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  1. Book ; Online: Characterization and Learning of Causal Graphs with Small Conditioning Sets

    Kocaoglu, Murat

    2023  

    Abstract: Constraint-based causal discovery algorithms learn part of the causal graph structure by systematically testing conditional independences observed in the data. These algorithms, such as the PC algorithm and its variants, rely on graphical ... ...

    Abstract Constraint-based causal discovery algorithms learn part of the causal graph structure by systematically testing conditional independences observed in the data. These algorithms, such as the PC algorithm and its variants, rely on graphical characterizations of the so-called equivalence class of causal graphs proposed by Pearl. However, constraint-based causal discovery algorithms struggle when data is limited since conditional independence tests quickly lose their statistical power, especially when the conditioning set is large. To address this, we propose using conditional independence tests where the size of the conditioning set is upper bounded by some integer $k$ for robust causal discovery. The existing graphical characterizations of the equivalence classes of causal graphs are not applicable when we cannot leverage all the conditional independence statements. We first define the notion of $k$-Markov equivalence: Two causal graphs are $k$-Markov equivalent if they entail the same conditional independence constraints where the conditioning set size is upper bounded by $k$. We propose a novel representation that allows us to graphically characterize $k$-Markov equivalence between two causal graphs. We propose a sound constraint-based algorithm called the $k$-PC algorithm for learning this equivalence class. Finally, we conduct synthetic, and semi-synthetic experiments to demonstrate that the $k$-PC algorithm enables more robust causal discovery in the small sample regime compared to the baseline algorithms.

    Comment: Published in NeurIPS'23. 41 pages
    Keywords Computer Science - Artificial Intelligence ; Computer Science - Machine Learning ; Statistics - Machine Learning
    Subject code 006
    Publishing date 2023-01-21
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: Modular Learning of Deep Causal Generative Models for High-dimensional Causal Inference

    Rahman, Md Musfiqur / Kocaoglu, Murat

    2024  

    Abstract: Pearl's causal hierarchy establishes a clear separation between observational, interventional, and counterfactual questions. Researchers proposed sound and complete algorithms to compute identifiable causal queries at a given level of the hierarchy using ...

    Abstract Pearl's causal hierarchy establishes a clear separation between observational, interventional, and counterfactual questions. Researchers proposed sound and complete algorithms to compute identifiable causal queries at a given level of the hierarchy using the causal structure and data from the lower levels of the hierarchy. However, most of these algorithms assume that we can accurately estimate the probability distribution of the data, which is an impractical assumption for high-dimensional variables such as images. On the other hand, modern generative deep learning architectures can be trained to learn how to accurately sample from such high-dimensional distributions. Especially with the recent rise of foundation models for images, it is desirable to leverage pre-trained models to answer causal queries with such high-dimensional data. To address this, we propose a sequential training algorithm that, given the causal structure and a pre-trained conditional generative model, can train a deep causal generative model, which utilizes the pre-trained model and can provably sample from identifiable interventional and counterfactual distributions. Our algorithm, called Modular-DCM, uses adversarial training to learn the network weights, and to the best of our knowledge, is the first algorithm that can make use of pre-trained models and provably sample from any identifiable causal query in the presence of latent confounders with high-dimensional data. We demonstrate the utility of our algorithm using semi-synthetic and real-world datasets containing images as variables in the causal structure.
    Keywords Computer Science - Machine Learning ; Computer Science - Artificial Intelligence ; Computer Science - Information Theory ; Statistics - Methodology ; Statistics - Machine Learning
    Subject code 006
    Publishing date 2024-01-02
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Direct visualization of crossing renal vessels on MRU achieved by splitting intravenous contrast dose.

    Kocaoğlu, Murat

    Pediatric radiology

    2016  Volume 46, Issue 7, Page(s) 1077–1078

    MeSH term(s) Contrast Media ; Humans ; Kidney ; Magnetic Resonance Imaging ; Ureteral Obstruction ; Urography
    Chemical Substances Contrast Media
    Language English
    Publishing date 2016
    Publishing country Germany
    Document type Letter ; Comment
    ZDB-ID 124459-0
    ISSN 1432-1998 ; 0301-0449
    ISSN (online) 1432-1998
    ISSN 0301-0449
    DOI 10.1007/s00247-015-3522-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Tentorial Venous Sinuses: A Cadaveric Study.

    Kocaoglu, Murat / Acar, Feridun

    Turkish neurosurgery

    2022  Volume 33, Issue 2, Page(s) 238–243

    Abstract: Aim: To present the configuration of the tentorial venous sinuses, and to determine the optimal incision zone on the tentorium cerebelli.: Material and methods: This study has been completed with 24 autopsied cadavers. For every cadaver, firstly, ... ...

