,CD8-Positive T-Lymphocytes ,Cell Lineage ,CD4-Positive T-Lymphocytes ,Thymocytes ,Multiomics ,Mice ,Transgenic ,Cell Differentiation ,Receptors ,Antigen ,T-Cell ,Thymus Gland ,Histocompatibility Antigens Class I ,CD4 Antigens - Abstract
The development of CD4+ T cells and CD8+ T cells in the thymus is critical to adaptive immunity and is widely studied as a model of lineage commitment. Recognition of self-peptide major histocompatibility complex (MHC) class I or II by the T cell antigen receptor (TCR) determines the CD8+ or CD4+ T cell lineage choice, respectively, but how distinct TCR signals drive transcriptional programs of lineage commitment remains largely unknown. Here we applied CITE-seq to measure RNA and surface proteins in thymocytes from wild-type and T cell lineage-restricted mice to generate a comprehensive timeline of cell states for each T cell lineage. These analyses identified a sequential process whereby all thymocytes initiate CD4+ T cell lineage differentiation during a first wave of TCR signaling, followed by a second TCR signaling wave that coincides with CD8+ T cell lineage specification. CITE-seq and pharmaceutical inhibition experiments implicated a TCR-calcineurin-NFAT-GATA3 axis in driving the CD4+ T cell fate. Our data provide a resource for understanding cell fate decisions and implicate a sequential selection process in guiding lineage choice.
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- 2023
17. Cerebrotendinous Xanthomatosis patients with late diagnosed in single orthopedic clinic: two novel variants in the CYP27A1 gene
- Author
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Köroğlu, Muhammed, Karakaplan, Mustafa, Gündüz, Enes, Kesriklioğlu, Betül, Ergen, Emre, Aslantürk, Okan, and Özdemir, Zeynep Maraş
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- 2024
- Full Text
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18. Globally Optimal Training of Neural Networks with Threshold Activation Functions
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Ergen, Tolga, Gulluk, Halil Ibrahim, Lacotte, Jonathan, and Pilanci, Mert
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
Threshold activation functions are highly preferable in neural networks due to their efficiency in hardware implementations. Moreover, their mode of operation is more interpretable and resembles that of biological neurons. However, traditional gradient based algorithms such as Gradient Descent cannot be used to train the parameters of neural networks with threshold activations since the activation function has zero gradient except at a single non-differentiable point. To this end, we study weight decay regularized training problems of deep neural networks with threshold activations. We first show that regularized deep threshold network training problems can be equivalently formulated as a standard convex optimization problem, which parallels the LASSO method, provided that the last hidden layer width exceeds a certain threshold. We also derive a simplified convex optimization formulation when the dataset can be shattered at a certain layer of the network. We corroborate our theoretical results with various numerical experiments., Comment: Accepted to ICLR 2023
- Published
- 2023
19. Effect of propofol induction on antioxidant defense system, cytokines, and cd4+ and cd8+ T cells in cats
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Didar AYDIN KAYA, Özlem GÜZEL, Duygu SEZER, Gülşen SEVİM, Erdal MATUR, Ezgi ERGEN, Feraye Esen GÜRSEL, and Gizem ATMACA
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antioxidant ,cat ,cytokine ,propofol ,t cells ,Veterinary medicine ,SF600-1100 - Abstract
We investigated the effects of propofol on the antioxidant defense mechanisms, pro and anti-inflammatory cytokine expressions and specific defense processes in the study since these parameters play a significant role in postoperative complications, regulation of immune reactions, and wound healing. Twenty male cats were included in the study, anesthesia protocol was induced by IV administration of 6 mg/kg of propofol. Blood samples were harvested right before (T0) and fifteen minutes after (T1) propofol injection. Serum malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), IL-4, IL-8, TNF-α, IL-1β, and IFN-γ levels; the number of CD4+, CD8+ T cells and CD4/CD8 ratio in peripheral blood were determined. Propofol reduced the serum MDA and GSH-Px, while CAT and SOD levels remained unchanged. Furthermore, propofol did not impact serum IL-8, TNF-α, and IL-1β levels. Contrastingly, IFN-γ level tended to elevate, and serum IL-4 level was significantly increased. On the other hand, the CD8+ T cell population was significantly decreased, while the number of CD4+ T cells and the CD4/CD8 ratio were unaffected. Briefly, propofol did not adversely affect oxidative defense mechanisms, proinflammatory and anti-inflammatory cytokine cascade, and cell mediated immunity. Considering the insufficiency of cats" hepatic drug metabolism, we may conclude that propofol is a safe product regarding the investigated parameters.
