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Publication Metadata only 3D face recognition(Institute of Electrical and Electronics Engineers (IEEE), 2006) Dutaǧaci, H.; Sankur, B.; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; 107907In this paper, we compare face recognition performances of various features applied on registered 3D scans of faces. The features we compare are DFT or DCT- based features, ICA-based features and NNMF-based features. We apply the feature extraction techniques to three different representations of registered faces: 3D point clouds, 2D depth images and 3D voxel representations. We also consider block-based DFT or DCT-based local features on 2D depth images and their fusion schemes. Experiments using different combinations of representation types and feature vectors are conducted on the 3D-RMA dataset. / Bu bildiride, kayıtlı 3B yüz taramalarında uygulanan çeşitli özelliklerin yüz tanıma performanslarını karşılaştırıyoruz. Karşılaştırdığımız özellikler, DFT veya DCT tabanlı özellikler, ICA tabanlı özellikler ve NNMF tabanlı özelliklerdir. Öznitelik çıkarma tekniklerini kayıtlı yüzlerin üç farklı temsiline uyguluyoruz: 3B nokta bulutları, 2B derinlik görüntüleri ve 3B voksel temsilleri. Ayrıca, 2D derinlik görüntüleri ve bunların füzyon şemaları üzerindeki blok tabanlı DFT veya DCT tabanlı yerel özellikleri de dikkate alıyoruz. 3D-RMA veri seti üzerinde farklı temsil türleri ve özellik vektörleri kombinasyonları kullanılarak deneyler yapılmıştır.Publication Open Access 3D face recognition by projection based methods(Society of Photo-optical Instrumentation Engineers (SPIE), 2006) Dutaǧaci, Helin; Sankur, Bülent; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of EngineeringIn this paper, we investigate recognition performances of various projection-based features applied on registered 3D scans of faces. Some features are data driven, such as ICA-based features or NNMF-based features. Other features are obtained using DFT or DCT-based schemes. We apply the feature extraction techniques to three different representations of registered faces, namely, 3D point clouds, 2D depth images and 3D voxel. We consider both global and local features. Global features are extracted from the whole face data, whereas local features are computed over the blocks partitioned from 2D depth images. The block-based local features are fused both at feature level and at decision level. The resulting feature vectors are matched using Linear Discriminant Analysis. Experiments using different combinations of representation types and feature vectors are conducted on the 3D-RMA dataset.Publication Metadata only 3D model retrieval using probability density-based shape descriptors(IEEE Computer Society, 2009) Akgul, Ceyhun Burak; Sankur, Buelent; Schmitt, Francis; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; 107907We address content-based retrieval of complete 3D object models by a probabilistic generative description of local shape properties. The proposed shape description framework characterizes a 3D object with sampled multivariate probability density functions of its local surface features. This density-based descriptor can be efficiently computed via kernel density estimation (KDE) coupled with fast Gauss transform. The nonparametric KDE technique allows reliable characterization of a diverse set of shapes and yields descriptors which remain relatively insensitive to small shape perturbations and mesh resolution. Density-based characterization also induces a permutation property which can be used to guarantee invariance at the shape matching stage. As proven by extensive retrieval experiments on several 3D databases, our framework provides state-of-the-art discrimination over a broad and heterogeneous set of shape categories.Publication Metadata only 3D progressive compression with octree particles(Akademische Verlagsgesellsch Aka Gmbh, 2002) Schmitt, Francis; Department of Computer Engineering; N/A; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; N/A; 107907; N/AThis paper improves the storage efficiency of the progressive particle-based modeling scheme presented in [14, 15] by using entropy coding techniques. This scheme encodes the surface geometry and attributes in terms of appropriately ordered oc-tree particles, which can then progressively be decoded and rendered by the-viewer by means of a fast direct triangulation technique. With the introduced entropy coding technique, the bitload of the multi-level representation for geometry encoding reduces to 9-14 bits per particle (or 4.5-7 bits per triangle) for 12-bit quantized geometry.Publication Metadata only 3D reconstruction of real objects with high resolution shape and texture(Elsevier, 2004) Schmitt, F; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; 107907We present a robust and accurate system for 3D reconstruction of real objects with high resolution shape and texture. Our reconstruction method is passive, the only information needed being 2D images obtained with a calibrated camera from different view angles as the object rotates on a turntable. The triangle surface model is obtained by a scheme combining octree construction and marching cubes algorithm, which is adapted to the shape from silhouette problem. We develop a texture mapping strategy based on surface particles to adequately address photography related problems such as inhomogeneous lighting, highlights and occlusion. Reconstruction results are included to demonstrate the attained quality.Publication Metadata only 3D shape correspondence by isometry-driven greedy optimization(IEEE Computer Soc, 2010) N/A; Department of Computer Engineering; Sahillioğlu, Yusuf; Yemez, Yücel; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; 215195; 107907We present an automatic method that establishes 3D correspondence between isometric shapes. Our goal is to find an optimal correspondence between two given (nearly) isometric shapes, that minimizes the amount of deviation from isometry. We cast the problem as a complete surface correspondence problem. Our method first divides the given shapes to be matched into surface patches of equal area and then seeks for a mapping between the patch centers which we refer to as base vertices. Hence the correspondence is established in a fast and robust manner at a relatively coarse level as imposed by the patch radius. We optimize the isometry cost in two steps. in the first step, the base vertices are transformed into spectral domain based on geodesic affinity, where the isometry errors are minimized in polynomial time by complete bipartite graph matching. the resulting correspondence serves as a good initialization for the second step of optimization in which we explicitly