    Abstract Aim: To present the configuration of the tentorial venous sinuses, and to determine the optimal incision zone on the tentorium cerebelli.
    Material and methods: This study has been completed with 24 autopsied cadavers. For every cadaver, firstly, supratentorial tissues were removed and tentorial measurements were noted, superior part of the tentorial sinuses was captured, and then infratentorial tissues were removed, and all the sinuses were checked and captured.
    Results: Average age of the studied 24 fresh cadavers was 50 years, wherein 4 were females and 20 were males. Tentorial sinus was presented in 87% of the cases, with 45% medial, 33% lateral, and 22% in the middle third of each tentorium half.
    Conclusion: This study showed the pattern, incidence, location, and distribution of tentorial venous sinuses and tried to find the optimum incision zone by identifying sparse areas for the venous sinuses during transtentorial surgical approaches.
    MeSH term(s) Male ; Female ; Humans ; Middle Aged ; Cranial Sinuses/surgery ; Dura Mater/surgery ; Cadaver ; Surgical Wound ; Head
    Language English
    Publishing date 2022-12-09
    Publishing country Turkey
    Document type Journal Article
    ZDB-ID 1203779-5
    ISSN 1019-5149
    ISSN 1019-5149
    DOI 10.5137/1019-5149.JTN.37725-22.5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Comparison of phase contrast magnetic resonance imaging and scintigraphy for determination of split pulmonary blood flow in children and young adults with congenital heart disease.

    Hafiz, Rawan / Kocaoglu, Murat / Trout, Andrew T

    Pediatric radiology

    2023  Volume 53, Issue 10, Page(s) 2040–2047

    Abstract: Background: Measurement of differential blood flow to the lungs is important to understanding flow dynamics in the setting of congenital heart disease. Split blood flow via the pulmonary arteries guides and demonstrates the effect of interventions. ... ...

    Abstract Background: Measurement of differential blood flow to the lungs is important to understanding flow dynamics in the setting of congenital heart disease. Split blood flow via the pulmonary arteries guides and demonstrates the effect of interventions. Minimally invasive imaging of pulmonary blood flow can be achieved with scintigraphy or magnetic resonance imaging (MRI).
    Objective: To assess agreement of pulmonary blood flow measurements obtained by scintigraphy and MRI in children and young adults.
    Materials and methods: We performed a retrospective review of patients < 21 years of age who had undergone both nuclear medicine pulmonary perfusion scans (Tc-99 m MAA) and cardiac MRI examinations from January 2012 to August 2021 at our tertiary pediatric hospital. Patient demographics, medical/surgical information, and estimates of split blood flow by both modalities were recorded. Pearson's correlation coefficient was used to determine the relationship between split blood flow measured by the two examinations. Agreement was calculated using interclass correlation coefficient (ICC) for absolute agreement and Bland-Altman difference analysis.
    Results: Correlation between split blood flow measured by scintigraphy and MRI using net flow was 0.90 (95% CI: 0.83-0.94, P < 0.001) and the ICC for agreement on split blood flow was 0.90 (95% CI: 0.84-0.94). Mean difference in split blood flow by Bland-Altman analysis was 0.79% with 95% limits of agreement (-11.2 to 12.8%).
    Conclusion: There is excellent agreement between Tc-99 m scintigraphy and phase contrast MRI for quantification of split pulmonary blood flow in children and young adults with congenital heart disease.
    MeSH term(s) Child ; Humans ; Young Adult ; Pulmonary Circulation/physiology ; Magnetic Resonance Imaging/methods ; Radionuclide Imaging ; Lung ; Heart Defects, Congenital/diagnostic imaging ; Reproducibility of Results
    Language English
    Publishing date 2023-06-05
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 124459-0
    ISSN 1432-1998 ; 0301-0449
    ISSN (online) 1432-1998
    ISSN 0301-0449
    DOI 10.1007/s00247-023-05693-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The Supracerebellar Transtentorial Approach in the Prone Position.

    Kocaoglu, Murat / Acar, Feridun

    Turkish neurosurgery

    2021  Volume 31, Issue 2, Page(s) 290–295

    Abstract: The mediobasal temporal region (MTR) is a deep part of the brain covered by eloquent structures. In certain cases, accessing this region is challenging. According to the literature, the supracerebellar transtentorial (SCTT) approach provides safe access ... ...