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- 2024
- Full Text
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20. Edge computing in future wireless networks: A comprehensive evaluation and vision for 6G and beyond
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Ergen, Mustafa, Saoud, Bilal, Shayea, Ibraheem, El-Saleh, Ayman A., Ergen, Onur, Inan, Feride, and Tuysuz, Mehmet Fatih
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- 2024
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21. Role of VDR gene polymorphisms and vitamin D levels in normal and overweight patients with PCOS
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Sağlam, Zümrüt Mine Işik, Bakir, Vuslat Lale, Ataş, Merve Nur, and Ergen, H. Arzu
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- 2024
- Full Text
- View/download PDF
22. Integration of 5G, 6G and IoT with Low Earth Orbit (LEO) networks: Opportunity, challenges and future trends
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Ibraheem Shayea, Ayman A. El-Saleh, Mustafa Ergen, Bilal Saoud, Riad Hartani, Derya Turan, and Adnan Kabbani
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Fifth generation (5G) ,Future mobile broadband networks ,Integration ,Land mobile satellite system ,Satellite ,Satellite challenges ,Technology - Abstract
The rapid growth of the massive smart Internet of Things (IoT) with mobile connections, the enhanced Mobile Broadband (eMBB) and the high demand for building a connected and intelligent world increase the probability of mobile satellite systems to be a major network in providing internet communication services in the future. Currently, the mobile satellite systems are envisioned as a significant solution for providing mobile services in different settings and for various vital objectives. These satellite systems have special qualities in each of these situations, including extensive coverage area, robustness, and ability to broadcast/multicast. The Low Earth Orbit (LEO) systems are the best promising technology that will offer internet services among the different types of satellite systems. However, the LEO systems are still experiencing certain restrictions with respect to connectivity, stability, and mobility support; because of which communication becomes unreliable. Therefore, the aim of this paper is to broadly explain the LEO systems and services in a comprehensive manner using a variety of perspectives. The paper focus is on key aspects of mobile internet based on satellite systems. This paper illustrates the integration of LEO systems with fifth and sixth generations of mobile cellular networks as well as with the IoT networks. It discusses the problems being faced as a result of the integration between cellular with IoT and satellite systems by comprehending which future research plans are outlined.
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- 2024
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23. Convexifying Transformers: Improving optimization and understanding of transformer networks
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Ergen, Tolga, Neyshabur, Behnam, and Mehta, Harsh
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Computer Science - Computation and Language ,Statistics - Machine Learning - Abstract
Understanding the fundamental mechanism behind the success of transformer networks is still an open problem in the deep learning literature. Although their remarkable performance has been mostly attributed to the self-attention mechanism, the literature still lacks a solid analysis of these networks and interpretation of the functions learned by them. To this end, we study the training problem of attention/transformer networks and introduce a novel convex analytic approach to improve the understanding and optimization of these networks. Particularly, we first introduce a convex alternative to the self-attention mechanism and reformulate the regularized training problem of transformer networks with our alternative convex attention. Then, we cast the reformulation as a convex optimization problem that is interpretable and easier to optimize. Moreover, as a byproduct of our convex analysis, we reveal an implicit regularization mechanism, which promotes sparsity across tokens. Therefore, we not only improve the optimization of attention/transformer networks but also provide a solid theoretical understanding of the functions learned by them. We also demonstrate the effectiveness of our theory through several numerical experiments.
- Published
- 2022
24. Latent Tuberculosis Infection Management in Solid Organ Transplantation Recipients: A National Snapshot
- Author
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Aylin Özgen Alpaydın, Tuba Yeter Turunç, Vildan Avkan-Oğuz, Füsun Öner-Eyüboğlu, Elif Tükenmez-Tigen, İmran Hasanoğlu, Güle Aydın, Yasemin Tezer-Tekçe, Seniha Şenbayrak, Filiz Kızılateş, Adalet Altunsoy Aypak, Sibel Altunışık-Toplu, Pınar Ergen, Behice Kurtaran, Meltem Işıkgöz Taşbakan, Ayşegül Yıldırım, Serkan Yıldız, Kenan Çalışkan, Ebru Ayvazoğlu, Ender Dulundu, Ebru Şengül Şeref Parlak, İrem Akdemir, Melih Kara, Sinan Türkkan, Kübra Demir-Önder, Ezgi Yenigün, Aslı Turgut, Sabahat Alışır Ecder, Saime Paydaş, Tansu Yamazhan, Tufan Egeli, Rüya Özelsancak, Arzu Velioğlu, Mehmet Kılıç, Alpay Azap, Erdal Yekeler, Tuğrul Çakır, Yaşar Bayındır, Asiye Kanbay, Ferit Kuşcu, Kemal Osman Memikoğlu, Nazan Şen, Erhan Kabasakal, and Gülden Ersöz
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Medicine - Abstract
OBJECTIVE: Latent tuberculosis infection (LTBI) screening is strongly recommended in the pre-transplant evaluation of solid organ transplant (SOT) recipients, although it remains inadequate in many transplant centers. We decided to investigate pre-transplant TB risk assessment, LTBI treatment, and registry rates in Turkey. MATERIAL AND METHODS: Adult SOT recipients who underwent tuberculin skin test (TST) and/or interferon-gamma release test (IGRA) from 14 centers between 2015 and 2019 were included in the study. An induration of ≥5 mm on TST and/or probable/positive IGRA (QuantiFERON-TB) was considered positive for LTBI. Demographic features, LTBI screening and treatment, and pre-/post-transplant TB history were recorded from the electronic database of transplantation units across the country and pooled at a single center for a unified database. RESULTS: TST and/or IGRA were performed in 766 (33.8%) of 2266 screened patients most of whom were kidney transplant recipients (n = 485, 63.4%). LTBI screening test was positive in 359 (46.9%) patients, and isoniazid was given to 203 (56.5%) patients. Of the patients treated for LTBI, 112 (55.2%) were registered in the national registry, and 82 (73.2%) completed the treatment. Tuberculosis developed in 6 (1.06%) of 563 patients who were not offered LTBI treatment. CONCLUSION: We determined that overall, only one-third of SOT recipients in our country were evaluated in terms of TB risk, only 1 of the 2 SOT recipients with LTBI received treatment, and half were registered. Therefore, we want to emphasize the critical importance of pretransplant TB risk stratification and registration, guided by revised national guidelines.
