====Schedule===== We meet on Tuesdays 11:00-12:30pm in 32-D407. Feel free to add papers to the paper stack. To join the reading group, feel free to: * subscribe to [[http://lists.csail.mit.edu/mailman/listinfo/v-golland | v-golland email list at csail]]. * To get access to the wiki, please contact Margherita Firenze at mfirenze at csail.mit.edu ===== Next meeting: ===== == May 21 == Cameras as Rays: Pose Estimation via Ray Diffusion \\ Zhang et al., ICLR 2024 \\ https://arxiv.org/abs/2402.14817 ===== Paper list Spring 2024 ===== 3D shape reconstruction of semi-transparent worms \\ Ilett et al., CVPR 2023 \\ https://arxiv.org/abs/2304.14841 NECA: Neural Customizable Human Avatar \\ Xiao et al., CVPR 2024 \\ https://arxiv.org/abs/2403.10335 Random Features for Large-Scale Kernel Machines \\ Rahimi and Recht, NeurIPS 2007 \\ https://proceedings.neurips.cc/paper/2007/hash/013a006f03dbc5392effeb8f18fda755-Abstract.html KAN: Kolmogorov-Arnold Networks \\ Liu et al. \\ https://arxiv.org/abs/2404.19756 ===== Past meetings: ===== ==== Spring 2024 ==== == May 14 == Towards Unbounded Machine Unlearning \\ https://openreview.net/pdf?id=OveBaTtUAT == May 7 == Learning with 3D rotations, a hitchhiker's guide to SO(3) \\ https://arxiv.org/abs/2404.11735 == Apr 30 == PWC-net \\ https://arxiv.org/pdf/1709.02371 == Apr 23 == MLP-Mixer \\ https://arxiv.org/abs/2105.01601 == Apr 16 == Particle Video Revisited: Tracking Through Occlusions Using Point Trajectories \\ https://particle-video-revisited.github.io == Apr 9 == DUSt3R: Geometric 3D Vision Made Easy \\ https://dust3r.europe.naverlabs.com/ == Apr 2 == Alias-Free Generative Adversarial Networks \\ https://arxiv.org/abs/2106.12423 == Mar 26 == 3D Gaussian Splatting for Real-Time Radiance Field Rendering \\ https://arxiv.org/abs/2308.04079 == Mar 19 == How Faithful is your Synthetic Data? Sample-level Metrics for Evaluating and Auditing Generative Models \\ https://arxiv.org/abs/2102.08921 == Mar 12 == "Bayes' Rays: Uncertainty Quantification for Neural Radiance Fields" \\ https://arxiv.org/abs/2309.03185 == Mar 5 == Hough transforms for geometrical shape detection: \\ https://link.springer.com/chapter/10.1007/978-3-031-43990-2_42 (we didn't get to this today) Structured State Space Models for Multiple Instance Learning in Digital Pathology \\ https://link.springer.com/chapter/10.1007/978-3-031-43907-0_57 == Feb 27 == Learning Deep Intensity Field for Extremely Sparse-View CBCT Reconstruction \\ https://link.springer.com/chapter/10.1007/978-3-031-43999-5_2 == Feb 20 == NISF: Neural Implicit Segmentation Functions \\ https://link.springer.com/chapter/10.1007/978-3-031-43901-8_70 == Feb 13 == snow day! suggested: https://www.sciencedirect.com/science/article/pii/S0165232X19302034 == January 30 == CamP: Camera Preconditioning for Neural Radiance Fields \\ https://arxiv.org/abs/2308.10902 == January 23 == Deep Kalman Filters \\ https://arxiv.org/pdf/1511.05121.pdf == January 16 == Nonparametric Object and Parts Modeling with Lie Group Dynamics \\ https://sli.csail.mit.edu/pdfs/publications/hayden2020cvpr.pdf == January 9 == Variational Learning for Switching State-Space Models \\ https://www.cs.toronto.edu/~hinton/absps/switch.pdf ==== Fall 2023 ==== == December 11 == Neural Kernel Surface Reconstruction \\ https://arxiv.org/pdf/2305.19590.pdf == December 4 == Neural Fields As Learnable Kernels for 3D Reconstruction \\ https://arxiv.org/abs/2111.13674 == November 27 == Bias and Generalization in Deep Generative Models \\ https://arxiv.org/pdf/1811.03259.pdf == November 20 == Curriculum Learning \\ https://dl.acm.org/doi/pdf/10.1145/1553374.1553380 == November 13 == Unified Brain MR-Ultrasound Synthesis using Multi-Modal Hierarchical Representations \\ DISA: DIfferentiable Similarity Approximation for Universal Multimodal Registration \\ == November 6 == Foundation Ark: Accruing and Reusing Knowledge for Superior and Robust Performance \\ https://link.springer.com/chapter/10.1007/978-3-031-43907-0_62 MultiTalent: A Multi-Dataset Approach to Medical Image Segmentation \\ https://link.springer.com/chapter/10.1007/978-3-031-43898-1_62 == October 30 == Bill Freeman and Ted Adelson, The design and use of steerable filters, IEEE TPAMI 1991 \\ http://people.csail.mit.edu/billf/www/papers/steerpaper91FreemanAdelson.pdf == October 23 == A Program to Build E(N)-Equivariant Steerable CNNs \\ ICLR 2022 \\ https://openreview.net/forum?id=WE4qe9xlnQw == October 16 == Vector Neurons: A General Framework for SO(3)-Equivariant Networks \\ ICCV 2021 \\ https://arxiv.org/abs/2104.12229 == October 2 == Closed-form solution of absolute orientation using unit quaternions \\ Journal of the Optical Society of America 1987 \\ https://www.cvl.iis.u-tokyo.ac.jp/~oishi/Papers/Alignment/Horn_Closed-form_JOSA1987.pdf == September 25 == Mastering the game of Go without human knowledge \\ Nature 2017 \\ https://ai6034.mit.edu/wiki/images/Nature24270_AlphaGoZero.pdf == September 18 == Evaluating reinforcement learning agents for anatomical landmark detection \\ MIDL 2018 \\ https://openreview.net/pdf?id=SyQK4-nsz == September 11 == Robust non-rigid registration through agent-based action learning \\ https://inria.hal.science/hal-01569447/document == August 30 == Deep Equilibrium Models \\ https://arxiv.org/abs/1909.01377 == August 23 == Self-Supervised Deep Equilibrium Models for Inverse Problems with Theoretical Guarantees \\ https://arxiv.org/abs/2210.03837 ==== Spring 2023 ==== == May 4 == Consistent Accelerated Inference via Confident Adaptive Transformers \\ https://arxiv.org/pdf/2104.08803.pdf == April 27 == Formal Limitations on the Measurement of Mutual Information \\ https://arxiv.org/pdf/1811.04251.pdf == April 20 == Understanding Contrastive Representation Learning through Alignment and Uniformity on the Hypersphere \\ https://arxiv.org/abs/2005.10242 == April 13 == Contrastive Learning Inverts the Data Generating Process \\ ICML 2021 \\ Zimmermann, Roland S., Yash Sharma, Steffen Schneider, Matthias Bethge, and Wieland Brendel \\ https://proceedings.mlr.press/v139/zimmermann21a.html == March 30 == Frequency Bias in Neural Networks for Input of Non-Uniform Density \\ ICML 2020 \\ Ronen Basri, Meirav Galun, Amnon Geifman, David Jacobs, Yoni Kasten, Shira Kritchman \\ https://arxiv.org/abs/2003.04560 == March 23 == On the Spectral Bias of Neural Networks \\ ICML 2019 \\ Nasim Rahaman, Aristide Baratin, Devansh Arpit, Felix Draxler, Min Lin, Fred A. Hamprecht, Yoshua Bengio, Aaron Courville \\ https://arxiv.org/abs/1806.08734 == March 16 == Combining Labeled and Unlabeled Data with Co-Training \\ COLT 1998 \\ Avrim Blum and Tom Mitchell \\ https://www.cs.cmu.edu/~avrim/Papers/cotrain.pdf == March 9 == Model-agnostic meta-learning for fast adaptation of deep networks. \\ ICML 2017 \\ Finn, Chelsea, Pieter Abbeel, and Sergey Levine \\ https://proceedings.mlr.press/v70/finn17a.html == March 2 == Spectral Representations for Convolutional Neural Networks \\ NeurIPS 2015 \\ Oren Rippel, Jasper Snoek, Ryan P. Adams \\ https://proceedings.neurips.cc/paper/2015/hash/536a76f94cf7535158f66cfbd4b113b6-Abstract.html == February 23 == Image-to-Image Regression with Distribution-Free Uncertainty Quantification and Applications in Imaging.\\ Anastasios N. Angelopoulos, Amit Kohli, Stephen Bates, Michael I. Jordan, Jitendra Malik.\\ https://arxiv.org/pdf/2202.05265.pdf == February 16 == A Practical Method for Constructing Equivariant Multilayer Perceptrons for Arbitrary Matrix Groups \\ ICML 2021 \\ Marc Finzi, Max Welling, Andrew Gordon Wilson \\ https://proceedings.mlr.press/v139/finzi21a.html == February 2 == EigenGame: PCA as a Nash Equilibrium \\ ICLR 2021 \\ Ian Gemp, Brian McWilliams, Claire Vernade, Thore Graepel \\ https://arxiv.org/abs/2010.00554 == January 26 == A Tutorial on Conformal Prediction. \\ JMRL 2008 \\ Glenn Shafer, Vladimir Vovk. \\ https://jmlr.csail.mit.edu/papers/volume9/shafer08a/shafer08a.pdf \\ Video on a follow up work from Berkeley: https://www.youtube.com/watch?v=nql000Lu_iE ==== Fall 2022 ==== == December 8 == Fourier PlenOctrees for Dynamic Radiance Field Rendering in Real-time \\ Liao Wang, Jiakai Zhang, Xinhang Liu, Fuqiang Zhao, Yanshun Zhang, Yingliang Zhang, Minye Wu, Lan Xu, Jingyi Yu \\ https://arxiv.org/abs/2202.08614v2 == November 17 == Nonuniform fast Fourier transforms using min-max interpolation. \\ Fessler, Jeffrey A., and Bradley P. Sutton. \\ IEEE transactions on signal processing 51.2 (2003): 560-574. {{fessler_nufft.pdf}} == November 3 == GLIDE: Towards Photorealistic Image Generation and Editing with Text-Guided Diffusion Models \\ https://proceedings.mlr.press/v162/nichol22a.html \\ == October 20, 2022 == Understanding Diffusion Models: A Unified Perspective \\ Calvin Luo \\ https://arxiv.org/abs/2208.11970 \\ == October 13, 2022 == Gaussian Processes for Machine Learning (Book - chapters 1 and 2) \\ Edward Rasmussen, Christopher Williams \\ https://gaussianprocess.org/gpml/ \\ == October 6, 2022 == Neural Tangent Kernel: Convergence and Generalization in Neural Networks \\ Arthur Jacot, Franck Gabriel, Clément Hongler \\ NeurIPS 2018 \\ https://arxiv.org/abs/1806.07572 \\ == September 29, 2022 == Neural Tangent Kernel: Convergence and Generalization in Neural Networks \\ Arthur Jacot, Franck Gabriel, Clément Hongler \\ NeurIPS 2018 \\ https://arxiv.org/abs/1806.07572 \\ == September 22, 2022 == A Structured Dictionary Perspective on Implicit Neural Representations \\ Gizem Yüce, Guillermo Ortiz-Jiménez, Beril Besbinar, Pascal Frossard \\ CVPR 2022 \\ https://arxiv.org/abs/2112.01917 \\ == September 15, 2022 == Vox2Cortex: Fast Explicit Reconstruction of Cortical Surfaces from 3D MRI Scans with Geometric Deep Neural Networks \\ Fabian Bongratz, Anne-Marie Rickmann, Sebastian Pölsterl, Christian Wachinger \\ CVPR 2022 \\ https://arxiv.org/abs/2203.09446 \\ == September 08, 2022 == We briefly discussed a stack of papers on self-supervision for image time-series: \\ Slow and steady feature analysis: higher order temporal coherence in video \\ Dinesh Jayaraman and Kristen Grauman \\ CVPR 2016 \\ https://openaccess.thecvf.com/content_cvpr_2016/papers/Jayaraman_Slow_and_Steady_CVPR_2016_paper.pdf Learning and using the arrow of time \\ Donglai Wei, Joseph J. Lim, Andrew Zisserman, and William T. Freeman \\ CVPR 2018 \\ https://openaccess.thecvf.com/content_cvpr_2018/papers/Wei_Learning_and_Using_CVPR_2018_paper.pdf Joint-task self-supervised learning for temporal correspondence \\ Xueting Li, Sifei Liu, Shalini De Mello, Xiaolong Wang, Jan Kautz, and Ming-Hsuan Yang\\ NeurIPS 2019 \\ https://proceedings.neurips.cc/paper/2019/file/140f6969d5213fd0ece03148e62e461e-Paper.pdf Learning correspondence from the cycle-consistency of time \\ Xiaolong Wang, Allan Jabri, and Alexei A. Efros \\ CVPR 2019 \\ https://openaccess.thecvf.com/content_CVPR_2019/papers/Wang_Learning_Correspondence_From_the_Cycle-Consistency_of_Time_CVPR_2019_paper.pdf Learning pixel trajectories with multiscale contrastive random walks \\ Zhangxing Bian, Allan Jabri, Alexei A. Efros, and Andrew Owens \\ CVPR 2022 \\ https://openaccess.thecvf.com/content/CVPR2022/papers/Bian_Learning_Pixel_Trajectories_With_Multiscale_Contrastive_Random_Walks_CVPR_2022_paper.pdf ==== Summer 2022 ==== == August 26, 2022 == Space-Time Correspondence as a Contrastive Random Walk \\ Allan Jabri, Andrew Owens, Alexei Efros \\ NeurIPS 2020 \\ https://proceedings.neurips.cc/paper/2020/file/e2ef524fbf3d9fe611d5a8e90fefdc9c-Paper.pdf == August 19, 2022 == Noether Networks: meta-learning useful conserved quantities \\ Alet, Ferran, Dylan Doblar, Allan Zhou, Josh Tenenbaum, Kenji Kawaguchi, Chelsea Finn \\ NeurIPS 2021 \\ https://proceedings.neurips.cc/paper/2021/file/886ad506e0c115cf590d18ebb6c26561-Paper.pdf == August 12, 2022 == BIGPrior: Towards Decoupling Learned Prior Hallucination and Data Fidelity in Image Restoration \\ Majed El Helou, Sabine Süsstrunk \\ IEEE TIP 2022 \\ https://arxiv.org/abs/2011.01406 == August 5, 2022 == Prototypical Networks for Few-shot Learning \\ Jake Snell, Kevin Swersky, Richard S. Zemel \\ NeurIPS 2017 \\ https://arxiv.org/abs/1703.05175 == July 29, 2022 == Fourier Features Let Networks Learn High Frequency Functions in Low Dimensional Domains \\ Matthew Tancik, Pratul P. Srinivasan, Ben Mildenhall, Sara Fridovich-Keil, Nithin Raghavan, Utkarsh Singhal, Ravi Ramamoorthi, Jonathan T. Barron, Ren Ng \\ NeurIPS 2020 \\ https://arxiv.org/abs/2006.10739 == July 22, 2022 == Neural Tangent Kernel: Convergence and Generalization in Neural Networks \\ Arthur Jacot, Franck Gabriel, Clément Hongler \\ NeurIPS 2018 \\ https://arxiv.org/abs/1806.07572 == July 15, 2022 == Reconstructing continuous distributions of 3D protein structure from cryo-EM images \\ Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger \\ ICLR 2020 \\ https://arxiv.org/abs/1909.05215 == July 8, 2022 == Chapter 6.1 of Numerical Optimization by Nocedal and Wright \\ The BFGS Method and its Convergence Analysis (pg. 135-143, 153-160) \\ {{nocedal-wright2006_book_numericaloptimization.pdf}} == July 1, 2022 == Chapter 5.2 of Numerical Optimization by Nocedal and Wright \\ Non-Linear Conjugate Gradient (pg. 121-134) \\ {{nocedal-wright2006_book_numericaloptimization.pdf}} == June 24, 2022 == Chapter 5.1 of Numerical Optimization by Nocedal and Wright \\ Convergence Rate and Preconditioning (pg. 112-120) \\ {{nocedal-wright2006_book_numericaloptimization.pdf}} == June 17, 2022 == Chapter 5.1 of Numerical Optimization by Nocedal and Wright \\ Linear Conjugate Gradient Method (pg. 101-111) \\ {{nocedal-wright2006_book_numericaloptimization.pdf}} == June 10, 2022 == DiffusionNet: Discretization Agnostic Learning on Surfaces \\ Nicholas Sharp, Souhaib Attaiki, Keenan Crane, Maks Ovsjanikov \\ https://arxiv.org/abs/2012.00888 == June 3, 2022 == Occupancy Flow: 4D Reconstruction by Learning Particle