    Abstract The mediobasal temporal region (MTR) is a deep part of the brain covered by eloquent structures. In certain cases, accessing this region is challenging. According to the literature, the supracerebellar transtentorial (SCTT) approach provides safe access to the MTR. Since this approach was introduced by Voigt and Yasargil, many researchers used SCTT in different positions. In particular, the sitting position was the most preferred as it allows the cerebellum to fall away from the tentorium. However, this position has disadvantages such as venous air embolism (VAE), paradoxical air embolism (PAE), and some non ergonomic conditions during surgery. We report two cases with tumors affecting the middle and posterior medial temporal regions. Both patients underwent surgeries in the prone position using the SCTT approach. There were no procedure-related complications. Histopathological results were as follows: psammomatous meningioma in the first case; adenocarcinoma metastasis in the second case. Thus, in this study, the efficacy, feasibility, and safety of accessing the MTR using the SCTT approach in the prone position were demonstrated.
    MeSH term(s) Brain Neoplasms/diagnostic imaging ; Brain Neoplasms/surgery ; Cerebellum/diagnostic imaging ; Cerebellum/surgery ; Humans ; Male ; Meningioma/surgery ; Middle Aged ; Neurosurgical Procedures/methods ; Patient Positioning/methods ; Prone Position/physiology ; Temporal Lobe/diagnostic imaging ; Temporal Lobe/surgery
    Language English
    Publishing date 2021-02-23
    Publishing country Turkey
    Document type Case Reports ; Journal Article
    ZDB-ID 1203779-5
    ISSN 1019-5149
    ISSN 1019-5149
    DOI 10.5137/1019-5149.JTN.31433-20.5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Imaging and clinical predictors of surgery in stricturing ileal Crohn's disease: a retrospective study from a large pediatric hospital.

    Debnath, Pradipta / Epstein, Katherine N / Kocaoglu, Murat / Towbin, Alexander J / Denson, Lee A / Dillman, Jonathan R

    Abdominal radiology (New York)

    2024  

    Abstract: Purpose: (1) To determine the frequency of surgical management in children with Crohn's Disease (CD) and a new radiologic ileal stricture, and (2) to identify imaging and clinical features that predict the need for surgery.: Methods: This ... ...

    Abstract Purpose: (1) To determine the frequency of surgical management in children with Crohn's Disease (CD) and a new radiologic ileal stricture, and (2) to identify imaging and clinical features that predict the need for surgery.
    Methods: This retrospective study included pediatric patients (< 21 years old) with CD and a new ileal stricture diagnosed by MRE, CTE, or CT between July 2018 and June 2023. Three board-certified radiologists recorded stricture length, maximum mural thickness, minimum lumen diameter, maximum upstream diameter, and simplified magnetic resonance index of activity (sMaRIA) score. Anthropometrics, laboratory data, and surgical interventions performed after stricture diagnosis were also recorded. Multivariable logistic regression was used to identify imaging and clinical variables associated with the need for surgery.
    Results: 44 pediatric CD patients (median age 16.5 years) presented with a new ileal stricture during the study period. 30 (68.2%) patients required surgery, with a median time of 87.5 days between stricture diagnosis and surgery. Median stricture measurements were length: 7.0 cm, maximum mural thickness: 7.3 mm, minimum lumen diameter: 0.2 cm, and maximum upstream diameter: 3.3 cm. Median sMaRIA score was 3.0, and 14 (31.8%) strictures had associated internal penetrating disease. Stricture ratio (ratio of maximum upstream lumen diameter to minimum lumen diameter) (OR = 1.15 [95% CI 1.02-1.30]; p = 0.02) and sMaRIA (OR = 2.12 [95% CI 0.87-5.17; p = 0.10) were associated with need for surgery.
    Conclusion: Surgery remains common in stricturing pediatric CD, with increasing stricture ratio and sMaRIA score associated with need for surgical management.
    Language English
    Publishing date 2024-04-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2839786-1
    ISSN 2366-0058 ; 2366-004X
    ISSN (online) 2366-0058
    ISSN 2366-004X
    DOI 10.1007/s00261-024-04314-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Cardiothoracic Magnetic Resonance Angiography.

    Kocaoglu, Murat / Pednekar, Amol / Fleck, Robert J / Dillman, Jonathan R

    Current problems in diagnostic radiology

    2023  Volume 53, Issue 1, Page(s) 154–165

    Abstract: Catheter-based angiography is regarded as the clinical reference imaging technique for vessel imaging; however, it is invasive and is currently used for intervention or physiologic measurements. Contrast enhanced magnetic resonance angiography (MRA) with ...