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- 2024
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25. GLEAM: Greedy Learning for Large-Scale Accelerated MRI Reconstruction
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Ozturkler, Batu, Sahiner, Arda, Ergen, Tolga, Desai, Arjun D, Sandino, Christopher M, Vasanawala, Shreyas, Pauly, John M, Mardani, Morteza, and Pilanci, Mert
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Unrolled neural networks have recently achieved state-of-the-art accelerated MRI reconstruction. These networks unroll iterative optimization algorithms by alternating between physics-based consistency and neural-network based regularization. However, they require several iterations of a large neural network to handle high-dimensional imaging tasks such as 3D MRI. This limits traditional training algorithms based on backpropagation due to prohibitively large memory and compute requirements for calculating gradients and storing intermediate activations. To address this challenge, we propose Greedy LEarning for Accelerated MRI (GLEAM) reconstruction, an efficient training strategy for high-dimensional imaging settings. GLEAM splits the end-to-end network into decoupled network modules. Each module is optimized in a greedy manner with decoupled gradient updates, reducing the memory footprint during training. We show that the decoupled gradient updates can be performed in parallel on multiple graphical processing units (GPUs) to further reduce training time. We present experiments with 2D and 3D datasets including multi-coil knee, brain, and dynamic cardiac cine MRI. We observe that: i) GLEAM generalizes as well as state-of-the-art memory-efficient baselines such as gradient checkpointing and invertible networks with the same memory footprint, but with 1.3x faster training; ii) for the same memory footprint, GLEAM yields 1.1dB PSNR gain in 2D and 1.8 dB in 3D over end-to-end baselines.
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- 2022
26. Retinal vascular and structural recovery analysis by optical coherence tomography angiography after endoscopic decompression in sellar/parasellar tumors
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Ergen, Anil, Kaya Ergen, Sebnem, Gunduz, Busra, Subasi, Sevgi, Caklili, Melih, Cabuk, Burak, Anik, Ihsan, and Ceylan, Savas
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- 2023
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27. Is the brightness- contrast level of virtual reality videos significant for visually induced motion sickness? Experimental real-time biosensor and self-report analysis
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Emel Ugur, Bahriye Ozlem Konukseven, Mehmet Ergen, Mehmet Emin Aksoy, and Serhat Ilgaz Yoner
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virtual reality ,visually induced motion sickness ,youtube VR ,electrodermal activity ,simulator sickness questionnaire ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
BackgroundVirtual reality is no longer created solely with design graphics. Real life 360° videos created with special shooting techniques are now offered as open access to users’ experience. As a result, this widespread use of VR systems has increased the incidence of visually induced motion sickness.ObjectiveIn the present study, we aimed to investigate impact of brightness-contrast levels of real-life 360° videos on susceptibility to visually induced motion sickness during immersive virtual reality headset viewing.MethodsIn this study, 360° real-world day and night driving videos publicly available on YouTube VR were used as stimuli. Stimuli were presented in 2-min segments. Electrodermal activity was recorded throughout the stimulus presentation, and SSQ was administered immediately afterward.ResultsNo significant difference was found between the experiments in terms of dermal activity. There is a statistically significant difference in total SSQ scores and in symptoms of fatigue, eye strain, head fullness, blurred vision, and dizziness (p < 0.005; p < 0.01) after then the night video.ConclusionThe present study examined the likely impact of brightness and contrast levels in VR environments on VIMS provocation.
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- 2024
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28. Unraveling Attention via Convex Duality: Analysis and Interpretations of Vision Transformers
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Sahiner, Arda, Ergen, Tolga, Ozturkler, Batu, Pauly, John, Mardani, Morteza, and Pilanci, Mert
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Computer Science - Machine Learning ,Computer Science - Computer Vision and Pattern Recognition ,Mathematics - Optimization and Control - Abstract
Vision transformers using self-attention or its proposed alternatives have demonstrated promising results in many image related tasks. However, the underpinning inductive bias of attention is not well understood. To address this issue, this paper analyzes attention through the lens of convex duality. For the non-linear dot-product self-attention, and alternative mechanisms such as MLP-mixer and Fourier Neural Operator (FNO), we derive equivalent finite-dimensional convex problems that are interpretable and solvable to global optimality. The convex programs lead to {\it block nuclear-norm regularization} that promotes low rank in the latent feature and token dimensions. In particular, we show how self-attention networks implicitly clusters the tokens, based on their latent similarity. We conduct experiments for transferring a pre-trained transformer backbone for CIFAR-100 classification by fine-tuning a variety of convex attention heads. The results indicate the merits of the bias induced by attention compared with the existing MLP or linear heads., Comment: 38 pages, 2 figures. To appear in ICML 2022
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- 2022
29. The Experiences of Classroom Teachers on the Homework Process in Teaching Mathematics: An Interpretative Phenomenological Analysis
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Ergen, Yusuf and Durmus, Mehmet Emin
- Abstract
This phenomenological study aimed to explore a group of classroom teachers' experiences with homework assignment in teaching mathematics. The participants of the study were 27 classroom teachers who were selected using the criterion-based sampling technique. The research data were collected with a semi-structured interview form developed by the researchers and subjected to interpretive phenomenological analysis. The results showed that the teachers plan the homework they would assign the evening before the class and use resources available on the internet while planning it. It was also revealed that they assign mathematics homework for various purposes such as ensuring comprehension of the subjects, knowledge retention and use of the learned subjects in daily life. They reported that they check and provide feedback on the assigned homework during the classes that the assigned homework is sometimes done by the family members of the students and that both preparing and checking the homework take an extensive amount of time. As a solution to these problems, they suggested communicating and negotiating with the parents, getting support from school counselors and reducing the number of the themes in the primary mathematics curriculum.