Dynamics \\ M Niemeyer, L Mescheder, M Oechsle, A Geiger \\ https://openaccess.thecvf.com/content_ICCV_2019/html/Niemeyer_Occupancy_Flow_4D_Reconstruction_by_Learning_Particle_Dynamics_ICCV_2019_paper.html {{fessler_nufft.pdf}} ==== Spring 2022 ==== == April 22, 2022 == Swin Transformer: Hierarchical Vision Transformer using Shifted Windows \\ Ze Liu, Yutong Lin, Yue Cao, Han Hu, Yixuan Wei, Zheng Zhang, Stephen Lin, Baining Guo \\ https://arxiv.org/abs/2103.14030 OR Emerging Properties in Self-Supervised Vision Transformers \\ Mathilde Caron, Hugo Touvron, Ishan Misra, Hervé Jégou, Julien Mairal, Piotr Bojanowski, Armand Joulin \\ https://arxiv.org/abs/2104.14294 OR Masked Autoencoders Are Scalable Vision Learners \\ Kaiming He, Xinlei Chen, Saining Xie, Yanghao Li, Piotr Dollár, Ross Girshick \\ https://arxiv.org/abs/2111.06377 == April 15, 2022 == An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale \\ Alexey Dosovitskiy, Lucas Beyer, Alexander Kolesnikov, Dirk Weissenborn, Xiaohua Zhai, Thomas Unterthiner, Mostafa Dehghani, Matthias Minderer, Georg Heigold, Sylvain Gelly, Jakob Uszkoreit, Neil Houlsby \\ https://arxiv.org/abs/2010.11929 == April 8 == Deep Diffeomorphic Normalizing Flows Hadi Salman, Payman Yadollahpour, Tom Fletcher, Kayhan Batmanghelich https://arxiv.org/abs/1810.03256 == April 1, 2022 == DeepGEM: Generalized Expectation-Maximization for Blind Inversion \\ Angela Gao, Jorge Castellanos, Yisong Yue, Zachary Ross, Katherine Bouman \\ https://proceedings.neurips.cc/paper/2021/hash/606c90a06173d69682feb83037a68fec-Abstract.html == March 18, 2022 == The Optimal Noise in Noise-Contrastive Learning Is Not What You Think \\ Chehab, Gramfort, Hyvarinen \\ https://arxiv.org/abs/2203.01110 == February 25, 2022 == Flood-Filling Networks \\ Michał Januszewski, Jeremy Maitin-Shepard, Peter Li, Jörgen Kornfeld, Winfried Denk, Viren Jain \\ https://arxiv.org/pdf/1611.00421.pdf ==== Fall 2021 ==== == Dec 1 == C. Chen et al., Realistic Adversarial Data Augmentation for MR Image Segmentation, MICCAI 2020{{chen-etal-realistic-aug.pdf}} == Nov 17 == A Semantic Loss Function for Deep Learning with Symbolic Knowledge, ICML 2018 (https://arxiv.org/pdf/1711.11157) == Nov 10 == R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker. Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps. PNAS, 2005. {{wiki:geometric-diffusion1.pdf}} **A survey of applications for background reading**: R. Talmon, I. Cohen, S. Gannot, and R. R. Coifman. Diffusion maps for signal processing. IEEE Signal Processing magazine, 2013. {{talmon_diffusion_sp.pdf}} == November 3 == Deformable Slice-to-Volume Registration for Motion Correction of Fetal Body and Placenta MRI by Uus et al., 2020 {{slice-to-volume-reg-placenta.pdf}} ** Background reading: ** - Reconstruction of fetal brain MRI with intensity matching and complete outlier removal by Kuklisova Murgasova Deprez et al., 2012 {{reconstruction_fetal_brain_mri_deprez2012.pdf}} - A survey on slice to volume reconstruction: Slice-to-volume medical image registration: a survey by Ferrante et al., 2017 {{slice-to-vol-survey.pdf}} == October 20 == Representation Learning with Contrastive Predictive Coding \\ [PDF] https://arxiv.org/pdf/1807.03748.pdf == October 6 == Estimation of Non-normalized Statistical Models by Score Matching \\ Aapo Hyvarinen \\ [PDF] https://jmlr.org/papers/volume6/hyvarinen05a/old.pdf == September 29 == Robust Compressed Sensing MRI with Deep Generative Priors \\ Ajil Jalal, et al. \\ https://arxiv.org/abs/2108.01368 == September 22 == Bayesian Learning via Stochastic Gradient Langevin Dynamics \\ Max Welling and Yee Whye Teh \\ https://www.stats.ox.ac.uk/~teh/research/compstats/WelTeh2011a.pdf For proof of convergence of Langevin dynamics (both continuous and discrete) to the posterior: \\ Langevin Diffusions and Metropolis-Hastings Algorithms \\ G.O. Roberts and O. Stramer \\ https://link.springer.com/content/pdf/10.1023/A:1023562417138.pdf == September 1 == HodgeNet: Learning Spectral Geometry on Triangle Meshes \\ Dmitriy Smirnov and Justin Solomon \\ https://arxiv.org/pdf/2104.12826.pdf ==== Summer 2021 ==== == August 25 == MeshCNN: A Network with an Edge \\ Rana Hanocka, Amir Hertz, Noa Fish, Raja Giryes, Shachar Fleishman, Daniel Cohen-Or \\ https://arxiv.org/pdf/1809.05910.pdf == August 11 == CyCADA: Cycle-Consistent Adversarial Domain Adaptation \\ Judy Hoffman, Eric Tzeng, Taesung Park, Jun-Yan Zhu, Phillip Isola, Kate Saenko, Alexei A. Efros, Trevor Darrell \\ https://arxiv.org/abs/1711.03213 == August 4 == Beyond pixel-wise supervision for segmentation: A few global shape descriptors might be surprisingly good! \\ Kervadec et al. 2021 (MIDL, Best Paper Award) \\ [pdf] https://2021.midl.io/proceedings/kervadec21.pdf ==== Spring 2021 ==== == May 10 == Deep Parametric Continuous Convolutional Neural Networks \\ Shenlong Wang,Simon Suo,Wei-Chiu Ma, Andrei Pokrovsky, and Raquel Urtasun \\ https://openaccess.thecvf.com/content_cvpr_2018/papers/Wang_Deep_Parametric_Continuous_CVPR_2018_paper.pdf == May 3 == Meta-Learning with Latent Embedding Optimization \\ Andrei A. Rusu, Dushyant Rao, Jakub Sygnowski, Oriol Vinyals, Razvan Pascanu, Simon Osindero, Raia Hadsell \\ https://arxiv.org/abs/1807.05960 == April 26 == Fourier Features Let Networks Learn High Frequency Functions in Low Dimensional Domains \\ Matthew Tancik, Pratul P. Srinivasan, Ben Mildenhall, Sara Fridovich-Keil, Nithin Raghavan, Utkarsh Singhal, Ravi Ramamoorthi, Jonathan T. Barron, Ren Ng \\ https://arxiv.org/abs/2006.10739 == April 12 == A Simple Framework for Contrastive Learning of Visual Representations \\ Ting Chen, Simon Kornblith, Mohammad Norouzi, Geoffrey Hinton \\ https://arxiv.org/abs/2002.05709 == April 5 == AutoInt: Automatic Integration for Fast Neural Volume Rendering \\ David B. Lindell, Julien N. P. Martel, Gordon Wetzstein \\ https://arxiv.org/abs/2012.01714 == March 29 == NeRF: Representing Scenes as Neural Radiance Fields for View Synthesis \\ Ben Mildenhall, Pratul P. Srinivasan, Matthew Tancik, Jonathan T. Barron, Ravi Ramamoorthi, Ren Ng \\ https://arxiv.org/abs/2003.08934 == March 22 == Image Registration via Stochastic Gradient Markov Chain Monte Carlo (https://doi.org/10.1007/978-3-030-60365-6_1) == March 15 == Evidential Deep Learning to Quantify Classification Uncertainty (https://arxiv.org/pdf/1806.01768.pdf) == March 8 == Spherical Deformable U-Net: Application to Cortical Surface Parcellation and Development Prediction \\ Zhao et al.{{spherical_unet.pdf}} == March 1 == RARE: Image Reconstruction using Deep Priors Learned without Ground Truth \\ Jiaming Liu, Yu Sun, Cihat Eldeniz, Weijie Gan, Hongyu An, Ulugbek S. Kamilov \\ https://arxiv.org/abs/1912.05854 == Feb 22 == The little engine that could: Regularization by denoising (RED) \\ Yaniv Romano, Michael Elad, and Peyman Milanfar \\ https://epubs.siam.org/doi/10.1137/16M1102884 {{RED.pdf}} == Feb 8 == B-spline Parameterized Joint Optimization of Reconstruction and K-space Trajectories (BJORK) for Accelerated 2D MRI \\ Guanhua Wang, Tianrui Luo, Jon-Fredrik Nielsen, Douglas C. Noll, Jeffrey A. Fessler \\ https://arxiv.org/abs/2101.11369 == Feb 1 == CBAM: Convolutional Block Attention Module \\ Sanghyun Woo, Jongchan Park, Joon-Young Lee, In So Kweon \\ ECCV 2018 \\ https://openaccess.thecvf.com/content_ECCV_2018/html/Sanghyun_Woo_Convolutional_Block_Attention_ECCV_2018_paper.html Attention Augmented Convolutional Networks \\ Irwan Bello, Barret Zoph, Ashish Vaswani, Jonathon Shlens, Quoc V. Le \\ ICCV 2019 \\ https://openaccess.thecvf.com/content_ICCV_2019/html/Bello_Attention_Augmented_Convolutional_Networks_ICCV_2019_paper.html == Jan 25 == Linear Predictability in Magnetic Resonance Imaging Reconstruction: Leveraging Shift-Invariant Fourier Structure for Faster and Better Imaging \\ Justin P. Haldar, Kawin Setsompop https://ieeexplore.ieee.org/abstract/document/8962389 == Jan 11 == * Attention is all you need: https://arxiv.org/pdf/1706.03762.pdf (introduces attention) * On the Relationship between Self-Attention and Convolutional Layers: https://arxiv.org/pdf/1911.03584.pdf (shows attention learns to perform a convolution) == Jan 4 == Information-Theoretic Segmentation by Inpainting Error Maximization https://arxiv.org/abs/2012.07287 ==== Fall 2020 ==== == Dec 14 == Dubois, Yann, Douwe Kiela, David J. Schwab, and Ramakrishna Vedantam. "Learning Optimal Representations with the Decodable Information Bottleneck." Advances in Neural Information Processing Systems 33 (2020). https://arxiv.org/pdf/2009.12789.pdf == November 23 == Geometric deep learning: going beyond Euclidean data \\ https://arxiv.org/pdf/1611.08097.pdf == November 2 == Dimensionality Reduction by Learning an Invariant Mapping \\ http://yann.lecun.com/exdb/publis/pdf/hadsell-chopra-lecun-06.pdf == October 26 == Deep Compressed Sensing \\ Wu et. al, in ICML 2019 \\ https://arxiv.org/abs/1905.06723 == October 19 == Domain Generalization for Medical Imaging Classification with Linear-Dependency Regularization \\ https://arxiv.org/abs/2009.12829 == September 21 == Invariant Risk Minimization \\ https://arxiv.org/abs/1907.02893 == September 14 == Neural Tangent Kernel: Convergence and Generalization in Neural Networks \\ https://arxiv.org/abs/1806.07572 ==== Summer 2020 ==== == August 31 == Semi-Supervised Learning with Ladder Networks \\ https://arxiv.org/abs/1507.02672 == August 24 == Structural Autoencoders Improve Representations for Generation and Transfer \\ https://arxiv.org/abs/2006.07796​ == August 17 == Training Generative Adversarial Networks with Limited Data, Karras et al. \\ https://arxiv.org/abs/2006.06676 == August 10 == A Fourier Perspective on Model Robustness in Computer Vision \\ Yin et al, 2020 \\ [pdf] https://arxiv.org/abs/1906.08988 == Summer 2020 Book == Elements of Causal Inference Peters, Janzing, and Scholkopf [pdf] https://library.oapen.org/bitstream/id/056a11be-ce3a-44b9-8987-a6c68fce8d9b/11283.pdf == July 27 == Chapters 6.1, 6.2, 6.3, 6.4, 6.5 of Elements of Causal Inference [pdf] https://library.oapen.org/bitstream/id/056a11be-ce3a-44b9-8987-a6c68fce8d9b/11283.pdf == July 20 == Chapter 4.2 and 5 of Elements of Causal Inference [pdf] https://library.oapen.org/bitstream/id/056a11be-ce3a-44b9-8987-a6c68fce8d9b/11283.pdf == July 13 == Chapter 4.1 of Elements of Causal Inference [pdf] https://library.oapen.org/bitstream/id/056a11be-ce3a-44b9-8987-a6c68fce8d9b/11283.pdf == June 29 == Chapter 3 of Elements of Causal Inference [pdf] https://library.oapen.org/bitstream/id/056a11be-ce3a-44b9-8987-a6c68fce8d9b/11283.pdf == June 22 == Chapters 1 and 2 of Elements of Causal Inference [pdf] https://library.oapen.org/bitstream/id/056a11be-ce3a-44b9-8987-a6c68fce8d9b/11283.pdf == June 15 == Tutorial on Variational Autoencoders, Carl Doesch, 2016: https://arxiv.org/pdf/1606.05908.pdf Auxiliary material, Kingma and Welling tutorial on VAEs, 2019: https://arxiv.org/pdf/1906.02691.pdf == June 8 === Yen-Chun Chen and Linjie Li and Licheng Yu and Ahmed El Kholy and Faisal Ahmed and Zhe Gan and Yu Cheng and Jingjing Liu. "UNITER: UNiversal Image-TExt Representation Learning." arXiv:1909.11740 (2019). https://arxiv.org/pdf/1909.11740.pdf == June 1 == Oord, Aaron van den, Yazhe Li, and Oriol Vinyals. "Representation learning with contrastive predictive coding." arXiv preprint arXiv:1807.03748 (2018). https://arxiv.org/abs/1807.03748 == May 25 == HOLIDAY - NO MEETING == May 18 == Noise2Noise: Learning Image Restoration without Clean Data https://arxiv.org/abs/1803.04189 Extending Stein's unbiased risk estimator to train deep denoisers with correlated pairs of noisy images https://arxiv.org/abs/1902.02452 ==== Spring 2020 ==== == May 11 == k-Space Deep Learning for Accelerated MRI. Yoseob Han, Leonard Sunwoo, Jong Chul Ye, IEEE TMI. https://arxiv.org/abs/1805.03779 == May 4 == DeepSphere: A graph-based spherical CNN Michael Defferrard, Martino Milani, and Frederick Gussett. ICLR 2020 {{deepsphere_cnn.pdf}} == April 27 == Louizos, Christos, Uri Shalit, Joris M. Mooij, David Sontag, Richard Zemel, and Max Welling. "Causal effect inference with deep latent-variable models." In Advances in Neural Information Processing Systems, pp. 6446-6456. 