    Abstract Catheter-based angiography is regarded as the clinical reference imaging technique for vessel imaging; however, it is invasive and is currently used for intervention or physiologic measurements. Contrast enhanced magnetic resonance angiography (MRA) with gadolinium-based contrast agents can be performed as a three-dimensional (3D) MRA or as a time resolved 3D (4D) MRA without physiologic synchronization, in which case cardiac and respiratory motion may blur the edges of the vessels and cardiac chambers. Ferumoxytol has recently been a popular contrast agent for MRA in patients with chronic renal failure. Noncontrast 3D MRA with ECG gating and respiratory navigation are safe and accurate noninvasive cross-sectional imaging techniques for the visualization of great vessels of the heart and coronary arteries in a variety of cardiovascular disorders including complex congenital heart diseases. Noncontrast flow dependent MRA techniques such as time of flight, phase contrast, and black-blood MRA techniques can be used as complementary or primary techniques. Here we review both conventional and relatively new contrast enhanced and non-contrast enhanced MRA techniques including ferumoxytol enhanced MRA, and bright-blood and water-fat separation based noncontrast 3D MRA techniques.
    MeSH term(s) Humans ; Magnetic Resonance Angiography/methods ; Ferrosoferric Oxide ; Contrast Media ; Heart ; Magnetic Resonance Imaging ; Imaging, Three-Dimensional/methods
    Chemical Substances Ferrosoferric Oxide (XM0M87F357) ; Contrast Media
    Language English
    Publishing date 2023-10-21
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 198954-6
    ISSN 1535-6302 ; 0363-0188
    ISSN (online) 1535-6302
    ISSN 0363-0188
    DOI 10.1067/j.cpradiol.2023.10.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online: Front-door Adjustment Beyond Markov Equivalence with Limited Graph Knowledge

    Shah, Abhin / Shanmugam, Karthikeyan / Kocaoglu, Murat

    2023  

    Abstract: Causal effect estimation from data typically requires assumptions about the cause-effect relations either explicitly in the form of a causal graph structure within the Pearlian framework, or implicitly in terms of (conditional) independence statements ... ...

    Abstract Causal effect estimation from data typically requires assumptions about the cause-effect relations either explicitly in the form of a causal graph structure within the Pearlian framework, or implicitly in terms of (conditional) independence statements between counterfactual variables within the potential outcomes framework. When the treatment variable and the outcome variable are confounded, front-door adjustment is an important special case where, given the graph, causal effect of the treatment on the target can be estimated using post-treatment variables. However, the exact formula for front-door adjustment depends on the structure of the graph, which is difficult to learn in practice. In this work, we provide testable conditional independence statements to compute the causal effect using front-door-like adjustment without knowing the graph under limited structural side information. We show that our method is applicable in scenarios where knowing the Markov equivalence class is not sufficient for causal effect estimation. We demonstrate the effectiveness of our method on a class of random graphs as well as real causal fairness benchmarks.
    Keywords Computer Science - Machine Learning ; Statistics - Methodology ; Statistics - Machine Learning
    Subject code 511
    Publishing date 2023-06-19
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Approximate Causal Effect Identification under Weak Confounding

    Jiang, Ziwei / Wei, Lai / Kocaoglu, Murat

    2023  

    Abstract: Causal effect estimation has been studied by many researchers when only observational data is available. Sound and complete algorithms have been developed for pointwise estimation of identifiable causal queries. For non-identifiable causal queries, ... ...

    Abstract Causal effect estimation has been studied by many researchers when only observational data is available. Sound and complete algorithms have been developed for pointwise estimation of identifiable causal queries. For non-identifiable causal queries, researchers developed polynomial programs to estimate tight bounds on causal effect. However, these are computationally difficult to optimize for variables with large support sizes. In this paper, we analyze the effect of "weak confounding" on causal estimands. More specifically, under the assumption that the unobserved confounders that render a query non-identifiable have small entropy, we propose an efficient linear program to derive the upper and lower bounds of the causal effect. We show that our bounds are consistent in the sense that as the entropy of unobserved confounders goes to zero, the gap between the upper and lower bound vanishes. Finally, we conduct synthetic and real data simulations to compare our bounds with the bounds obtained by the existing work that cannot incorporate such entropy constraints and show that our bounds are tighter for the setting with weak confounders.

    Comment: Published in ICML 2023
    Keywords Statistics - Machine Learning ; Computer Science - Artificial Intelligence ; Computer Science - Information Theory ; Computer Science - Machine Learning
    Publishing date 2023-06-22
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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