- Published
- 2021
30. Experience of Primary School Teachers with Inclusion Students in the Context of Teaching Mathematics: A Case Study
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Durmus, Mehmet Emin and Ergen, Yusuf
- Abstract
This study investigated experiences of primary school teachers with inclusion students in the context of teaching mathematics. In the study the phenomenology design, which is one of the qualitative research designs, was used. The participants were determined by criterion-based sampling method. The participants of the study consisted of 21 primary school teachers with inclusion students. Research data were collected by a semi-structured interview form developed by the researchers. Content analysis method was used for data analysis. The study found that the participants mostly used rough evaluation forms in order to determine the gains when preparing IEP. In addition, most of the participants stated that they needed help in preparing IEP and they received the most of the help from school counselors. The participants stated that they mostly used demonstration, teaching with play and drama methods and that they could practice with inclusion students only during breaks, during social activities times or in the hours in the support training room apart from mathematic class. Moreover, it was found that most of the participants measured verbally gains of the inclusion students by question and answer method. It was also concluded that inadequacy of the time was the most common problem they encountered in the process of learning-teaching and assessment for the mathematics class.
- Published
- 2021
31. DestVI identifies continuums of cell types in spatial transcriptomics data
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Lopez, Romain, Li, Baoguo, Keren-Shaul, Hadas, Boyeau, Pierre, Kedmi, Merav, Pilzer, David, Jelinski, Adam, Yofe, Ido, David, Eyal, Wagner, Allon, Ergen, Can, Addadi, Yoseph, Golani, Ofra, Ronchese, Franca, Jordan, Michael I, Amit, Ido, and Yosef, Nir
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Bioengineering ,Human Genome ,1.1 Normal biological development and functioning ,Underpinning research ,Generic health relevance ,Animals ,Gene Expression Profiling ,Mice ,Neoplasms ,Single-Cell Analysis ,Software ,Transcriptome ,Exome Sequencing - Abstract
Most spatial transcriptomics technologies are limited by their resolution, with spot sizes larger than that of a single cell. Although joint analysis with single-cell RNA sequencing can alleviate this problem, current methods are limited to assessing discrete cell types, revealing the proportion of cell types inside each spot. To identify continuous variation of the transcriptome within cells of the same type, we developed Deconvolution of Spatial Transcriptomics profiles using Variational Inference (DestVI). Using simulations, we demonstrate that DestVI outperforms existing methods for estimating gene expression for every cell type inside every spot. Applied to a study of infected lymph nodes and of a mouse tumor model, DestVI provides high-resolution, accurate spatial characterization of the cellular organization of these tissues and identifies cell-type-specific changes in gene expression between different tissue regions or between conditions. DestVI is available as part of the open-source software package scvi-tools ( https://scvi-tools.org ).
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- 2022
32. Integration of 5G, 6G and IoT with Low Earth Orbit (LEO) networks: Opportunity, challenges and future trends
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Shayea, Ibraheem, El-Saleh, Ayman A., Ergen, Mustafa, Saoud, Bilal, Hartani, Riad, Turan, Derya, and Kabbani, Adnan
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- 2024
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33. Cerebrotendinous Xanthomatosis patients with late diagnosed in single orthopedic clinic: two novel variants in the CYP27A1 gene
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Muhammed Köroğlu, Mustafa Karakaplan, Enes Gündüz, Betül Kesriklioğlu, Emre Ergen, Okan Aslantürk, and Zeynep Maraş Özdemir
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Cerebrotendinous Xanthomatosis ,Novel mutation ,Achilles ,Tendon xanthomas ,Medicine - Abstract
Abstract Background Cerebrotendinous Xanthomatosis (CTX) is a rare autosomal recessive lipid storage disorder caused by loss of function variants in the CYP27A1 gene which encodes sterol 27-hydroxylase, on chromosome 2q35. Although the symptoms begin commonly in infancy, CTX diagnosis is often delayed. The aim of this study is to review the orthopedic findings of the disease by providing an overview of the clinical features of the disease. It is to raise awareness of this condition for which early diagnosis and treatment are important. Methods We retrospectively evaluated the clinical, laboratory, radiological, and genetic findings of eight patients from four families who were admitted to our Orthopedics and Traumatology Department between 2017 and 2022 due to bilateral Achilles tendon xanthomas, were found to have high cholestanol and CYP27A1 gene mutations. Results The mean age of patients was 37, and five of them were male. The mean age at the onset of symptoms was 9.25 years. The mean age of initial diagnosis was 33.75 years. Between symptom onset and clinical diagnosis, an average delay of 24.5 years was observed. All patients had bilateral Achilles tendon xanthoma. Notably, a novel variant (c.670_671delAA) in CYP27A1 gene was identified in three patients who also presented with peripheral neuropathy and bilateral pes cavus. One patient had osteoporosis and four patients had osteopenia. Five patients had a history of bilateral cataracts. Furthermore, three of the patients had early-onset chronic diarrhea and three of the patients had ataxia. Two of the patients had epilepsy and seven of the patients had behavior-personality disorder. All patients had low intelligence, but none of them had cardiac disease. Conclusion We present the diagnostic process and clinical features which the largest CTX case series ever reported from single orthopedic clinic. We suggest that patients with normal cholesterol levels presenting with xanthoma being genetically analyzed by testing at their serum cholestanol level, and that all siblings of patients diagnosed with CTX be examined.