2017. https://arxiv.org/pdf/1705.08821.pdf == April 13 == UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction Leland McInnes, John Healy, James Melville https://arxiv.org/abs/1802.03426 == April 6, 2020== Neural Discrete Representation Learning Aaron van den Oord, Oriol Vinyals, Koray Kavukcuoglu https://arxiv.org/abs/1711.00937 == March 30, 2020 == Unsupervised Learning with Stein's Unbiased Risk Estimator https://arxiv.org/abs/1805.10531 == March 16, 2020 == How Good is the Bayes Posterior in Deep Neural Networks Really? https://arxiv.org/pdf/2002.02405.pdf == March 9, 2020 == Invert to Learn to Invert https://papers.nips.cc/paper/8336-invert-to-learn-to-invert.pdf == March 2, 2020 == Deep Complex Networks https://arxiv.org/abs/1705.09792 == February 24, 2020 == Learning to Explain: An Information-Theoretic Perspective on Model Interpretation https://arxiv.org/abs/1802.07814 == February 10, 2020 == Towards Automatic Concept-based Explanations https://arxiv.org/abs/1902.03129 == February 2, 2020 == Explanation by Progressive Exaggeration Sumedha Singla, Brian Pollack, Junxiang Chen, Kayhan Batmanghelich https://arxiv.org/abs/1911.00483.pdf Updated version: https://openreview.net/forum?id=H1xFWgrFPS == January 27, 2020 == Noise-contrastive estimation: A new estimation principle for unnormalized statistical models http://proceedings.mlr.press/v9/gutmann10a/gutmann10a.pdf == January 13, 2020 == Putting An End to End-to-End:Gradient-Isolated Learning of Representations https://arxiv.org/pdf/1905.11786.pdf == January 6, 2020 == Burda et al, Importance weighted autoencoders (ICLR 2016): https://arxiv.org/abs/1509.00519 ==== Fall 2019 ==== == 16 December == The Thermodynamic Variational Objective (NeurIPS 2019): https://arxiv.org/abs/1907.00031 == 9 December == Domain-Adversarial Training of Neural Networks, JMLR 2016: http://www.jmlr.org/papers/volume17/15-239/15-239.pdf == 25 November == Zhou et al, Prior-aware Neural Network for Partially-Supervised Multi-Organ Segmentation, ICCV 2019 https://arxiv.org/abs/1904.06346 == 2 December == Show, attend and tell: Neural image caption generation with visual attention http://proceedings.mlr.press/v37/xuc15.pdf == 18 November == Compositional Attention Networks for Machine Reasoning: https://arxiv.org/abs/1803.03067 == 4 November == Models Genesis: Generic Autodidactic Models for 3D Medical Image Analysis https://arxiv.org/abs/1908.06912 == 28 October == Neural Persistence: A Complexity Measure for Deep Neural Networks Using Algebraic Topology https://arxiv.org/abs/1812.09764 A Topological Loss Function for Deep-Learning based Image Segmentation using Persistent Homology https://arxiv.org/abs/1910.01877 == 21 October == A Topology Layer for Machine Learning https://arxiv.org/abs/1905.12200 == 15 October == Predicting Slice-to-Volume Transformation in Presence of Arbitrary Subject Motion, Hou et al., MICCAI 2018 https://arxiv.org/abs/1702.08891 Fast Volume Reconstruction From Motion Corrupted Stacks of 2D Slices https://ieeexplore.ieee.org/abstract/document/7064742 == 7 October == High Accuracy Optical Flow Estimation Based on a Theory for Warping https://lmb.informatik.uni-freiburg.de/people/brox/pub/brox_eccv04_of.pdf Determining Optical Flow http://image.diku.dk/imagecanon/material/HornSchunckOptical_Flow.pdf == 30 September == Group Equivariant Convolutional Networks, Taco S. Cohen, Max Welling https://arxiv.org/abs/1602.07576# == September 23 == Andrearczyk et al, Exploring local rotation invariance in 3D CNNs with steerable filters, MIDL 2019. http://proceedings.mlr.press/v102/andrearczyk19a/andrearczyk19a.pdf == September 16 == Freeman and Adelson, The design and use of steerable filters, IEEE PAMI 1991 {{design_and_use_of_steerable_filters.pdf}} == September 9 == Weiler et al, 3D Steerable CNNs: Learning RotationallyEquivariant Features in Volumetric Data, NeurIPS 2018. http://papers.nips.cc/paper/8239-3d-steerable-cnns-learning-rotationally-equivariant-features-in-volumetric-data.pdf ==== Summer 2019 ==== == August 21 == Dihn et al, Density estimation using Real NVP, ICLR 2017 https://arxiv.org/abs/1605.08803 Gomez et al, The reversible residual network: Backpropagation without storing activations, NeurIPS 2017 https://papers.nips.cc/paper/6816-the-reversible-residual-network-backpropagation-without-storing-activations == August 14 == Diederik P. Kingma, Prafulla Dhariwal: Glow: Generative Flow with Invertible 1×1 Convolutions, NeurIPS 2018 https://papers.nips.cc/paper/8224-glow-generative-flow-with-invertible-1x1-convolutions.pdf == August 7 == Francesco Locatello, Stefan Bauer, Mario Lucic, Gunnar Raetsch, Sylvain Gelly, Bernhard Schölkopf, Olivier Bachem; Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations; Proceedings of the 36th International Conference on Machine Learning, PMLR 97:4114-4124, 2019. https://arxiv.org/abs/1811.12359 == July 17 == Computational Optimal Transport by Gabriel Peyre and Marco Cuturi: Finish 2.4-2.5; 3.1-3.4 https://arxiv.org/pdf/1803.00567.pdf == July 3 == Computational Optimal Transport by Gabriel Peyre and Marco Cuturi: Read up to the end of 2.4 https://arxiv.org/pdf/1803.00567.pdf == June 24 == Justin Solomon's slides from his tutorial talk on optimal transport http://people.csail.mit.edu/polina/papers/ot_tutorial.pptx == June 27 == Automated Treatment Planning in Radiation Therapy using Generative Adversarial Networks; Mahmood et al. {{mahmood18a.pdf}} ==== Spring 2019 ==== == May 13 == The Neuro-Symbolic Concept Learner: Interpreting Scenes, Words, and Sentences From Natural Supervision; Jiayuan Mao et al. https://openreview.net/forum?id=rJgMlhRctm == April 29 == Fully Automatic 3D Reconstruction of the Placenta and its Peripheral Vasculature in Intrauterine Fetal MRI; Torrents-Barrena et al. {{automatic_placenta_seg.pdf}} == April 22 == Semi-supervised learning for segmentation under semantic constraint; Pierre-Antoine Ganaye et al. https://link.springer.com/content/pdf/10.1007%2F978-3-030-00931-1_68.pdf == Mar 18 == Improved Training of Wasserstein GANs https://arxiv.org/pdf/1704.00028.pdf == Mar 11 == Wasserstein GAN https://arxiv.org/pdf/1701.07875.pdf == Mar 4 == Understanding and Improving Interpolation in Autoencoders via an Adversarial Regularizer https://openreview.net/pdf?id=S1fQSiCcYm https://openreview.net/forum?id=S1fQSiCcYm == Feb 25 == Spectral Representations for Convolutional Neural Networks: https://arxiv.org/pdf/1506.03767.pdf == Feb 11 == Greff et al., "Highway and Residual Networks learn Unrolled Iterative Estimation". [[https://arxiv.org/abs/1612.07771]]. == Jan 14 and Jan 22 == Note: we're meeting on Tue, Jan 22, 1pm for a one-time off-schedule meeting (because Mon Jan 21 is a holiday), focusing on Sec 4 and 5 of: Neural Ordinary Differential Equations\\ Ricky T. Q. Chen, Yulia Rubanova, Jesse Bettencourt, David Duvenaud\\ NeurIPS 2018. [[https://arxiv.org/pdf/1806.07366.pdf|pdf]]\\ \\ Related papers for further reading: \\ - Rousseau et al, Residual Networks as Geodesic Flows of Diffeomorphisms, ArXiv 2018. [[https://arxiv.org/pdf/1805.09585.pdf|pdf]] \\ Seems very related concurrent development by different authors. \\ - Grathwohl et al, FFJORD: Free-form continuous dynamics for scalable reversible generative models, ICLR 2019. [[https://arxiv.org/pdf/1810.01367.pdf|pdf]] \\ Continuation of the continuous flows from the Neural-ODEs == Jan 7 == A Deep Cascade of Convolutional Neural Networks for Dynamic MR Image Reconstruction. Jo Schlemper, Jose Caballero, Joseph V. Hajnal, Anthony Price and Daniel Rueckert. IEEE TMI 2017. {{https://arxiv.org/pdf/1704.02422.pdf}} ==== Fall 2018 ==== == Dec. 10 == K. Hammernik, T. Klatzer, E. Kobler, M.P. Recht, D.K. Sodickson, T. Pock, F. Knoll \\ arning a Variational Network for Reconstructionof Accelerated MRI Data. \\ Magnetic Resonance in Medicine, 2018 \\ {{Hammernik_et_al-2018-Magnetic_Resonance_in_Medicine.pdf}} == Dec. 3 == Bo Zhu, Jeremiah Z. Liu, Stephen F. Cauley, Bruce R. Rosen, Matthew S. Rosen \\ Image reconstruction by domain-transform manifold learning. \\ Nature Letters \\ {{zhu_nature25988.pdf}} == Nov. 19 == Simon A. A. Kohl, Bernardino Romera-Paredes, Clemens Meyer, Jeffrey De Fauw, Joseph R. Ledsam, Klaus H. Maier-Hein, S. M. Ali Eslami, Danilo Jimenez Rezende, Olaf Ronneberger \\ A Probabilistic U-Net for Segmentation of Ambiguous Images. \\ NIPS 2018 \\ https://arxiv.org/abs/1806.05034 == Nov. 5 == Finn, C., Abbeel, P., Levine, S. Model-agnostic meta-learning for fast adaptation of deep networks. In: ICML. (2017) https://arxiv.org/abs/1703.03400 == Oct. 29 == Gabriel Maicas, Andrew P. Bradley, Jacinto C. Nascimento, Ian Reid, Gustavo Carneiro "Training Medical Image Analysis Systems like Radiologists" MICCAI 2018 https://arxiv.org/abs/1805.10884 == Oct. 22 == Martin Szummer and Tommi Jaakkola. "Information Regularization with Partially Labeled Data." Advances in neural information processing systems. 2003. https://people.csail.mit.edu/tommi/papers/SzuJaa-nips02.pdf Follow up paper: https://arxiv.org/abs/1212.2466 == Oct. 1 & Oct. 15 == Grandvalet, Yves, and Yoshua Bengio. "Semi-supervised learning by entropy minimization." Advances in neural information processing systems. 2005. http://papers.nips.cc/paper/2740-semi-supervised-learning-by-entropy-minimization.pdf ==== Summer 2018 ==== == Aug 28 == Ramprasaath R. Selvaraju, Michael Cogswell, Abhishek Das, Ramakrishna Vedantam, Devi Parikh, and Dhruv Batra, "Grad-CAM: Visual Explanations from Deep Networks via Gradient-Based Localization", ICCV 2017, https://arxiv.org/pdf/1610.02391 Bolei Zhou, Aditya Khosla, Agata Lapedriza, Aude Oliva, and Antonio Torralba, "Learning Deep Features for Discriminative Localization", CVPR 2016, https://arxiv.org/pdf/1512.04150 == Aug 21 == David Bau*, Bolei Zhou*, Aditya Khosla, Aude Oliva, Antonio Torralba. Network dissection: Quantifying interpretability of deep visual representations. CVPR 2017. http://netdissect.csail.mit.edu/final-network-dissection.pdf Other papers of interest from Bolei Zhou's webpage: * Bolei Zhou*, David Bau*, Aude Oliva, Antonio Torralba. Interpreting deep visual representations via network dissection. PAMI 2018. https://arxiv.org/pdf/1711.05611 * Bolei Zhou, Aditya Khosla, Agata Lapedriza, Aude Oliva, Antonio Torralba. Learning deep features for discriminative localization. CVPR 2016. http://cnnlocalization.csail.mit.edu/Zhou_Learning_Deep_Features_CVPR_2016_paper.pdf * Bolei Zhou*, Yiyou Sun*, David Bau*, Antonio Torralba. Interpretable basis decomposition for visual explanation. ECCV 2018. http://people.csail.mit.edu/bzhou/publication/eccv18-IBD == Aug 7 and Aug 14 == S. Bach, A. Binder, G. Montavon, F. Klauschen, K.-R. Müller, W. Samek: On Pixel-wise Explanations for Non-Linear Classifier Decisions by Layer-wise Relevance Propagation. PLOS ONE, 10(7): e0130140 (2015) http://dx.doi.org/10.1371/journal.pone.0130140 == July 31 == Bob D. de Vos, Floris F. Berendsen, Max A. Viergever, Marius Staring, and Ivana Isgum, "End-to-End Unsupervised Deformable Image Registration with a Convolutional Neural Network ." DLMIA-MICCAI, 2017. https://arxiv.org/pdf/1704.06065.pdf == July 24 == Geoffrey E Hinton, Sara Sabour, Nicholas Frosst. Matrix capsules with EM routing. https://openreview.net/pdf?id=HJWLfGWRb == July 17 == Sabour, Sara, Nicholas Frosst, and Geoffrey E. Hinton. "Dynamic routing between capsules." Advances in Neural Information Processing Systems. 2017. https://arxiv.org/pdf/1710.09829.pdf Additional papers for more reading: {{BrainTumorTypeClassificationviaCapsuleNetworks.pdf}} {{MATRIX-CAPSULES-WITH-EM-ROUTING.pdf}} {{CapsulesforObjectSegmentation.pdf}} === July 10 === {{CapsulesforObjectSegmentation.pdf}} ==== Spring 2018 ==== === May 1 and May 16 === Kingma, Diederik P., et al. "Semi-supervised learning with deep generative models." Advances in Neural Information Processing Systems. 2014. http://papers.nips.cc/paper/5352-semi-supervised-learning-with-deep-generative-models.pdf === April 24 === Kainz et al.: "Fast Volume Reconstruction From Motion Corrupted Stacks of 2D Slices" {{discussion:kainz2015.pdf}} === April 10 === Mengye Ren and Richard S. Zemel. "End-to-End Instance Segmentation with Recurrent Attention." arXiv preprint arXiv:1605.09410 (2015). https://arxiv.org/pdf/1605.09410.pdf === April 3 === Lipton, Zachary C., et al. "Learning to diagnose with LSTM recurrent neural networks." arXiv preprint arXiv:1511.03677 (2015). https://arxiv.org/pdf/1511.03677.pdf === March 27 === Evangelos Kalogerakis, Siddhartha Chaudhuri, Daphne Koller, and Vladlen Koltun "A Probabilistic Model for Component-Based Shape Synthesis" SIGGRAPH / ACM Transactions on Graphics 31(4), 2012 http://vladlen.info/papers/shape-synthesis.pdf === Mar 13 === Conjugate gradient algorithm and gradient preconditioning. Chapters 11.2 and 11.3 in [[http://people.csail.mit.edu/jsolomon/share/book/numerical_book.pdf|Numerical Algorithms by Justin Solomon]] We will briefly discuss conjugate gradients then focus on preconditioning. === Mar 6 === Conjugate gradient algorithm. A (shorter) section from the numerical recipes book: {{wiki:c10-6.pdf}} More background: Jonathan Richard Shewchuk. An Introduction to the Conjugate Gradient Method Without the Agonizing Pain. This is a nice (although long) tutorial paper: {{wiki:painless-conjugate-gradient.pdf}} === Feb 13 === From Label Maps to Generative Shape Models: A Variational Bayesian Learning Approach; IPMI 2017 {{elhabian2017.pdf}} === Feb 06 === Unsupervised Anomaly Detection with Generative Adversarial Networks to Guide Marker Discovery; IPMI 2017 {{schlegl2017.pdf}} === Jan 30 === Error correction boosting for learning fully Convolutional networks with limited data; MICCAI 2017, Roy et al. {{Roy.pdf}} === Jan 23 === Christoph Baur, Shadi Albarqouni, Nassir Navab. Semi-supervised Deep Learning for Fully Convolutional Networks. {{Baur.pdf}} ==== Fall 2017 ==== === Dec 12 === Zhang Y., Yang L., Chen J., Fredericksen M., Hughes D.P., Chen D.Z. (2017) Deep Adversarial Networks for Biomedical Image Segmentation Utilizing Unannotated Images. === Dec 5 === Kingma, Diederik P., and Max Welling. "Auto-encoding variational bayes." arXiv preprint arXiv:1312.6114 (2013). {{vae_2013.pdf}} Useful lecture notes for reviewing variational approximation: {{437_approximations.pdf}} === Nov 28 === Juan Eugenio Iglesias - Globally optimal coupled surfaces for semi-automatic segmentation of medical images {{iglesias2017.pdf}} === Nov 14 === Topology-controlled Reconstruction of Multi-labelled Domains from Cross-sections; Ed Chien (Justin's postdoc) will present. {{multitopo_tog.pdf}} === Nov 07 === We will focus on: * Ravishankar et al - Learning and Incorporating Shape Models for Semantic Segmentation {{Ravishankar2017.pdf}} * Milletari et al - Integrating Statistical Prior Knowledge into Convolutional Neural Networks {{Milletari2017.pdf}} This reading will be related to that of Oct 24th, when we discussed: * Oktay et al - Anatomically Constrained Neural Networks (ACNN): Application to Cardiac Image Enhancement and Segmentation {{oktay2017a.pdf}} === Oct 31 === Phillips Tech Talk: Computational Neurology and Computational Pathology. The talk is at 4PM in 32-G882. The link to register is [[https://www.eventbrite.com/e/philips-tech-talk-computational-neurology-and-computational-pathology-tickets-39016916648|here]]. === Oct 24 - Shape priors with CNNs === * Oktay et al - Anatomically Constrained Neural Networks (ACNN): Application to Cardiac Image Enhancement and Segmentation {{oktay2017a.pdf}} * Milletari et al - Integrating Statistical Prior Knowledge into Convolutional Neural Networks {{Milletari2017.pdf}} * Ravishankar et al - Learning and Incorporating Shape Models for Semantic Segmentation {{Ravishankar2017.pdf}} === Oct 17 === Vertex Clustering model for disease progression: Application to Cortical Thickness Images; Marinescu et al. {{marinescu2017.pdf}} === Sep 26 === We will read Sections 5.3 to 5.4 of {{bv_cvxbook.pdf}}. === Sep 19 === We will read Sections 5.1 to 5.2. === Sep 12 === We will read from section 4.2.3 onwards. === Sep 5 === We reviewed the first third of Ch. 4 (read through section 4.2.3) ==== Summer 2017 ==== We will be reading Convex Optimization by Stephen Boyd this summer. {{bv_cvxbook.pdf}} === Aug 1 === Read section 2.6 on Dual Cones === July 27 === We will continue reading Ch. 2 (read through section 2.5). See also a [[http://www.ics.uci.edu/~xhx/courses/ConvexOpt/convex_sets.pdf|helpful set of slides for Chapter 2]]. === July 18 === We will start Ch. 2 on Convex Sets (read through section 2.3) ==== Spring 2017 ==== === May 9 === We will go back to the paper we started with: Chen et al., Sparse Projections of Medical Images onto Manifolds [http://people.csail.mit.edu/polina/papers/Chen-IPMI-2013.pdf] === May 2 === Nonlinear Component Analysis as a Kernel Eigenvalue Problem Bernhard Scholkopf, Alexander Smola, Klaus-Robert Muller. AKA Kernel PCA. {{kpca.pdf}} For those who want to take a look at a more formal treatment of the Sobolev kernel and such, here is another tutorial: AN INTRODUCTION TO THE THEORY OF REPRODUCING KERNEL HILBERT SPACES VERN I. PAULSEN{{rkhs.pdf}} === April 25 === We will go over the second part of the notes. === April 11 === RKHS Material: Text notes: http://www.mit.edu/~9.520/scribe-notes/class03_gdurett.pdf Slides: http://www.mit.edu/~9.520/fall14/index.html Class 4 and class 5. === March 21 === Fowlkes, Charless, Serge Belongie, Fan Chung, and Jitendra Malik. "Spectral grouping using the Nystrom method." IEEE transactions on pattern analysis and machine intelligence 26, no. 2 (2004): 214-225. {{fowlkes_spectralgrouping_nystrom.pdf}} === Mar 7 === Chen et al., Sparse Projections of Medical Images onto Manifolds [http://people.csail.mit.edu/polina/papers/Chen-IPMI-2013.pdf] === Feb 28 === Daniel Moyer, Boris A. Gutman, Joshua Faskowitz, Neda Jahanshad, and Paul M. Thompson. A Continuous Model of Cortical Connectivity. MICCAI 2016 [http://www-scf.usc.edu/~moyerd/pubs/continuous-connectivity.pdf] === Feb 21 === Yang Xiao, Roland Kwitt, and Marc Niethammer. "Fast Predictive Image Registration." International Workshop on Large-Scale Annotation of Biomedical Data and Expert Label Synthesis. Springer International Publishing, 2016. [https://arxiv.org/abs/1607.02504] === Feb 7 === Isola et al., Image-to-Image Translation with Conditional Adversarial Networks, [https://arxiv.org/pdf/1611.07004.pdf] ==== IAP 2017 ==== === Jan 31 === Ronneberger et al. U-Net: Convolutional Networks for Biomedical Image Segmentation. MICCAI 2015. {{unet.pdf}} === Jan 24 === Oktay et al. Multi-Input Cardiac Image Super-Resolution using Convolutional Neural Networks. MICCAI 2016. [https://www.doc.ic.ac.uk/~oo2113/publications/MICCAI2016_camera_ready.pdf] === Jan 17 === * HeMIS: Hetero-Modal Image Segmentation [https://arxiv.org/pdf/1607.05194v1.pdf] === Jan 10 === Barycentric Subspace Analysis: a new Symmetric Group-wise Paradigm for Cardiac Motion Tracking. [https://hal.inria.fr/hal-01373706/document] ==== Fall 2016 ==== === Nov 22 === Unsupervised Freeview Groupwise Cardiac Segmentation Using Synchronized Spectral Network {{unsupervised.pdf}} === Nov 15 === Bilateral Weighted Adaptive Local Similarity Measure for Registration in Neurosurgery {{kochan16.pdf}} === Nov 8 === Fast Fully Automatic Segmentation of the Human Placenta from Motion Corrupted MRI. {{kainz_miccai106a.pdf}} === Nov 1 === SpineNet: Automatically Pinpointing Classification Evidence in Spinal MRIs. {{jamaludin16.pdf}} === Oct 25 === MICCAI 2016 debrief. Please come with 1-3 papers that you liked at MICCAI 2016 and want to discuss about! === Oct 11 === Aditya Khosla will talk about his work on CNN for Medical Tasks. Potentially relevant paper: http://people.csail.mit.edu/khosla/papers/arxiv2016_Wang.pdf === Oct 4 === Antonio Torralba will discuss his experience with NNs. === Sep 27 === We'll continue with Goodfellow et al's book. http://www.deeplearningbook.org/, chapter 9 (CNNs) === Sep 13 === We'll continue with Goodfellow et al's book. http://www.deeplearningbook.org/, up to and including 6.5 (Backprop) ==== Summer 2016 ==== === Aug 25 === We'll continue with Goodfellow et al's book. http://www.deeplearningbook.org/, up to and including 6.4 === Aug 11 === We're starting a series of discussions on Deep learning. We'll start with Goodfellow et al's book. http://www.deeplearningbook.org/ (Please scan through Part I and review whatever is necessary) **On Aug 11th, we'll read Part II, Chapter 6.** === July 28 === Adrien Depeursinge will tell us about his work on texture classification. === June 17, June 23, July 14 === Vercauteren et al, Diffeomorphic Demons: Efficient Non-parametric Image Registration: {{diffeodemons-neuroimage08-vercauteren.pdf}} For those interested in further development: {{symlogdemons-miccai08-vercauteren.pdf}} For those need basic background of demons algorithm: {{thirion98.pdf}} === June 9 === Avants, Brian B., Charles L. Epstein, Murray Grossman, and James C. Gee. "Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain." Medical image analysis 12, no. 1 (2008): 26-41. MedIA version: {{Avants-MedIA.pdf}} {{symmetric_diffeomorphic_image_registration.pdf}} === June 2 === C. Studholme, D.L.G. Hill, D.J. Hawkes, "An overlap invariant entropy measure of 3D medical image alignment", Pattern Recognition 32 (1999) 71—86 {{normalizedMI.pdf}} (Discussion leader: Danielle) === July 21 === Horn et al, Determining Optical Flow: {{opticalflow.pdf}} ==== Spring 2016 ==== === May 17 === Nonrigid Registration Using Free-Form Deformations: Application to Breast MR Images. D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach, and D. J. Hawkes. IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 18, NO. 8, AUGUST 1999. {{wiki:rueckert-ffd.pdf}} === May 10 === Floris F. Berendsen, Uulke A. van der Heide, Thomas R. Langerak, Alexis N.T.J. Kotte, Josien P.W. Pluim. Free-form image registration regularized by a statistical shape model: application to organ segmentation in cervical MR. CVIU 2013. {{Plum-2013.pdf}} === May 3 === Papież, B. W., Heinrich, M. P., Fehrenbach, J., Risser, L., & Schnabel, J. A. (2014). An implicit sliding-motion preserving regularisation via bilateral filtering for deformable image registration. Medical image analysis, 18(8), 1299-1311. {{1-s2.0-S1361841514000784-main.pdf}} === April 26 === Tanya Schmah, Laurent Risser, and Franncois-Xavier Vialard, 2013 - Left-Invariant Metrics for Diffeomorphic Image Registration with Spatially-Varying Regularisation. {{leftinvariantmetrics.pdf}} {{diffeomorphic_image_matching_with_left-invariant_metrics.pdf}}(Discussion Leader - Miaomiao) === April 19 === Tong et al, 2013 - Segmentation of MR images via discriminative dictionary learning and sparse coding: Application to hippocampus labeling. {{dictLearning.pdf}} (Discussion Leader - Danielle) === April 12 === Bhatia et al, 2014 - Hierarchical Manifold Learning for Regional Image Analysis. {{bhatia2014.pdf}} - Discussion Leader: Adrian === April 5 === Kim, Jaechul, Ce Liu, Fei Sha, and Kristen Grauman. "Deformable spatial pyramid matching for fast dense correspondences." Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition. 2013. {{2013CVPR_DSP.pdf}} - Discussion Leader: Ray One of its applications in image-guided radiotherapy: Mazur, Thomas R., et al. "SIFT-based dense pixel tracking on 0.35 T cine-MR images acquired during image-guided radiation therapy with application to gating optimization." Medical physics 43.1 (2016): 279-293. {{SIFT-based dense pixel tracking on 0.35 T cine-MR images acquired during imageguided radiation therapy with application to gating optimization.pdf}} === March 29 === Matthieu Lê, Jan Unkelbach, Nicholas Ayache, Hervé Delingette. GPSSI: Gaussian Process for Sampling Segmentations of Images. MICCAI 2015. {{Le-MICCAI-2015.pdf}} === Feb 23 === Mapping Stacked Decision Forests to Deep and Sparse Convolutional Neural Networks for Semantic Segmentation http://arxiv.org/pdf/1507.07583v2.pdf Disc. leader: Greg, {{discussion:20160209_ciccarelli_rfdnn.pdf}} === Feb 2 === Conditional Regression Forests for Human Pose Estimation, Sun et al, CVPR 2012 {{skt_cvpr2012.pdf}} Discussion Leader: Danielle If you'd like some background on Regression Forests, you can look at these chapters from "Decision Forests for Computer Vision and Medical Image Analysis", Criminisi and Shotton, eds.: {{decisionForestsChap3.pdf}}, {{decisionForestsChap5.pdf}} ==== IAP 2016 ==== === Jan 25 == We will have Mert Sabuncu present his work on longitudinal analysis: {https://calendar.csail.mit.edu/events/161223} related on his MICCAI 2015 paper {{Sabuncu-MICCAI-2015.pdf}}. === Jan 4 === We will march off to Sarang Joshi's tutorial on diffeomorphic registration. Here's some holiday reading: François-Xavier Vialard , Laurent Risser, Daniel Rueckert, Colin J. Cotter. Diffeomorphic 3D Image Registration via Geodesic Shooting Using an Efficient Adjoint Calculation. IJCV 2011. {{Vialard-IJCV.pdf}} Note from the tutorial: {{LieGroups.pdf}} Matlab code used in the tutorial: {{GaussianSPlines.txt}} and {{Flow.txt}} ==== Fall 2015 ==== === Dec 10 === Simultaneous Longitudinal Registration with Group-Wise Similarity Prior. Greg M. Fleishman , Boris A. Gutman, P. Thomas Fletcher, Paul M. Thompson. IPMI 2015 {{Fleishman-IPMI-2015.pdf}} === Nov 19 === [MICCAI2015] Uncertainty-driven Forest Predictors for Vertebra Localization and Segmentation. David Richmond, Dagmar Kainmueller, Ben Glocker, Carsten Rother, Gene Myers.\\ {{forest.pdf}} === Nov 12 === q-Space Deep Learning for Twelve-Fold Shorter and Model-Free Diffusion MRI Scans {{golkov15.pdf}}. === Nov 5 === Neher et. al. A Machine Learning Based Approach to Fiber Tractography Using Classifier Voting. MICCAI 2015. {{neher15.pdf}} === Oct 29 === Soheil Hor, Mehdi Moradi. Scandent Tree: A Random Forest Learning Method for Incomplete Multimodal Datasets. MICCAI 2015. {{scandent-trees-miccai-2015.pdf}} === Oct 19 (Monday) === We sorted out the list to read. === Sep 24 === We will be reading Miaomiao Zhang's latest paper: {{zhang_ipmi2015.pdf}} For more context we have, Ashburner and Friston's paper: {{ashburner_ni11.pdf}} And also the paper we read last week! === Sep 17 === We will read Miller et al's paper on the application of geodesic shooting in diffeomorphic image registration: {{miller_jmiv06.pdf}} A more recent paper by Ashburner and Friston is also available for further reading: {{ashburner_ni11.pdf}} ==== Summer 2015 ==== === Aug 27, Sep 3 === We will read Vercauteren et al, Diffeomorphic Demons: Efficient Non-parametric Image Registration: {{diffeodemons-neuroimage08-vercauteren.pdf}} For those interested in further development of this line of research: {{symlogdemons-miccai08-vercauteren.pdf}} === Aug 20 === No meeting === Aug 13 === We will continue reading Beg et al. Additional resources: Review of calculus of variations: {{calculusOfVariations.pdf}} Danielle's notes on Beg et al: {{dfpace_Beg_etal.pdf}} === Aug 6 === We will read Beg et al, Computing large deformation metric mappings via geodesic flows of diffeomorphisms, IJCV 2005. {{beg_lddmm.pdf}} === July 30 === We will continue going over Danial Lashkari's notes. === July 23 === We will continue going over Danial Lashkari's notes. Additionally, this is another resource: {{diffgeo.pdf}} === July 16 === We will go over Danial Lashkari's notes from the last time we all learned about lie algebra and manifolds. http://groups.csail.mit.edu/vision/golland/group_meeting/doku.php?id=discussion:oct_1_2007 ==== Spring 2015 ==== === May 8, 22 === Durrleman, Stanley, et al. "Toward a comprehensive framework for the spatiotemporal statistical analysis of longitudinal shape data." International journal of computer vision 103.1 (2013): 22-59. {{durrleman_et_al_2013.pdf}} === April 24, May 1 == Reshef DN, Reshef YA, Finucane HK, et al. Detecting Novel Associations in Large Datasets. Science (New York, N.y). 2011;334(6062):1518-1524. doi:10.1126/science.1205438. {{MIC.pdf}} The supplementary material that we will discuss: {{som.pdf}} Section 3 discussed the approximation algorithm, though sections 1 and 2 are likely to also be useful for the discussion! === April 17 === MICCAI: Zhang, Miaomiao, and P. Thomas Fletcher. "Bayesian Principal Geodesic Analysis in Diffeomorphic Image Registration." Medical Image Computing and Computer-Assisted Intervention–MICCAI 2014. Springer International Publishing, 2014. 121-128. {{bayesian-principal-geodesic-analysis-in-diffeomorphic-image-registration.pdf}} NIPS: Zhang, Miaomiao, and P. Thomas Fletcher. "Probabilistic principal geodesic analysis." Advances in Neural Information Processing Systems. 2013. {{5133-probabilistic-principal-geodesic-analysis.pdf}} === April 10 == Sabuncu, Mert R. "A Universal and Efficient Method to Compute Maps from Image-Based Prediction Models." Medical Image Computing and Computer-Assisted Intervention–MICCAI 2014. Springer International Publishing, 2014. 