minimize the isometry cost via an iterative greedy algorithm in the original 3D Euclidean space. We demonstrate the performance of our method on various isometric (or nearly isometric) pairs of shapes for some of which the ground-truth correspondence is available.Publication Metadata only 3D Shape recovery and tracking from multi-camera video sequences via surface deformation(IEEE, 2006) Skala, V.; N/A; Department of Computer Engineering; Sahillioğlu, Yusuf; Yemez, Yücel; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; 215195; 107907This paper addresses 3D reconstruction and modeling of time-varying real objects using multicamera video. The work consists of two phases. In the first phase, the initial shape of the object is recovered from its silhouettes using a surface deformation model. The same deformation model is also employed in the second phase to track the recovered initial shape through the time-varying silhouette information by surface evolution. The surface deformation/evolution model allows us to construct a spatially and temporally smooth surface mesh representation having fixed connectivity. This eventually leads to an overall space-time representation that preserves the semantics of the underlying motion and that is much more efficient to process, to visualize, to store and to transmit.Publication Metadata only 3D shape recovery and tracking from multi-camera video sequences via surface deformation(Institute of Electrical and Electronics Engineers (IEEE), 2006) Skala, V.; N/A; Department of Computer Engineering; Sahillioğlu, Yusuf; Yemez, Yücel; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; 215195; 107907This paper addresses 3D reconstruction and modeling of time-varying real objects using multicamera video. The work consists of two phases. In the first phase, the initial shape of the object is recovered from its silhouettes using a surface deformation model. The same deformation model is also employed in the second phase to track the recovered initial shape through the time-varying silhouette information by surface evolution. The surface deformation/evolution model allows us to construct a spatially and temporally smooth surface mesh representation having fixed connectivity. This eventually leads to an overall space-time representation that preserves the semantics of the underlying motion and that is much more efficient to process, to visualize, to store and to transmit. / Bu makale, çok kameralı video kullanarak zamanla değişen gerçek nesnelerin 3B yeniden yapılandırılmasını ve modellenmesini ele almaktadır. Çalışma iki aşamadan oluşmaktadır. İlk aşamada, nesnenin ilk şekli, bir yüzey deformasyon modeli kullanılarak silüetlerinden kurtarılır. Aynı deformasyon modeli, ikinci aşamada, yüzey evrimi yoluyla zamanla değişen siluet bilgisi yoluyla geri kazanılan ilk şekli izlemek için de kullanılır. Yüzey deformasyonu/evrimi modeli, sabit bağlantıya sahip uzamsal ve zamansal olarak pürüzsüz bir yüzey ağ temsili oluşturmamıza izin verir. Bu, sonunda, altta yatan hareketin anlamını koruyan ve işlemesi, görselleştirmesi, depolaması ve iletmesi çok daha verimli olan genel bir uzay-zaman temsiline yol açar.Publication Open Access 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients(Public Library of Science, 2019) Dinçer, Cansu; Kaya, Tuğba; Tunçbağ, Nurcan; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; 26605; 8745Glioblastoma multiforme (GBM) is the most aggressive type of brain tumor. Molecular heterogeneity is a hallmark of GBM tumors that is a barrier in developing treatment strategies. In this study, we used the nonsynonymous mutations of GBM tumors deposited in The Cancer Genome Atlas (TCGA) and applied a systems level approach based on biophysical characteristics of mutations and their organization in patient-specific subnetworks to reduce inter-patient heterogeneity and to gain potential clinically relevant insights. Approximately 10% of the mutations are located in "patches" which are defined as the set of residues spatially in close proximity that are mutated across multiple patients. Grouping mutations as 3D patches reduces the heterogeneity across patients. There are multiple patches that are relatively small in oncogenes, whereas there are a small number of very large patches in tumor suppressors. Additionally, different patches in the same protein are often located at different domains that can mediate different functions. We stratified the patients into five groups based on their potentially affected pathways, revealed from the patient-specific subnetworks. These subnetworks were constructed by integrating mutation profiles of the patients with the interactome data. Network-guided clustering showed significant association between each group and patient survival (P-value = 0.0408). Also, each group carries a set of signature 3D mutation patches that affect predominant pathways. We integrated drug sensitivity data of GBM cell lines with the mutation patches and the patient groups to analyze the therapeutic outcome of these patches. We found that Pazopanib might be effective in Group 3 by targeting CSF1R. Additionally, inhibiting ATM that is a mediator of PTEN phosphorylation may be ineffective in Group 2. We believe that from mutations to networks and eventually to clinical and therapeutic data, this study provides a novel perspective in the network-guided precision medicine.Publication Metadata only A calculus of atomic actions(N/A, 2009) Qadeer, Shaz; N/A; Department of Computer Engineering; Elmas, Tayfun; Taşıran, Serdar; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/AWe present a proof calculus and method for the static verification of assertions and procedure specifications in shared-memory concurrent programs. The key idea in our approach is to use atomicity as a proof tool and to simplify the verification of assertions by rewriting programs to consist of larger atomic actions. We propose a novel, iterative proof style in which alternating use of abstraction and reduction is exploited to compute larger atomic code blocks in a sound manner. This makes possible the verification of assertions in the transformed program by simple sequential reasoning within atomic blocks, or significantly simplified application of existing concurrent program verification techniques such as the Owicki-Gries or rely-guarantee methods. Our method facilitates a clean separation of concerns where at each phase of the proof, the user worries only about only either the sequential properties or the concurrency control mechanisms in the program. We implemented our method in a tool called QED.We demonstrate the simplicity and effectiveness of our approach on a number of benchmarks including ones with intricate concurrency protocols.