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- 2024
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34. Yerli Malı Yurdun Malı Mı? Tüketicilerin Yerel Ürünlere Ödeme Yapma İstekliliği Üzerine Bir Araştırma
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Dilşad Güzel, Tayfun Ergen, and Gülşah Korkmaz
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Political science (General) ,JA1-92 ,Social sciences (General) ,H1-99 - Abstract
Bu araştırma, yerel gıda ürünlerine yönelik tüketicilerin ödeme yapma istekliliğini etkileyen faktörleri kapsamlı bir şekilde incelemektedir. Çalışma, özellikle fiyat bilinci, ürün ilgilenimi ve fiyat/kalite çıkarımı gibi kritik değişkenleri ele almakta ve bu faktörlerin yerel gıdalara olan talep üzerindeki etkilerini değerlendirmektedir. Erzurum ilinde gerçekleştirilen anket çalışması, 410 katılımcı ile yürütülmüş olup, katılımcılara yerel gıdaların seçiminde bu değişkenlerin etkilerini sorgulayan detaylı sorular yöneltilmiştir. Araştırma sonuçları, fiyat bilinci ve fiyat/kalite çıkarımının yanı sıra ürün ilgileniminin de tüketicilerin yerel gıdalara yönelik ödeme istekliliğinde önemli bir rol oynadığını göstermektedir. Bu bulgular, yerel gıda pazarlamasının stratejilerini belirlerken ve tüketicilere yönelik bilgilendirme kampanyalarını tasarlarken dikkate alınmalıdır. Ayrıca, çalışma, yerel ürünlerin çevreye olan etkilerinin ve çevre dostu üretim pratiklerinin tüketici tercihlerine etkisini de göz önünde bulundurmuştur. Sonuç olarak, tüketicilere yerel ürünler hakkında yeterli bilgi sağlanması ve çevreye zarar vermeyen ürünlerin üretiminin artırılması yoluyla tüketicilerin yerel ürünlere yönelik ödeme istekliliğinin artırılması önerilmektedir. Bu yaklaşım, yerel ekonomilere destek olmanın yanı sıra sürdürülebilir tüketim pratiklerini teşvik etmektedir.
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- 2023
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35. Framing the Study of Digital Religion: Waves of Academic Research, Theoretical Approaches and Themes
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Yunus Ergen
- Subjects
digital religion ,research waves ,theoretical approaches ,themes ,dijital din ,araştırma dalgaları ,teorik yaklaşımlar ,temalar ,Communication. Mass media ,P87-96 ,Religions. Mythology. Rationalism ,BL1-2790 ,Philosophy of religion. Psychology of religion. Religion in relation to other subjects ,BL51-65 - Abstract
The phenomenon of “digital religion” has emerged as a research field over the past quarter century as religious experiences integrate into the digital sphere. Within this field, researchers have adopted various theoretical frameworks and empirical methodologies to illuminate the complex dynamics that arise from the interaction between digital culture and religion. However, the existing literature on this topic is characterized by fragmentation, which makes a comprehensive understanding of its trajectory difficult. This fragmentation is particularly noticeable in the absence of a coherent narrative that outlines the field’s development. This study aims to provide a scholarly framework for understanding the trajectory of Digital Religion Studies (DRSs), encompassing successive waves of academic research, theoretical paradigms, and thematic foci. This study provides a qualitative assessment of existing literature on the relationship between digital culture and religion through a comprehensive review. A thorough literature review reveals that research in the field of digital religion can be classified into four distinct phases: descriptive, categorical, theoretical, and integrative. The prominent theoretical frameworks that have emerged media ecology, mediation, mediatization, religious-social shaping of technology (RSST), and hypermediation. Finally, the thematic categorization of research primarily revolves around topics, such as rituals, authenticity, identity, community, authority, and embodiment.
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- 2023
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36. YARI İLETKEN YONGA PLAKASI HARİTALARINDAKİ KUSUR SINIFLANDIRMALARI İÇİN DERİN ÖĞRENME TEMELLİ BİR KARAR DESTEK YÖNTEMİNİN GELİŞTİRİLMESİ
- Author
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Ekrem Düven and Gökhan Ergen
- Subjects
semiconductor wafer defect classification ,deep learning ,decision support system ,yarı iletken yonga plakası kusur sınıflandırma ,derin öğrenme ,karar destek sistemi ,Technology ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
Yarı iletken devre elemanı üretim teknolojilerinde gerçekleşen gelişimler, bu elemanların üzerinde yer aldığı yonga plakası üretim süreçlerini daha karmaşık ve hassas hale getirmektedir. Üretim ile ilişkili çevresel koşullar, malzeme kalitesi gibi çeşitli faktörler, yonga plakası üzerinde kusursuz olarak nitelendirilebilecek alan miktarını yani verimi doğrudan etkilemektedir. Bir yarı iletken yonga plakası üzerindeki kusurlu alanların oluşturabileceği desenler standart olarak tanımlanmış durumdadır. İncelenen bir yonga plakası yüzeyindeki kusurların bu tanımlara göre sınıflandırılması, üretim süreçlerinde oluşan problemlerin kaynaklarının belirlenmesi için önemli bilgiler sağlayabilmektedir. Bu çalışmada, mevcut uygulamalarda her yarı iletken yonga levhası için insan operatörler tarafından yapılan kusur deseni sınıflandırma işlemini belirli bir güvenlik değerine kadar otomatik olarak gerçekleştiren ve böylece toplam işlem süresini azaltan bir karar destek yöntemi geliştirilmiştir. Bu yöntemde temel sınıflandırma işlemi için derin öğrenme metotlarıyla eğitilmiş bir ağ yapısı kullanılmaktadır. İstenilen güvenlik değerinin üzerinde bir doğrulukla sınıflandırılan yonga plakaları doğru sınıflandırılmış olarak kabul edilmekte, bu değerin altında kalan yonga plakaları ise insan operatörün incelemesine tabi tutulmaktadır. Yöntemin kullanılması ile; ortalama büyüklükte bir yonga plakası üretim tesisi için geçerli günlük toplam inceleme süresi, tüm incelemenin insan operatör tarafından yapıldığı durumda geçerli sürenin %10’una indirilebilmekte, ayrıca insan operatörün yapabileceği öznel değerlendirmelerin de önüne geçilebilmektedir.