353-360. {{mappingimagebasedpredictionmodels_sabuncu_miccai14_final.pdf}} === March 27 == Maxime Taquet, Benoıt Scherrer, Jurriaan M. Peters, Sanjay P. Prabhu, and Simon K. Warfield. A Fully Bayesian Inference Framework for Population Studies of the Brain Microstructure. MICCAI 2014. {{Taquet-MICCAI2014.pdf}} ==== Fall 2014 ==== === November 18: === Ramesh, Adrian and Danielle will lead: ICML tutorial on Submodularity in Machine learning - Part I http://www.cs.berkeley.edu/~stefje/submodularity_icml.html === November 4: === Danielle will lead: Zhu, Zhang, Liu and Metaxas, Scalable histopathological image analysis via active learning. {{Zhu_MICCAI2014.pdf}} === October 21 == George will lead: Herve Lombaert, Darko Zikic, Antonio Criminisi, and Nicholas Ayache. Laplacian Forests: Semantic Image Segmentation by Guided Bagging. {{miccai-laplacian-forest.pdf}} **(Update 10/24/2014)** Notes are now available. {{reading-group-random-forests-laplacian-forests-2014-10-21-draft1.pdf}} === October 7 === We will meet in *32-D451*. Daniel C. Alexander, Darko Zikic, Jiaying Zhang, Hui Zhang, Antonio Criminisi. Image Quality Transfer via Random Forest Regression: Applications in Diffusion MRI. {{alexander_miccai2014.pdf}} === September 30 === We will meet in *32-G431*. Xiaoxiao Liu, Marc Niethammer, Roland Kwitt, Matthew McCormick, and Stephen Aylward. Low-Rank to the Rescue – Atlas-based Analyses in the Presence of Pathologies. {{liu2014_miccai_low_rank_to_the_rescue.pdf}} Code: https://github.com/KitwareMedical/pyLAR ==== Summer 2014 ==== === June 31 (aka July 1) === Rohlfing T1, Sullivan EV, Pfefferbaum A. Regression models of atlas appearance. {{ipmi2009_rohlfing.pdf}} === June 24 === O. Veksler, Star shape prior for graph-cut image segmentation. ECCV 2008, Lecture Notes in Computer Science Volume 5304, 2008, pp 454-467. {{starshapeprior.pdf}} ==== Spring 2014 ==== == May 6 == Since we didn't have dessert, this is my suggestion for next week. I hope you enjoy it. SUNGKYU JUNG, IAN L. DRYDEN and J. S. MARRON. "Analysis of principal nested spheres (PNS)", Biometrika (2012), http://www.stat.pitt.edu/sungkyu/papers/Biometrika-2012-Jung-551-68.pdf == April 29 == The reading is split into an amuse-bouche and an entree. I intend on only discussing the entree at length. Amuse-bouche: To whet your appetite, skim chapter 8 of Boyd's ADMM monograph for a sampler of applications where ADMM is used (among these are a few I sketched last time: lasso, group lasso, SVM's): http://www.stanford.edu/~boyd/papers/pdf/admm_distr_stats.pdf Entree: Concentrate your fire power on reading the following paper by Yedidia and friends who show how ADMM can be implemented as a message-passing algorithm and how to modify the algorithm to tackle some large nonconvex problems: http://arxiv.org/abs/1305.1961 **Update 4/30/2014 2:28am**: Notes by me (George) for last reading group are now up! {{reading-group-admm-intro-2014-04-15-notes.pdf}} (lasted updated 4/30 to fix some typos caught by Danielle) == April 15 == We begin our series on distributed optimization, with a preliminary focus on a method called ADMM. Please read chapters 1-3 of the following: http://www.stanford.edu/~boyd/papers/pdf/admm_distr_stats.pdf A resource webpage that might be helpful: http://www.stanford.edu/~boyd/papers/admm_distr_stats.html == April 8 == Ben Glocker, A Sotiras, N Komodakis, Nikos Paragios. "Deformable Medical Image Registration: Setting the State of the Art with Discrete Methods", Annual Review Biomedical Engineering, 2011, 13: 219-244. {{glocker11.pdf}} == Apr 1 == Wang et al, "Markov Random Field modeling, inference & learning in computer vision & image understanding: A survey", CVIU, 2013. Technical report (42pages) [[http://hal.inria.fr/docs/00/73/49/83/PDF/GraphicalModelSurvey.pdf]], or CVIU paper (18 pages) {{wang13.pdf}} == Mar 25 == Yang et al, Neighbor-Constrained Segmentation With Level Set Based 3-D Deformable Models, IEEE TMI 2004 {{yang_neighborConstrainedSegmentation.pdf}} == Mar 18 == Firdaus Janoos, Shantanu Singh, Raghu Machiraju, William M. Wells III, István Ákos Mórocz. State-Space Models of Mental Processes from fMRI. IPMI 2011. {{janoos-ipmi2011.pdf}} And here is the journal paper: {{Janoos_2013.pdf}} == Mar 11 == Harini Eavani, Theodore Satterthwaite, Raquel Gur, Ruben Gur, Christos Davatzikos; Unsupervised Learning of Functional Network Dynamics in Resting State fMRI http://www.rad.upenn.edu/sbia/Harini.Eavani/ipmi13/IPMI_2013_Harini_camera_ready_ver2.pdf == Feb 11 == Ioannidis, J.P.A. Why most published research findings are false {{why_most_published_research_findings.pdf}} (see also [[http://arxiv.org/pdf/1301.3718v1.pdf|this rebuttal paper]] and [[http://andrewgelman.com/2013/01/i-dont-believe-the-paper-empirical-estimates-suggest-most-published-medical-research-is-true-that-is-the-claim-may-very-well-be-true-but-im-not-at-all-convinced-by-the-analysis-being-used/|Andrew Gelman's counter-rebuttal]]). ==== Fall 2013 ==== == Dec 9 == Probabilistic inference of regularisation in non-rigid registration. Ivor J.A. Simpson, Julia A. Schnabel, Adrian R. Groves, Jesper L.R. Andersson, Mark W. Woolrich. {{simpson-neuroimage-2012.pdf}} == Dec 2 == Simpson et al, //A Bayesian Approach for Spatially Adaptive Regularisation in Non-rigid Registration//{{bayes_reg.pdf}} (MICCAI) == Nov 18 == We continue our patch series by moving from super-resolution to segmentation. Wang et al, 2013, //Patch-Based Segmentation without Registration: Application to Knee MRI// {{Wang_Seg_2013.pdf}} (MLMI-MICCAI) == Nov 4 == We will start a series of patch-based methods. For Nov 4th, we'll look at: Shi et al, 2013. //Cardiac Image Super-Resolution with Global Correspondence Using Multi-Atlas PatchMatch// {{shi_et_al_2013.pdf}} (MICCAI) As an **optional** read, many algorithms use or refer to [[http://gfx.cs.princeton.edu/pubs/Barnes_2009_PAR/|patchMatch - Barnes, 2009]]. === Oct 28 === We will discuss interesting papers from IPMI and MICCAI. Everyone should come with a couple of papers they are interested in exploring. === Oct 21 === We will read Tree-space statistics and approximations for large-scale analysis of anatomical trees, by A. Feragen, M. Owen, J. Petersen, M.M.W. Wille, L.H. Thomsen, A. Dirksen and M. de Bruijne http://image.diku.dk/aasa/papers/tree_stats_ipmi2012_cameraready.pdf === Oct 7 === Matched Signal Detection on Graphs: Theory and Application to Brain Network Classification, by C. Hu, L. Cheng, J. Sepulcre, G. El Fakhri, Y. M. Lu, and Q. Li. {{quanzhengli_matchedsignaldetectionongraphs_ipmi2013.pdf}} ==== Spring 2013 ==== ===May 7th.=== Chapter 5 of this book: "Handbook of Markov Chain Monte Carlo", which can be found [[http://www.mcmchandbook.net/HandbookChapter5.pdf|here]] ===April 23th.=== Chapter 27 of this Book: "Bayesian Reasoning and Machine Learning" ===April 9th.=== Globerson and Roweis, Nightmare at Test Time: Robust Learning by Feature Deletion, ICML, 2006 [{{globerson_and_roweis_2006.pdf}}] === March 12 === Kayhan and I (George) will talk about a new approach to nonnegative matrix factorization (NMF) that is NOT based on iterative hill-climbing type algorithms that may only reach a local optima; instead, under a separability assumption which is empirically observed in real topic modeling data, NMF for learning topic models can be solved in polynomial time. The paper that we'll look at is on arXiv, and we'll focus on everything up to and including Section 3.1 (mid way through page 8--basically we'll focus on the case where there are true anchor words): [[http://arxiv.org/abs/1204.1956|"Learning Topic Models -- Going Beyond SVD"]]\\ Sanjeev Arora, Rong Ge, Ankur Moitra\\ Foundations of Computer Science 2012 **Update (3/11/2013 5:10pm).** I just put together some preliminary notes going over some key high-level ideas; hopefully this is helpful: {{reading-group-learning-topic-models-2013-03-12-draft1.pdf}} === March 5 === We met to plan what we'll read for the spring. Here are the results of the voting: * Non-negative matrix factorization (6) * Learning with missing features (5) * Tutorial on sampling methods (MCMC, HMC, etc) (5) * Type I vs Type II sparsity (4): David Wipf and Yi Wu. "Dual-Space Analysis of the Sparse Linear Model" NIPS 2012 [[http://nips.cc/Conferences/2012/Program/event.php?ID=3436]] * Video Magnification (4) [[http://people.csail.mit.edu/mrub/vidmag/|Initial paper]] * Tutorial on deep learning (4) * Compressed sensing (3) Paper? * Learning distributions from composition of marginals (3): F. Sanchez-Vega, J. Eisner, L. Younes, and D. Geman. "Learning Multivariate Distributions by Competitive Assembly of Marginals" IEEE PAMI, 2012. * Network/time clustering in fmri (3): Identification of Recurrent Patterns in the Activation of Brain Networks * ADMM for distribution optimization (3) * sym diffeomorphism long. (3) * significant for lasso (2) * Tutorial on Indian Buffet processes (2) * Non-quadratic priors (0) * Multidimensional Spectral Hashing (0) * Ordered based search (0) ==== Fall 2012 ==== === Nov 20 - Dec === We will read (Mert will lead): A. Criminisi, J. Shotton, and E. Konukoglu, "Decision Forests: A Unified Framework for Classification, Regression, Density Estimation, Manifold Learning and Semi-Supervised Learning" The file is big so here's a link: http://research.microsoft.com/apps/pubs/default.aspx?id=158806 Depending on interest, this reading might span several weeks. In our first session, let's plan to read up to the end of chapter 4, namely the one on regression. On an unrelated note, Ender, one of the co-authors of this paper, will be present. We also read the following MICCAI paper: E. Konokoglu, B. Glocker, D. Zikic, A. Criminisi, "Neighbourhood Approximation Forests", MICCAI 2012: {{neighbourhood_approximation_forests.pdf}}. === Nov 13 === We will continue with MICCAI 2012 papers and read: "Hierarchical Manifold Learning" by Kanwal K. Bhatia, Anil Rao, Anthony N. Price, Robin Wolz, Joseph V. Hajnal, Daniel Rueckert: {{hierarchicalmanifoldlearning.pdf}} === Nov 6 === We will read this paper: "SVM based significance maps" by Bilwaj Gaonkar, Christos Davatzikos {{bilwaj2012.pdf}} === Oct 30 === We will read our first paper from the MICCAI 2012 series: “Evaluating segmentation error without ground truth” by Timo Kohlberger, Vivek Singh, Chris Alvino, Claus Bahlmann, Leo Grady: {{kohlberger2012_GT.pdf}} === Oct 23 === MICCAI Discussion Decided for next week: “Evaluating segmentation error without ground truth” To invite for talk --- Neighborhood approximation forests, 10 Later reading series - Reading up on random forests (Antonio's book), 10 Other readings: Evaluating segmentation error without ground truth, 9 SVM based significance maps, 8 Geodesic information flow, 5 Hierarchical manifold learning, 5 === October 16 === We will read Chapter 3 of Tom Minka's thesis on Expectation Propagation {{minka-thesis.pdf}}. There is a fair amount of derivation, so hopefully, we can get a clear picture of the algorithm. Additional references on EP and other approximate inference algorithms can be found at: http://research.microsoft.com/en-us/um/people/minka/papers/ep/roadmap.html === October 9 (originally September 25) === We'll expand on the spatially dependent Pitman-Yor processes we covered a couple of weeks ago, and read: Soumya Ghosh and Erik B. Sudderth, Nonparametric Learning for Layered Segmentation of Natural Images, CVPR 2012. {{ghoshsudderth12cvpr.pdf}} The supplementary materials cover some detail that we probably won't have time to cover, but I've uploaded them for completeness. {{ghoshsudderth12cvpr-supplement.pdf}} Also relevant is a video lecture on the topic by Erik Sudderth from a NIPS 2011 workshop: [[http://videolectures.net/nipsworkshops2011_sudderth_segmentation]] === September 19 === We will read the original Hierarchical Dirichlet Process paper: Teh, Jordan, Beal, Blei: Hierarchical Dirichlet Processes {{wiki:hierarchical_nonparametric.pdf}} Here are some helpful notes written up by Danial: {{wiki:DP_brief_notes.pdf}}. === September 11 === We'll look at a paper that uses layers approach to image segmentation: Sudderth and Jordan, Shared Segmentation of Natural Scenes Using Dependent Pitman-Yor Processes, NIPS 2008. {{sudderth-jordan-nips08.pdf}} ==== Summer 2012 ==== === September 4 === We'll look at two papers that use/extend SWA, and cover a little more detail on supernode/seed selection: Alpert, S., Galun, M., Basri, R. and Brandt, A., Image segmentation by probabilistic bottom-up aggregation and cue integration, PAMI 2012. {{alpert_aggregating_pami_2012.pdf}} Goldschmidt, Y., Galun, M., Sharon, E., Basri, R. and Brandt, A. Fast multiscale clustering by integrating collective features, NIPS 2007 {{goldschmidt2007nips.pdf}} Note that the first paper has the same title as their 2007 CVPR submission, so be careful if searching. === August 28 === We will look at a paper on tumor segmentation via superpixel hierarchy: {{corso_et_al.pdf}} J. J. Corso, E. Sharon, S. Dube, S. El-Saden, U. Sinha, and A. Yuille. Efficient Multilevel Brain Tumor Segmentation with Integrated Bayesian Model Classification. IEEE Transactions on Medical Imaging, 27(5):629-640, 2008 If you want to read into the SWA algorithm: Hierarchy and adaptivity in segmenting visual scenes, {{nature04977.pdf}} === July 24 === We will discuss S. C. Zhu’s paper on image segmentation: {{zhu_pami96.pdf}} A brief review of the snakes is provided in Sec. 2.1 and in the Appendix of the paper, and active contours are explained in more details in {{kass_ijcv88.pdf}} and {{caselles_ijcv97.pdf}}. === July 17 === We will finish chapter 5 and go over chapter 6. === July 3 === This week, we will go over the 5'th chapter (Filtering on Graphs) of the "Discrete Calculus" by Leo Grady. === June 19 === We'll start with Sebastian's nature paper: [[http://www.nature.com/nature/journal/v401/n6755/pdf/401788a0.pdf]] The paper gives intuition for non-negative matrix factorization and compares it to several other approaches. For reference, the detailed algorithms paper is here: [[http://hebb.mit.edu/people/seung/papers/nmfconverge.pdf]] === Future potential papers === To understand the algorithms: [[http://www.dam.brown.edu/people/geman/am261-2008/Tutorial%20on%20MM.pdf|A Tutorial on MM Algorithms]] [[http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=06045343a|Unified Development of Multiplicative Algorithms for Linear and Quadratic Nonnegative Matrix Factorization]] [[http://www.appliedmathematician.net/proceedings/datamining/2005/dm05_70dingc.pdf|On the Equivalence of NMF and Spectral Clustering]] Understanding the similarities and the differences between probabilistic topic models and NMF will be useful. A potential paper is: [[http://www.hindawi.com/journals/cin/2008/947438/|Probabilistic Latent Variable Models as Nonnegative Factorizations]] ==== Spring 2012 ==== === May 15 === We'll read: 4D registration of serial brain's MR images: a robust measure of changes applied to Alzheimer's disease. Marco Lorenzi, Nicholas Ayache, Giovanni Frisoni, and Xavier Pennec. MICCAI STIA Workshop, 2010 {{4d_registration_lorenzi.pdf}} === Apr 24 === We’ll be reading on determinantal point processes. More precisely, we will read chapter 2 of Alex' thesis: A. Kulesza, Learning with Determinantal Point Processes, thesis draft. {{alex_thesis_draft.pdf}} ------ Additional material. Conference papers: A. Kulesza, and B. Taskar, Structured Determinantal Point Processes, Neural Information Processing Systems Conference (NIPS), Vancouver, BC, December 2010. {{sdpp_nips10-1.pdf}} k-DPPs: Fixed-Size Determinantal Point Processes, A. Kulesza, and B. Taskar. International Conference on Machine Learning (ICML), Bellevue, WA, June 2011. {{kdpps_icml11-1.pdf}} Learning Determinantal Point Processes, A. Kulesza, and B. Taskar. Conference on Uncertainty in Artificial Intelligence (UAI), Barcelona, Spain, July 2011. {{ldpps_uai11.pdf}} Math DPP surveys: Ben Hough, Manjunath Krishnapur, Yuval Peres, Bálint Virág, Determinantal Processes and Independence, Probability Surveys, 2006. {{determinantal_processes_and_independence_-_hough.pdf}} Alexei Borodin, Determinantal point processes, 2009. {{determinantal_point_processes_-_borodin.pdf}} === Apr 10 === Switching gears, we'll read - Vounou M, Nichols TE, Montana G; Alzheimer's Disease Neuroimaging Initiative. Discovering genetic associations with high-dimensional neuroimaging phenotypes: A sparse reduced-rank regression approach. Neuroimage, 53(3):1147-59, 2010 {{vounou_et_al_2010_-_neuroimage.pdf}}. === Mar 20 === We will read Dan Feldman's NIPS paper. Here's an **updated** PDF that includes supplemental material: {{nips11coresets-supplemental.pdf}} Here's the NIPS talk: http://videolectures.net/nips2011_faulkner_coresets/ **Update (3/19/2012, 10:17pm)** Preliminary notes that I (George) typed up for last week's discussion are here: {{reading_group_2012_03_13_notes.pdf}} Unfortunately, from what I can tell, some constants from the lecture notes don't quite match constants in literature cited at times. I tried to reconcile these discrepancies. The main message is *not* any different though; basically the k-center coreset construction algorithm has a horrendous running time in terms of the number of clusters k. === Mar 13 === We will finish reading the survey paper from last week, emphasizing clustering (section 6) and the high-dimensional setting (section 7). **Update (3/13/2012, 2:34am)** Preliminary notes that I (George) typed up for last week's discussion are here: {{reading_group_2012_03_06_notes.pdf}} Unfortunately, these may not be terribly helpful for this week's reading as the clustering material is quite different... === Mar 6 === In preparation for Dan Feldman's coresets talk in April, we'll be reading a (dated) survey on the basics of coresets from computational geometry. Basically the idea is that we want to approximate some interesting metric of a bunch of data points by using a hopefully substantially smaller subsample (called a coreset) of the data points. The reading: P.K. Agarwal, S. Har-Peled, and K.R. Varadarajan. "Geometric Approximation via Coresets". (2005) {{coresets_survey_2005.pdf}} As a preview for what's to come, here's Dan's paper at NIPS 2011 on how to build a coreset for a (huge) training dataset of a mixture model while retaining an $\epsilon$-approximation to the data likelihood; the result is that you can run, say, the EM algorithm for Gaussian mixture models on the coreset instead (**this is NOT part of the reading for Mar 6** although I'd recommend looking over the abstract to see what coresets can achieve now): D. Feldman, M. Faulkner, and A. Krause. "Scalabe Training of Mixture Models via Coresets". (2011) {{coresets_nips11.pdf}} === Feb 28 === We'll be reading a paper on a model and algorithm for Gaussian process classification: Urtasun, R. and Darrell, T.: Discriminative Gaussian Process Latent Variable Model for Classification. ICML '07 {{urtasun-icml-gaussian-process-classification.pdf}} === Feb 21 === We will read Mackay's tutorial on Gaussian processes: {{mackay-gaussian-processes.pdf}} Thanks to Iman for finding an updated version: {{mackay-gaussian-processes-frombook.pdf}} We'll focus on the first 6 sections. Another useful reference is Williams' tutorial: {{williams-gaussian-process.pdf}} (only Sections 3 and 4 are relevant to this week's discussion). === Feb 14 === We will read the first 4 sections of "A Riemannian Framework for Tensor Computing" {{riemannian_framework_for_tensor_computing_2005.pdf}}. === Jan 31 === We will be reading the paper "Smooth relevance vector machine: a smoothness prior extension of the RVM" by Alexander Schmolck and Richard Everson (Mach Learn (2007) 68: 107–135) {{smoothrvm.pdf}} We'll discuss and compare it to papers we covered earlier, Mert's MICCAI {{sabuncumiccai2011.pdf}} and journal paper (coming soon) as well as Tipping's original work on RVM {{tippingjmlr2001_sparsebayesianlearningandtherelevancevectormachine.pdf}}. === Jan 24 === Spatially regularized SVM for the detection of brain areas associated with stroke outcome. Remi Cuingnet, Charlotte Rosso, Stephane Lehericy, Didier Dormont, Habib Benali, Yves Samson1, and Olivier Colliot. MICCAI 2010. {{miccai2010_cuingnet.pdf}} === Jan 17 === UPDATE: Annotations added. I recommend reading most of the introduction for context and background, so I've left it without annotations. In the Methods section, I've highlighted titles of subsections that are pertinent to the results I intend to cover. Similarly, in the Results section, I've highlighted subsections I intend to cover and struck through everything we won't discuss. Despite this, there is still a fairly large amount of text to read, some of which is somewhat technical (in a neuroscientific sense). Therefore, I recommend initially focusing on the results figures, which are highly illustrative and well described in their respective captions, then referring back to the text. Annotated PDF: {{j_neurophys-2011-yeo-annot-print.pdf}} We plan to read parts of Thomas' (and others') paper on a large scale study of resting state functional connectivity in healthy subjects. The discussion should mostly be centred around particularly interesting results that could serve as motivation for future work in our group. Once I've read all of the paper in detail, I'll try to narrow down the results sections so that the amount of material is reasonable. B. T. Thomas Yeo, Fenna M. Krienen, Jorge Sepulcre, Mert R. Sabuncu, Danial Lashkari, Marisa Hollinshead, Joshua L. Roffman, Jordan W. Smoller, Lilla Zöllei, Jonathan R. Polimeni, Bruce Fischl, Hesheng Liu and Randy L. Buckner; The organization of the human cerebral cortex estimated by intrinsic functional connectivity {{j_neurophys-2011-yeo.pdf}} ==== Fall 2011 ==== === Dec 7 === {{met-mlbayes.pdf}} We're going back in time and covering a tutorial in Bayesian inference in Machine Learning by Tipping. It offers a nice build-up from least squares regression to the RVM. The Models in Section 4 are very related to the RVoxM readings from the previous 2 weeks. {{rvmpath.pdf}} I put together a quick list of papers and references for learning the RVM and RVoxM. If you are interested in this topic, take a look at the file for more information/paths to take. For the curios, here{{tipping.pdf}}'s some results from a quick (potentially buggy) implementation. I tried to keep the colors as those Tipping's Figure 5, although I had to guess some of the parameters so the curves are slightly different. The new blue line shows the (-log) joint that we were wondering about, and the red is the (-log) marginal likelihood from the paper (these later two curves were rescaled). Although they differ slightly, all three estimations of lambda (validation, joint, marginal) seem ~equally decent. === Dec 1 === ** Note special time this week: Thursday, Dec 1, 4pm ** \\ We'll go into the hyperparameter estimation derivations from the Relevance Voxel Machine. I've emailed a draft of the journal RVoxM paper to V-Golland. We will concentrate on Sections II, III and VI (Theory and Appendix). For the interested, more reading into RVM: Michel Tipping maintains a website on "Sparse Bayesian Models (& the RVM)": http://www.miketipping.com/index.php?page=rvm \\ One of the papers, "Sparse Bayesian learning and the relevance vector machine" {{tipping01a.pdf}} has relevant derivations in sec 1, 2, 5. (see http://www.miketipping.com/index.php?page=corrections for corrections) \\ Fletcher {{fletcher_-_rvm_explained.pdf}} also dives right into the theory (much less discussion on motivation/application/etc) \\ See {{2004-Wipf-IEEESigProc.pdf}} for another perspective on sparsity === Nov 22 === ** Note special time this week: Tuesday, Nov 22, 4pm ** We'll be reading Mert's MICCAI paper - Sabuncu and Leemput, The Relevance Voxel Machine (RVoxM): A Bayesian Method for Image-based Prediction, MICCAI, 2011 - {{sabuncumiccai2011.pdf}} === Nov 16 === We will read "Connectivity-Informed fMRI Activation Detection" by Bernard Ng, Rafeef Abugharbieh, Gael Varoquaux, Jean Baptiste Poline and Bertrand Thirion. {{ng_connectivityinformedfmri_miccai11.pdf}} === Nov 2 and 9 === We'll read up on RKHSs. We'll start with this tutorial: {{daume04rkhs.pdf}} Sections 1-5 are straightforward and should be mostly review, so we'll just be discussing Section 6. There are a few typos: At the end of 6.2, the first sentence of the last paragraph is more clear as "The property of reproducing kernels that we need is = f(\cdot)." The right-hand side of the equation in 6.4.1 should read $\lambda\phi(x)$ (instead of x^\prime). The notes that George posted are also relevant; here are the notes and the blurb: On an unrelated note, here are some notes I hacked up about basics of Reproducing Kernel Hilbert Spaces and Kernel Ridge Regression: {{reading_group_prep_rkhs_2011_10_14.pdf}} This is NOT related to the 10/19 reading; it's related to the 10/12 reading. This could be useful for when we return to talking about kernel methods. **Update 10/13**: A few minor typos have been corrected. **Update 10/14**: The proof for the closed-form solution for kernel ridge regression has been extended to allow for possibly non-invertible kernel matrices. === Oct 26 === We will go through the details of INLA and discuss applications. Please read Section 4 in addition to the first part of the paper. Here's a write-up on the Laplace's approximation from 6.437: {{Laplace.pdf}} === Oct 19 === We will read about integrated nested Laplace approximations (it's a 74-page beast, but references begin on page 32 followed by discussions that happened after publication): Håvard Rue, Sara Martino, and Nicolas Chopin. "Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations." JRSS 2009. {{inla.pdf}} * **Update 10/18**: Just read through the end of section 3; this amounts to ~13.3 pages of reading. * **Update 10/19 1:38am**: Notes I (George) will use today at reading group. It's high-level and almost surely has bugs: {{reading_group_inla_notes_2011_10_19_0137.pdf}} === Oct 12 === Nicolas Duchateau, Mathieu De Craene, Gemma Piella, and Alejandro F. Frangi. Characterizing Pathological Deviations from Normality using Constrained Manifold-Learning. miccai 2011. {{Duchateau-miccai2011.pdf}} === Sep 14 === Rómer Rosales and Brendan Frey. Learning Generative Models of Affinity Matrices: UAI 2003 {{rosales_frey_similarity.pdf}} ==== Summer 2011 ==== === August 23 === Firdaus Janoos, Shantanu Singh, Raghu Machiraju, William M. Wells III, István Ákos Mórocz. State-Space Models of Mental Processes from fMRI. IPMI 2011. {{janoos-ipmi2011.pdf}} === August 16 === Fani Deligianni, Gael Varoquaux, Bertrand Thirion, Emma Robinson, David J Sharp, A David Edwards, and Daniel Rueckert. A Probabilistic Framework to Infer Brain Functional Connectivity from Anatomical Connections. IPMI 2011. {{deligianni2011.pdf }} === August 9 === Gaël Varoquaux, Alexandre Gramfort, Fabian Pedregosa, Vincent Michel, Bertrand Thirion. "Multi-subject Dictionary Learning to Segment an Atlas of Brain Spontaneous Activity." IPMI 2011. {{ipmi2011-multi-subject-dict-learning-fmri.pdf}} === August 2 === We'll cover Stanley Durrleman, Marcel Prastawa, Guido Gerig, Sarang C. Joshi. "Optimal Data-Driven Sparse Parameterization of Diffeomorphisms for Population Analysis." IPMI 2011. {{ipmi2011-sparse-diffeomorphisms.pdf}} === July 26 === We will continue covering Wainwright's notes on sparse linear models (i.e. same reading as July 12 and 19). In particular, we will blow up the plot on Page 92, work through the proof for Theorem 5.3 and Example 5.7, and finish discussion about pairwise incoherence and the restricted isometry property (RIP). As an illustrative example, I (George) will also discuss Exercise 5.2 at the end of the chapter (showing that pairwise incoherence implies the restricted nullspace property, without using RIP results). Non-trivial probabilistic results that are used in Example 5.7 and Exercise 5.2c will be briefly discussed. Definition 5.3. and Theorem 5.3 are in hard-to-read shaded boxes, which are reproduced here: {{reading_group_july_26.pdf}} Page 92 plot, blown up (1.7MB): http://people.csail.mit.edu/georgehc/pg92_plot_blown_up.jpg **Update (July 24, 1:48pm)**: Notes from the previous reading group are now available: {{reading_group_2011_07_19_notes.pdf}} **Update (July 25, 11:43am)**: Preliminary supplemental notes for this week's reading group are now available: {{reading_group_2011_07_26_notes_draft2.pdf}} === July 19 === We will read the notes on sparse linear models, focusing on the conditions, their relationships, and the proofs. Try to come up with or keep in mind a roadmap of where to go from here as you read. === July 12 === We will cover Martin Wainwright's notes on sparse linear models up to and including section 5.3.2. {{wainwright-sparse-linear-models.pdf}} The gray boxes are kind of hard to read, so they're reproduced in this supplement: {{wainwright-theorems-1.pdf}} === June 21st === We will continue the discussion on CCA. In addition to the June 14th reading, see I. Rustandi Thesis, Predictive fMRI Analysis for Multiple Subjects and Multiple Studies - Section 3.3. {{cmu-cca-ch3.pdf}} (see section 3.3) === June 14th === D. R. Hardoon , S. Szedmak and J. Shawe-Taylor, Canonical correlation analysis; An overview with application to learning methods, T.R. 2003{{Hardoon-03.pdf}} Further reading F.R. Bach and M.I. Jordan, A Probabilistic Interpretation of Canonical Correlation Analysis, T.R. 2005 {{BachJordan05.pdf}} H. Hotelling, Relations Between Two Sets of Variates, Biometrika, 1936{{Hotelling36.pdf}} ==== Spring 2011 ==== === May 16 === Original Infomax paper. Bell and Sejnowski, Neural Computation, 1995. {{wiki:infomax.pdf}} Cardoso '97 paper that connects Infomax to Max. Likelihood: {{cardoso1997_infomax_ml.pdf}} === May 9 === We'll talk about ICA. The paper will be: ICA Tutorial (with sections devoted to Infomax ICA): * Independent Component Analysis: Algorithms and Applications, Aapo Hyvärinen and Erkki Oja, 2000. {{wiki:icatutorial.pdf}} === May 2 === We'll talk about an ICA method for evaluating fMRI and genetic data. The paper will be: * J.Liu et al, Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA, HBM 2009. {{2009_liu-hbm.pdf}} A relevant review paper (optional): * Calhoun et al. A review of group ICA for fMRI data and ICA for joint inference of imaging, genetic, and ERP data, NeuroImage, 2009 {{calhoun2009.pdf}} === Apr 11 (no meeting Apr 4, we will have a talk instead) === We will be discussing "Joint Bayesian Cortical Sulci Recognition and Spatial Normalization" by Perrot et al. from IPMI 2009. {{perrot_ipmi_09.pdf}} === Mar 28 (no meeting March 21, spring break) === Gael Varoquaux, Alexandre Gramfort, Jean-Baptiste Poline, Bertrand Thirion; Brain covariance selection: better individual functional connectivity models using population prior. NIPS 2011 {{varoquax-fmri-nips10.pdf}} [[Discussion_Mar_29_2011|Discussion]] === Mar 14 === We'll look at "Fitting a graph to vector data" {{fitting_a_graph_to_vector_data.pdf}}, which gives an alternate approach to K-nearest neighbors and epsilon radius for creating the initial graph. === Feb 28 (no meeting on Feb 21 -- Presidents' Day) === We will look more closely at the derivation that leads to the eigenvector problem in one of the references in the paper we read last time. Specifically, we will discuss theorems 14.2.1 and 14.4.2 in Multivariate Analysis by Mardia, Kent and Bibby. {{multivariate_analysis.pdf}} Proof that the SVD is the best low rank approximation and the exercise in Mardia {{svdproof.pdf}} **Remark**: Given the discussion during reading group, it seems that a Cholesky decomposition would work. In particular, for real, positive semi-definite B, using Cholesky decomposition would produce lower-triangular, real-valued L such that: B = L * L^T As an example, if B is full-rank, then the columns of L would all be independent forming a basis (which may not be orthonormal; although we could say that the original data points also need not be orthonormal). More information: http://en.wikipedia.org/wiki/Cholesky_decomposition#Statement === Feb 14 === Actually, we will discuss Tenebaum, J.B., de Silva, V., and Langford, J.C., A global geometric framework for nonlinear dimensionality reduction, Science, 290, p 2319-2323, 2000. {{wiki:isomap.pdf}} Contrary to the first notice, we will NOT discuss: R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker. Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps. PNAS, 2005. {{wiki:geometric-diffusion1.pdf}} This paper demonstrates gradient-based implementation of MDS (known as Sammon mapping): JOHN W. SAMMON, A Nonlinear Mapping for Data Structure Analysis. IEEE TRANSACTIONS ON COMPUTERS, VOL. C-18, NO. 5, MAY 1969 {{mds-numerical.pdf}} === Feb 7 === We will discuss a view of spectral embedding via diffusion processes. Please read carefully the first paper and go over the second paper. Both present similar approaches to the problem. A wandom walk view of spectral segmentation. Meila and Shi, AIstats 2001. {{meila-aistats-2001.pdf}}. R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker. Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps. PNAS, 2005. {{wiki:geometric-diffusion1.pdf}} U. Luxburg. A tutorial on spectral clustering. Statistics and Computing 2007. {{luxburg_spectralclustering_tutorial.pdf}}. === Jan 31 === J. Shi, J. Malik: Normalized Cuts and Image Segmentation {{wiki: ShiMalik-NormalizedCuts.pdf}} We'll mainly be focusing on section 2 - i.e. why it is that minimizing the normalized cut turns out to be a generalized eigenvalue problem. We might also want to discuss how we can interpret this by forming a Markov chain on the graph, so I've added a relevant paper {{meila-aistats-2001.pdf}}. === Jan 25 === We'll be continuing Sharpnack's paper on graph labeling, focusing on Theorem 1 and its proof: J. Sharpnack, A. Singh; Identifying graph-structured activation patterns in networks {{sharpnack-graph-nips10.pdf}} A video of the conference talk is here: http://videolectures.net/nips2010_sharpnack_igs/ (the talk doesn't go into detail on the proofs, but does give a little bit of intuition for the terms in the theorem). We'll also look briefly at these papers on other spectral methods: {{wiki: ShiMalik-NormalizedCuts.pdf}} {{wiki:Ng-SpectralClustering.pdf}} {{wiki: Belkin-LaplacianEigenmaps.pdf}} === Jan 18 === We'll be reading Sharpnack's paper on graph labeling: J. Sharpnack, A. Singh; Identifying graph-structured activation patterns in networks {{sharpnack-graph-nips10.pdf}} A video of the conference talk is here: http://videolectures.net/nips2010_sharpnack_igs/ ===January 11=== We will take another look at the paper by M. Nielsen, L. Florack and R. Deriche {{nielsen_regscalespace_jmathimage1997.pdf}} through Section 5. ==== Fall 2010 ==== === Dec 2 === We will clean up our discussion of the demons algorithms. The leftover items is the second-order optimization and the relationship between regularization and smoothing. 1) For the ESM method, we will look at section 3 of this paper: Insight Into Efficient Image Registration Techniques and the Demons Algorithm. Tom Vercauteren, Xavier Pennec, Ezio Malis, Aymeric Perchant, and Nicholas Ayache. IPMI 2007. {{insighteffregdemons-ipmi07-vercauteren.pdf}} 2) For the regularization, we will look at these papers: *Iconic Feature Based Non-Rigid Registration: The PASHA Algorithm. P. Cachier et. al. (Appendix A only) {{cachier_pasha_cviu2003.pdf}} *Regularization, Scale-Space and Edge Detection Filters. M. Nielsen, L. Florack, R. Deriche {{nielsen_regscalespace_jmathimage1997.pdf}} === Nov 17 === Diffeomorphic demons: Efficient non-parametric image registration. Tom Vercauteren, Xavier Pennec, Aymeric Perchant, Nicholas Ayache. NeuroImage, 2009. {{Vercauteren-2009.pdf}} The original demons paper: J.-P. Thirion, Image matching as a diffusion process: an analogy with Maxwell's demons. Medical Image Analysis (1998), volume 2, number 3. {{thirion98.pdf}} === Nov 10 === From MICCAI, 2010: L. Risser, F.-X. Vialard, R. Wolz, D. Holm, D. Rueckert; Simultaneous Fine and Coarse Diffeomorphic Registration: Application to Atrophy Measurement in Alzheimer's Disease; MICCAI 2010 {{miccai2010_risser.pdf}} === Nov 3 === From MICCAI, 2010: P. Risholm, S. Pieper, E. Samset and W. M. Wells; Summarizing and visualizing uncertainty in non-rigid registration {{miccai2010_risholm.pdf}} Background paper: P. Risholm et al. Bayesian Estimation of Deformation and Elastic Parameters in Non-rigid Registration {{wibr2010_risholm.pdf}} === Oct 27 === From MICCAI, 2010: G. Varoquaux, F. Baronnet, A. Kleinschmidt, P. Fillard, and B. Thirion; Detection of Brain Functional-Connectivity Difference in Post-stroke Patients Using Group-Level Covariance Modeling {{varoquaux_grouplevelcovariance_miccai10.pdf}} === Oct 20 === We will read Chapter 22 "Analysis of variance" (ANOVA) of Andrew Gelman's "Data Analysis Using Regression and Multilevel/Hierarchical Models" book {{gelman.pdf}}. In particular, we will just be looking at pages 487-501 in the book (PDF pages 513-527). **Update 10/15/10 9:04PM**: The high quality PDF of just Chapter 22 is now available {{gelman-ch22.pdf}}. Notes by George: {{reading-group-anova-2010-10-20-notes.pdf}} === Oct 13 === We will read Bernardo and Smith's coverage of reference priors. The relevant section from the book is here: {{bernardo_smith_referencepriors.pdf}}. * Pages 298-316 (PDF pages 1-19) cover the basics of 1-dimensional reference priors, * pages 316-320 (PDF pages 19-23) cover restricted reference priors (from a restricted family of distributions), * pages 320-333 (PDF pages 23-36) cover reference priors with nuisance parameters, * and pages 333-339 (PDF pages 36-42) cover the multidimensional case. ==== Summer 2010 ==== === Aug 17-31 === The next three meetings will provide an overview of Multilevel Regression and ANOVA using the book, "Data analysis using regression and multilevel/hierarchical models" by Andrew Gelman. The chapters posted below come from the publisher's website and have a few formatting issues. A short summary of these issues has been made {{format_errors.pdf}} The material for the first 2 weeks comes from Part 2A {{gelman_pt2A.pdf}} Aug 17th: Please read chapter 12, pgs.251-276, as an introduction to multilevel linear models. Also, please read pgs.244-247 from chapter 11, which attempts to explain the difference between "random" and "fixed" effects. Aug 24th and 31st (pick one to attend): Please read chapter 13, pgs.279-297, which covers some more complex multilevel linear models with varying slopes and "non-nested" data. Sep 7th: Multilevel regression applied to fMRI. Please read {{woolrich_behrens_multilevel.pdf}} === Aug 3 === Gerber et al. Manifold modeling for brain population analysis. Medical Image Analysis 14 (2010) 643–653. {{wiki:Gerber-MedIA-2010.pdf}} === Aug 10 === Jia et al. ABSORB: Atlas building by self-organized registration and bundling. NeuroImage 51 (2010) 1057–1070. {{jia_neuroimage_2010.pdf}} === July 13 - July 27 === We will start a 3-4 week overview of Neural Networks and Deep Belief Networks. The rough schedule is as follows: July 13th: We will introduce the standard Neural Network setup, as presented in Bishop's "Pattern Recognition and Machine Learning" {{Bishop_PatternRecognitionandMachineLearning_Ch5.pdf}}. Please read Sections 5.1 and 5.2. In addition, please skim 5.3.1 and 5.3.2, as we may get started on Back-Propagation. July 20th: We will talk about back propagation. Please read Section 5.3 of Bishop and the original Back-Propogation paper by Rumelhart {{Rumelhart_BackPropagatingErrors_Nature86.pdf}}). If time permits, we may go over computing the Hessian (Section 5.4 of Bishop). July 27th: We will discuss Hinton's learning algorithm for Deep Belief networks {{Hinton_FastLearningDeepBelief_NeuralComp06.pdf}}. ==== Spring 2010 ==== === May 17 === We will finish the LP paper from Mar 29. === May 10 === We will discuss the meanfield solvers for MRFs. Background from Wanmei's thesis: {{wiki:meanfield.pdf}} Exerts from course notes: {{wiki:variational.pdf}} === Apr 26 == __Graph cuts for energy minimization; Min Cut Max Flow:__ Yuri Boykov, Olga Veksler, and Ramin Zabih. Fast Approximate Energy Minimization via Graph Cuts. //IEEE PAMI// 23(11), 2001. {{wiki:boykov2001.pdf}} Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest and Clifford Stein. Min Cut Max Flow and the Ford-Fulkerson method. //Introduction to Algorithms, Second Edition// {{minmax.pdf}} === Apr 12 === We will discuss primal-dual algorithms for solving linear programs. The first chapter of "Primal-Dual Interior-Point Methods" by Stephen Wright provides a good overview of the subject: {{wright_primaldual_1997.pdf}} The tutorial on convex optimization by Haitham Hindi is a more complete overview of duality and optimality conditions: {{hindi_tutorialconvexopt.pdf}} === Apr 5 === We will discuss primal-dual formulation in more detail. See pages 215-227 and 232-234 of Convex Optimization by Boyd and Vandenberghe: {{boyd_duality.pdf}} A PDF of the full book is available at http://www.stanford.edu/~boyd/cvxbook/bv_cvxbook.pdf. Book pages 215-227,232-234 correspond to PDF pages 229-241,246-248. We will also try to finish the labeling from last time. === Mar 29 === Nikos Komodakis and Georgios Tziritas: Approximate Labeling via Graph Cuts Based on Linear Programming. in PAMI 2007 {{komodakis07linprog.pdf}} we will stick to the PAMI paper, but a concise listing of the most important ideas is in: Nikos Komodakis et al. ICCV 2005 {{komodakis_iccv2005.pdf}} [[http://www.example.com|External Link]] === Feb 22 === Olivier Commowick, Simon K. Warfield, and Gregoire Malandain. Using Frankenstein’s Creature Paradigm to Build a Patient Specific Atlas; MICCAI 2009 {{miccai2009_commowick.pdf}} === Feb 16 (monday schedule for classes) === We continued the discussion of the paper from the previous week. === Feb 8 === Nematollah Batmanghelich, Ben Taskar, and Christos Davatzikos. A general