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- 2023
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37. Load balancing in 5G heterogeneous networks based on automatic weight function
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Emre Gures, Ibraheem Shayea, Sawsan Ali Saad, Mustafa Ergen, Ayman A. El-Saleh, Nada M.O. Sid Ahmed, and Mohammad Alnakhli
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Load balancing ,Handover ,Heterogeneous networks ,Mobility management ,Millimetre wave communication ,Information technology ,T58.5-58.64 - Abstract
Load balancing is a major challenge in heterogeneous networks (HetNets) consisting of 5G and 6G ultra-dense small cells with long-term evaluation advanced (LTE-A) networks. A key factor in achieving efficient load balancing during user mobility is creating appropriate optimisation for handover control parameters (HCP). This paper proposes a coordinated load balancing algorithm for LTE-A/fifth generation (5G) HetNets. The algorithm automatically optimises HCP settings for a given user based on three bounded functions (the signal-to-interference-plus-noise ratio (SINR) of the user equipment (UE), the number of physical resource blocks (PRBs) per UE and the UE’s speed) as well as their automatic weight levels. A two-step target cell determination strategy is implemented according to the cell load level and RSRP criteria, ensuring that users are handed over to low-loaded target cells. A new HO procedure that considers the pilot signal power is also proposed, which includes the number of PRBs per UE and the RSRP. Cells with freer PRBs are prioritised in user association to provide load balance and enhanced throughput. The proposed load balancing algorithm is compared with five other load balancing algorithms selected from the literature. The simulation results reveal that under various mobile speed scenarios, the proposed load balancing scheme enhances network performance in terms of load level, throughput, spectral efficiency and call dropping ratio (CDR).
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- 2023
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38. Path Regularization: A Convexity and Sparsity Inducing Regularization for Parallel ReLU Networks
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Ergen, Tolga and Pilanci, Mert
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Statistics - Machine Learning - Abstract
Understanding the fundamental principles behind the success of deep neural networks is one of the most important open questions in the current literature. To this end, we study the training problem of deep neural networks and introduce an analytic approach to unveil hidden convexity in the optimization landscape. We consider a deep parallel ReLU network architecture, which also includes standard deep networks and ResNets as its special cases. We then show that pathwise regularized training problems can be represented as an exact convex optimization problem. We further prove that the equivalent convex problem is regularized via a group sparsity inducing norm. Thus, a path regularized parallel ReLU network can be viewed as a parsimonious convex model in high dimensions. More importantly, since the original training problem may not be trainable in polynomial-time, we propose an approximate algorithm with a fully polynomial-time complexity in all data dimensions. Then, we prove strong global optimality guarantees for this algorithm. We also provide experiments corroborating our theory., Comment: Accepted to NeurIPS 2023
- Published
- 2021
39. Parallel Deep Neural Networks Have Zero Duality Gap
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Wang, Yifei, Ergen, Tolga, and Pilanci, Mert
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Computer Science - Machine Learning ,Mathematics - Optimization and Control - Abstract
Training deep neural networks is a challenging non-convex optimization problem. Recent work has proven that the strong duality holds (which means zero duality gap) for regularized finite-width two-layer ReLU networks and consequently provided an equivalent convex training problem. However, extending this result to deeper networks remains to be an open problem. In this paper, we prove that the duality gap for deeper linear networks with vector outputs is non-zero. In contrast, we show that the zero duality gap can be obtained by stacking standard deep networks in parallel, which we call a parallel architecture, and modifying the regularization. Therefore, we prove the strong duality and existence of equivalent convex problems that enable globally optimal training of deep networks. As a by-product of our analysis, we demonstrate that the weight decay regularization on the network parameters explicitly encourages low-rank solutions via closed-form expressions. In addition, we show that strong duality holds for three-layer standard ReLU networks given rank-1 data matrices.
- Published
- 2021
40. Global Optimality Beyond Two Layers: Training Deep ReLU Networks via Convex Programs
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Ergen, Tolga and Pilanci, Mert
- Subjects
Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Computer Science - Computational Complexity ,Statistics - Machine Learning - Abstract
Understanding the fundamental mechanism behind the success of deep neural networks is one of the key challenges in the modern machine learning literature. Despite numerous attempts, a solid theoretical analysis is yet to be developed. In this paper, we develop a novel unified framework to reveal a hidden regularization mechanism through the lens of convex optimization. We first show that the training of multiple three-layer ReLU sub-networks with weight decay regularization can be equivalently cast as a convex optimization problem in a higher dimensional space, where sparsity is enforced via a group $\ell_1$-norm regularization. Consequently, ReLU networks can be interpreted as high dimensional feature selection methods. More importantly, we then prove that the equivalent convex problem can be globally optimized by a standard convex optimization solver with a polynomial-time complexity with respect to the number of samples and data dimension when the width of the network is fixed. Finally, we numerically validate our theoretical results via experiments involving both synthetic and real datasets., Comment: Accepted to ICML 2021
- Published
- 2021
41. Processing 2D barcode data with metaheuristic based CNN models and detection of malicious PDF files
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Toğaçar, Mesut and Ergen, Burhan
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- 2024
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42. Resilience in service firms: the impact of social capital on firm performance during turmoil
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Ergen Keleş, Fatma Hilal and Keleş, Emrah
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- 2023
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43. Empirical cefepime+vancomycin versus ceftazidime+vancomycin versus meropenem+vancomycin in the treatment of healthcare-associated meningitis: results of the multicenter Ephesus study
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Sipahi, Oguz Resat, Akyol, Deniz, Ormen, Bahar, Cicek-Senturk, Gonul, Mermer, Sinan, Onal, Ugur, Amer, Fatma, Saed, Maysaa Abdallah, Ozdemir, Kevser, Tukenmez-Tigen, Elif, Oztoprak, Nefise, Altin, Ummugulsum, Kurtaran, Behice, Popescu, Corneliu Petru, Sakci, Mustafa, Suntur, Bedia Mutay, Gautam, Vikas, Sharma, Megha, Kaya, Safak, Akcil, Eren Fatma, Kaya, Selcuk, Turunc, Tuba, Ergen, Pınar, Kandemir, Ozlem, Cesur, Salih, Bardak-Ozcem, Selin, Ozgiray, Erkin, Yurtseven, Taskın, Erdem, Huseyin Aytac, Sipahi, Hilal, Arda, Bilgin, Pullukcu, Hüsnü, Tasbakan, Meltem, Yamazhan, Tansu, Aydemir, Sohret, and Ulusoy, Sercan
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- 2023
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44. DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection
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Hausmann, Fabian, Ergen, Can, Khatri, Robin, Marouf, Mohamed, Hänzelmann, Sonja, Gagliani, Nicola, Huber, Samuel, Machart, Pierre, and Bonn, Stefan
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- 2023
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45. Assessment of estimated and measured resting metabolic rates in type 1 and type 2 diabetes mellitus
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Akin Dayan, Nilay Ergen, and Sami Sabri Bulgurlu
- Subjects
Calorimetry ,Indirect ,Energy expenditure ,Diabetes mellitus ,Insulin-dependent ,Science (General) ,Q1-390 ,Social sciences (General) ,H1-99 - Abstract
Aim: This study aimed to compare the estimated and measured resting metabolic rates of patients with type 1 and type 2 diabetes mellitus in an outpatient clinical setting. Material and methods: Participants were categorized into three groups that included type 1 diabetes, type 2 diabetes, and individuals without diabetes. Bland–Altman analysis was used to identify the equation that most accurately predicted the measured resting metabolic rates. Multiple regression analysis was used to identify the factors affecting resting metabolic rates. Results: Resting metabolic rates was observed to be higher in subjects with type 2 diabetes compared to that of the other groups. There was a proportional bias between predicted and measured resting metabolic rates. Type 1 diabetes, type 2 diabetes, male sex, body weight, waist circumference, and triglyceride level were factors that positively predicted resting metabolic rates, and age was a factor that negatively predicted it. Conclusions: Although there was a bias between estimated and measured RMR, the most accurate results were achieved with the Mifflin–St Jeor equation for women with type 1 diabetes, with the Owen equation for men with type 1 diabetes, with the Harris Benedict equation for women with type 2 diabetes, and with the Ikeda equation for men with type 2 diabetes as well as for women and men in the control group.
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- 2024
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46. Hidden Convexity of Wasserstein GANs: Interpretable Generative Models with Closed-Form Solutions
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Sahiner, Arda, Ergen, Tolga, Ozturkler, Batu, Bartan, Burak, Pauly, John, Mardani, Morteza, and Pilanci, Mert
- Subjects
Computer Science - Machine Learning ,Computer Science - Computer Vision and Pattern Recognition ,Electrical Engineering and Systems Science - Image and Video Processing ,Mathematics - Optimization and Control ,Statistics - Machine Learning - Abstract
Generative Adversarial Networks (GANs) are commonly used for modeling complex distributions of data. Both the generators and discriminators of GANs are often modeled by neural networks, posing a non-transparent optimization problem which is non-convex and non-concave over the generator and discriminator, respectively. Such networks are often heuristically optimized with gradient descent-ascent (GDA), but it is unclear whether the optimization problem contains any saddle points, or whether heuristic methods can find them in practice. In this work, we analyze the training of Wasserstein GANs with two-layer neural network discriminators through the lens of convex duality, and for a variety of generators expose the conditions under which Wasserstein GANs can be solved exactly with convex optimization approaches, or can be represented as convex-concave games. Using this convex duality interpretation, we further demonstrate the impact of different activation functions of the discriminator. Our observations are verified with numerical results demonstrating the power of the convex interpretation, with applications in progressive training of convex architectures corresponding to linear generators and quadratic-activation discriminators for CelebA image generation. The code for our experiments is available at https://github.com/ardasahiner/ProCoGAN., Comment: Published as paper in ICLR 2022. First two authors contributed equally to this work; 34 pages, 11 figures
- Published
- 2021
47. Functional outcomes of titanium elastic nail procedure after femoral shaft fracture in pediatric patients
- Author
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Muhammed Koroglu, Mustafa Karakaplan, Emre Ergen, Enes Gunduz, Huseyin Utku Ozdes, and Okan Aslanturk
- Subjects
femur diaphyseal fractures ,elastic nails ,pediatric ,Medicine - Abstract
Pediatric femur diaphyseal fractures are seen after serious traumas such as traffic accidents and fall from height. Although treatment algorithms are made according to age groups, treatment planning is individualized according to the patient and the degree of injury. In our study, we evaluated functional outcomes of pediatric femur fractures treated with titanium elastic nail (TEN). This is a retrospective study including pediatric femoral diaphyseal fractures treated with TEN between 2012 and 2021. Open fractures, pathological fractures, distal fractures involving the femoral condyles, and proximal fractures involving the trochanteric region were not included in our study. Thirty-three femoral diaphyseal fractures with complete data were identified as stable and unstable in length, and functional results and post-treatment complications were recorded by performing TEN in fracture fixation. Clinical functional results were analyzed with Flynn criteria. Thirty-three femoral fractures of 29 patients were included. Eighteen (62.1%) of our patients were boys and 11 (37.9%) were girls. The mean age was 6.51 years (4-13 years). The most common injury mechanism was traffic accidents seen in 19 patients (24.51%). The mean follow-up period after surgery was 26.6 (6-90 months) months. Stable fractures (transverse and short oblique) were found in 26 cases (78.7%) and unstable fractures (spiral/long oblique and comminuted) in 7 cases (21.7%). According to Flynn criteria, excellent results were found in 20 fractures (60.6%) and satisfactory results in 10 fractures (30.3%) and 3 poor (%9.09). There was no significant difference between stable and unstable fractures in terms of functional outcome (p=0.12). Femoral diaphyseal fractures are serious injuries that require surgery. Regardless of the type of fracture, stable or unstable in length, the results of treatment with TEN are very successful. Major complications such as nonunion and re-fracture are rarely seen with this treatment. [Med-Science 2023; 12(3.000): 746-52]
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- 2023
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48. Assessment of estimated and measured resting metabolic rates in type 1 and type 2 diabetes mellitus
- Author
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Dayan, Akin, Ergen, Nilay, and Bulgurlu, Sami Sabri
- Published
- 2024
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- View/download PDF
49. Demystifying Batch Normalization in ReLU Networks: Equivalent Convex Optimization Models and Implicit Regularization
- Author
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Ergen, Tolga, Sahiner, Arda, Ozturkler, Batu, Pauly, John, Mardani, Morteza, and Pilanci, Mert
- Subjects
Computer Science - Machine Learning ,Mathematics - Optimization and Control ,Statistics - Machine Learning - Abstract
Batch Normalization (BN) is a commonly used technique to accelerate and stabilize training of deep neural networks. Despite its empirical success, a full theoretical understanding of BN is yet to be developed. In this work, we analyze BN through the lens of convex optimization. We introduce an analytic framework based on convex duality to obtain exact convex representations of weight-decay regularized ReLU networks with BN, which can be trained in polynomial-time. Our analyses also show that optimal layer weights can be obtained as simple closed-form formulas in the high-dimensional and/or overparameterized regimes. Furthermore, we find that Gradient Descent provides an algorithmic bias effect on the standard non-convex BN network, and we design an approach to explicitly encode this implicit regularization into the convex objective. Experiments with CIFAR image classification highlight the effectiveness of this explicit regularization for mimicking and substantially improving the performance of standard BN networks., Comment: Accepted to ICLR 2022. First two authors contributed equally to this work; 36 pages, 13 figures
- Published
- 2021
50. Vector-output ReLU Neural Network Problems are Copositive Programs: Convex Analysis of Two Layer Networks and Polynomial-time Algorithms
- Author
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Sahiner, Arda, Ergen, Tolga, Pauly, John, and Pilanci, Mert
- Subjects
Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Computer Science - Computational Complexity ,Statistics - Machine Learning - Abstract
We describe the convex semi-infinite dual of the two-layer vector-output ReLU neural network training problem. This semi-infinite dual admits a finite dimensional representation, but its support is over a convex set which is difficult to characterize. In particular, we demonstrate that the non-convex neural network training problem is equivalent to a finite-dimensional convex copositive program. Our work is the first to identify this strong connection between the global optima of neural networks and those of copositive programs. We thus demonstrate how neural networks implicitly attempt to solve copositive programs via semi-nonnegative matrix factorization, and draw key insights from this formulation. We describe the first algorithms for provably finding the global minimum of the vector output neural network training problem, which are polynomial in the number of samples for a fixed data rank, yet exponential in the dimension. However, in the case of convolutional architectures, the computational complexity is exponential in only the filter size and polynomial in all other parameters. We describe the circumstances in which we can find the global optimum of this neural network training problem exactly with soft-thresholded SVD, and provide a copositive relaxation which is guaranteed to be exact for certain classes of problems, and which corresponds with the solution of Stochastic Gradient Descent in practice., Comment: 25 pages, 6 figures
- Published
- 2020
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