and unifying framework for feature construction in image-based patter classification; IPMI 2009 {{ipmi2009_batmanghelich.pdf}} === Jan 26 === Davis, B.C., Fletcher, P.T., Bullitt, E., Joshi, S. Population Shape Regression From Random Design Data. ICCV 2007. {{wiki:davis-iccv2007.pdf}} === Jan 19 === T. Rohlfing et al. Regression models for atlas appearance. IPMI 2009. {{ipmi2009_rohlfing.pdf}} ==== Fall 2009 ==== === Nov 17 === Ou; DRAMMS: Deformable registration via Attribute Matching and mutual-saliency weighting; IPMI 2009 {{ipmi2009_ou.pdf}} === Oct 27 === Criminisi; Decision Forests with Long-Range Spatial Context for Organ Localization in CT Volumes, MICCAI/PMMIA 2009 {{criminisipmmia2009_decisionforests.pdf}} Additional reading: Breimann 01 Random Forests: {{breiman01randomforests.pdf}} === Oct 13 === Murgasova, A spatio-temporaral atlas of the growing brain for fMRI studies, MICCAI/IADB 2009 {{murgasova09development.pdf}} === Oct 6 === D. R. Hardoon , S. Szedmak and J. Shawe-Taylor, Canonical correlation analysis; An overview with application to learning methods, T.R. 2003{{Hardoon-03.pdf}} Further reading H. Hotelling, Relations Between Two Sets of Variates, Biometrika, 1936{{Hotelling36.pdf}} F.R. Bach and M.I. Jordan, A Probabilistic Interpretation of Canonical Correlation Analysis, T.R. 2005 {{BachJordan05.pdf}} === Sep 29 === We will continue discussing the Elastic Net paper by Zou and Hastie: {{elastic_net_zou_hastie_2005.pdf}} === Sep 15 === We will discuss the Elastic Net paper by Zou and Hastie: {{elastic_net_zou_hastie_2005.pdf}} === Sep 1 === Will finish the sparse PCA paper. ==== Summer 2009 ==== === Aug 25 === We will discuss the Sparse PCA paper by Zou, Hastie, and Tibshirani: {{sparsepca.pdf}} **The published version of the paper (which we'll discuss) is here: {{spca_jcgs.pdf}}** === Aug 18 === We continued discussing the IBP papers. === Aug 11 === Indian Buffet Process: we will discuss Griffith and Ghahramani, Infinite latent feature models and the Indian buffet process, NIPS 2006. {{wiki:ibp-1.pdf}} There are two other important papers: IBP and the hierarchical Beta processes. {{wiki:hbp-2.pdf}} Stick-breaking Construction for the IBP. {{wiki:stickbreakingibp.pdf}} === July 21 and 28 === We will discuss Discriminative Shape Alignment. Marco Loog and Marleen de Bruijne. IPMI 2009. {{Loog-IPMI2009.pdf}} Thomas will lead the discussion. Proof of complex representations: {{wiki:procrusts-complex-representation.pdf}} Two tutorials found by Tammy: {{wiki:procrustes-ch-04.pdf}} {{procrustes_tutorial.pdf}} === June 16 === We will be discussing Stochastic Tractography {{friman_bayesianstochtract_2006.pdf| Friman, Bayesian Stochastic Tractography}}. This paper references the work by Behrens et. al. {{behrens_propagofuncertainty_2003.pdf| Behrens, Propagation of Uncertainty}}. Since both papers are fairly straightforward, if time permits, we will talk about both models. === June 9 === We discussed the PAMI paper during our Reading Group; the MICCAI paper was listed for further reading. {{finsler_active_contours_ieee_pami_2008.pdf|Finsler Active Contours}}, J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, IEEE PAMI 2008. {{finsler_tractography_for_white_matter_connectivity_analysis_of_the_cingulum_bundle_j._melonakos_v._mohan_m._niethammer_k._smith_m._kubicki_a._tannenbaum_miccai_2007.pdf| Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle}} J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, A. Tannenbaum, MICCAI 2007. === June 2 === We used the MICCAI paper as the basis of the discussion; the thesis has much more detail. {{fan_miccai07_published.pdf| MCMC Curve Sampling for Image Segmentation}}, Fan, A., J. Fisher, W. Wells, J. Levitt, A. Willsky, MICCAI 2007. {{fan_phdthesis.pdf| Curve Sampling and Geometric Conditional Simulation}}, Fan, A., MIT PhD Thesis, Nov. 2007. ==== Spring 2009 ==== === May 12 === Dirichlet Processes (contd.) We plan to read and understand the variational approximations from Kurihara et al. Kurihara, Welling, Teh: Collapsed Variational Dirichlet Process Mixture Models {{wiki:cvdp.pdf}}. === May 5 === Dirichlet Processes (contd.) We are continuing with the hierarchical Dirichlet processes from Teh et al. === April 21 (no meeting April 7, 14) === Dirichlet Processes. We plan to read and understand Teh et al. But for the first session, we will spend time going through the basics of the nonparametric methods from the tutorial {{wiki:Dirichlet_processes.pdf}}. Here is some brief notes on DPs: {{wiki:DP_brief_notes.pdf}}. Teh, Jordan, Beal, Blei: Hierarchical Dirichlet Processes {{wiki:hierarchical_nonparametric.pdf}} === March 31 (no meeting March 24 -- springbreak) === We will finish the shapes paper from last time. === March 17 === E. Klassen, A. Srivastava, W. Mio, and S. Joshi, Analysis of Planar Shapes Using Geodesic Paths in Shape Spaces, PAMI 2004 {{{klassensrivastavamiojoshipami04.pdf}} === Feb 24 === We will start by finishing the paper from last time. The homework is to derive the coefficients from the next level of splines from the coefficients of the previous level. We will then discuss the thin-plate splines. Principal Warps: Thin-Plate Splines and the Decomposition of Deformations. FRED L. BOOKSTEIN. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE. VOL.II. NO. 6. JUNE 1989. {{wiki:bookstein-89.pdf}} Wanmei and Mert will lead the discussion. === Feb 10 === We will finish the registration paper and discuss multi-level splines in a bit more detail. Michal will lead the discussion on the registration paper. Scattered Data Interpolation with Multilevel B-Splines. Seungyong Lee, George Wolberg, and Sung Yong Shin. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, VOL. 3, NO. 3, JULY–SEPTEMBER 1997. {{wiki:bsplines-2.pdf}} Archana will lead the discussion on splines. === Feb 3 === Nonrigid Registration Using Free-Form Deformations: Application to Breast MR Images. D. Rueckert, L. I. Sonoda, C. Hayes, D. L. G. Hill, M. O. Leach, and D. J. Hawkes. IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 18, NO. 8, AUGUST 1999. {{wiki:rueckert-ffd.pdf}} These are several background papers on splines: Surface Fitting with Hierarchical Splines DAVID R. FORSEY and RICHARD H. BARTELS. ACM Transactions on Graphics, Vol. 14, No. 2, April 1995, Pages 134-161. {{wiki:bsplines-1.pdf}} Scattered Data Interpolation with Multilevel B-Splines. Seungyong Lee, George Wolberg, and Sung Yong Shin. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, VOL. 3, NO. 3, JULY–SEPTEMBER 1997. {{wiki:bsplines-2.pdf}} Principal Warps: Thin-Plate Splines and the Decomposition of Deformations. FRED L. BOOKSTEIN. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE. VOL.II. NO. 6. JUNE 1989. {{wiki:bookstein-89.pdf}} ==== Fall 2008 ==== === Dec 16 === K. K. Bhatia, P. Aljabar, J. P. Boardman, L. Srinivasan, M. Murgasova, S. J. Counsell, M. A. Rutherford, J. Hajnal, A. D. Edwards, and D. Rueckert, Groupwise Combined Segmentation and Registration for Atlas Construction, MICCAI 2007 {{BahtiaMiccai07.pdf}} === Dec 12 (note unnusual day, still 12-1:30) === We will go over section V of the same paper. === Dec 2 === We will work on details of geometry of the cost function and Lemma 2 in the sparse bayesian learning paper. === Nov 25 -- no meeting (Thanksgiving week) === === Nov 18 === David P. Wipf and Bhaskar D. Rao. Sparse Bayesian Learning for Basis Selection. IEEE TRANSACTIONS ON SIGNAL PROCESSING, 2004. {{2004-Wipf-IEEESigProc.pdf}} has some theoretical explanation about why the sparse Bayesian learning is indeed sparse. Section II shows the formulation, which is the same as Tipping's ARD paper, and an EM algorithm to optimize the objective function. Section III and IV are the theoretical analysis of why the model favors sparse solution. In particular, IV A proposes a very interesting proof. === Nov 11 -- no meeting, Veterans' day === === Nov 4 === We will continue with the currents. === Oct 21 === S. Durrleman, X. Pennec, A. Trouve, P. Thompson, N. Ayache. Inferring brain variability from diffeomorphic deformations of currents: An integrative approach {{wiki:durrleman_currents.pdf}} M. Vaillant and J. Glaunes" Surface Matching via Currents {{wiki:vaillant_currents.pdf}} === Oct 14 === S. Durrleman, X. Pennec, A. Trouve, P. Thompson, N. Ayache. Inferring brain variability from diffeomorphic deformations of currents: An integrative approach {{wiki:durrleman_currents.pdf}} === Oct 7 === We are going to read Tipping's paper on Sparse Bayesian Learning \\ {{tipping2003_fastmarginallikelihoodmaximisationforsparcemachinemodels.pdf}}. It is closely related to some other learning schemes. {{2001-Tipping-JMLR.pdf}} lays out the fundamental concepts for sparse Bayesian learning, and it may assist you to understand the above paper. {{2004-Wipf-IEEESigProc.pdf}} has some theoretical explanation about why the sparse Bayesian learning is indeed sparse. === Sep 23 ==== Using the logarithm of odds to define a vector space on probabilistic atlases. Kilian M. Pohl , John Fisher , Sylvain Bouix , Martha Shenton , Robert W. McCarley , W. Eric L. Grimson , Ron Kikinis , William M. Wells Medical Image Analysis 2007. {{pohl-media-2007.pdf}} === Sep 16 === Label Space: A Multi-object Shape Representation. James Malcolm, Yogesh Rathi, and Allen Tannenbaum. MICCAI 2008. {{wiki:malcolm-miccai08.pdf}} ==== Summer 2008 ==== === Aug 27 (just this time, 11-12:30) === Salima Makni, Philippe Ciuciu, Jérôme Idier, and Jean-Baptiste Poline. Joint Detection-Estimation of Brain Activity in Functional MRI: A Multichannel Deconvolution Solution. IEEE Trans. Sig. Proc., 53(9):3488-502, Sept. 2005. {{makni-tsp.pdf}} === Aug 20 === Davis, B.C., Fletcher, P.T., Bullitt, E., Joshi, S. Population Shape Regression From Random Design Data. ICCV 2007. {{wiki:davis-iccv2007.pdf}} === Aug 13 === Yonggang Shi, Zhuowen Tu, Allan L. Reiss, Rebecca A. Dutton, Agatha D. Lee, Albert M. Galaburda, Ivo D. Dinov, Paul M. Thompson, Arthur W. Toga: Joint Sulci Detection Using Graphical Models and Boosted Priors. IPMI 2007. {{wiki:shi-ipmi07.pdf}} === Aug 6 === We will finish the GLM paper this time. === July 30 === Friston, L., et al.: Assessing the significance of focal activations using their spatial extent. Human Brain Mapping, 1994. {{wiki:Friston_FocalActivations.pdf}} === July 23 === Friston, K., et al.: Statistical parametric maps in functional imaging: A general linear approach. Human Brain Mapping, 1995.{{wiki:friston_glm.pdf}} Worsley, KJ, Friston, KJ.: Analysis of fMRI Time-Series Revisited—Again. Neuroimage, 1995. {{wiki:worsley_fmriagain.pdf}} Myers, RH, Montgomery, DC. A tutorial on Generalized Linear Models. Journal of Quality Technology, 1997. {{wiki:myers_tutorialOnGLM.pdf}} === July 16 === We will finish the paper from last week. === July 9 === Joshua E. Cates, P. Thomas Fletcher, Martin Andreas Styner, Martha Elizabeth Shenton, Ross T. Whitaker: Shape Modeling and Analysis with Entropy-Based Particle Systems. IPMI 2007. {{wiki:cates-ipmi07.pdf}} === July 1 (Tuesday, 12-1:30, just this one time) === We will continue to discuss the LDDMM paper. The goal is to find a geometric interpretation of the first term in the sum in eq. 4, finish the theorem and talk about the metric (Sec 6). === June 18 === We will discuss the computation behind LDDMM {{wiki:beg-lddmm.pdf}}. It will be an easier start than understanding the more theoretical underpinnings of the other LDDMM papers. Note that the first lemma is the hardest part of the paper, but things get a lot easier after that. === June 4 (12:30-2pm) === We will discuss the Nystrom Method, which can be used to approximate the eigendecomposition of large matrices. An application of this technique to Spectral Clustering is presented in Fowlkes et al. {{fowlkes_spectralgrouping_nystrom.pdf}} ==== Spring 2008 ==== === May 13 === We will discuss Rao's paper on the uniqueness of the decomposition into a Gaussian and a non-Gausian part. New paper {{1966-Rao-SankhyaSerA.pdf}}. === May 6 === We will discuss Rao's paper on the uniqueness of the decomposition into a Gaussian and a non-Gausian part {{1969-Rao-AnnMathStatist.pdf}}. === Apr 28 (Monday, 12:30-1:30) === We will continue with the ICA paper. === Apr 22 === We will discuss Beckmann et al.'s Probabilistic ICA for fMRI paper {{beckmann2003.pdf}} === Apr 15 === We will continue with the LDA discussion. === Apr 9 (Wednesday, 2:30pm) === We will discuss Blei et al.'s Latent Dirichlet Allocation paper {{bleingjordan2003.pdf}} We will also discuss [[http://www.nataliedee.com/091605/poison-cupcakes.jpg|this.]] === Apr 2 (Wednesday, 2:30pm) === We will discuss Lilla Zollei's paper. A Marginalized MAP Approach and EM Optimization for Pair-Wise Registration: {{2007-zollei-ipmi.pdf}} === Mar 18 === We will continue on the Wisharts paper; the homework is to get more comfortable with that particular distribution. === Mar 11 === Bing Jian, Baba C. Vemuri: Multi-fiber Reconstruction from Diffusion MRI Using Mixture of Wisharts and Sparse Deconvolution. IPMI 2007. {{wiki:jian-vemuri-ipmi07.pdf}} Anastasia will lead the discussion. === Feb 26 === Schapire. Boosting overview {{wiki:schapire_msri.pdf}} [[Discussion_Feb_26|Discussion]] Additional papers: Jerome Friedman, Trevor Hastie, Robert Tibshirani. Additive Logistic Regression: a Statistical View of Boosting (1998). {{wiki:friedman98additive.pdf}} Torralba, Murphy and Freeman. Sharing visual features for multiclass and multiview object detection. {{wiki:sharing.pdf}} === Feb 19 === Boosting Image Retrieval (Tieu, Viola, IJCV 2004) {{wiki:tieu_BoostingImageRetrieval.pdf}} === Feb 12 === We will continue the discussion about the paper from last meeting. === Feb 1 (Friday) === Chris McIntosh and Ghassan Hamarneh. Is a Single Energy Functional Sufficient? Adaptive Energy Functionals and Automatic Initialization. MICCAI 2007. {{wiki:mcintosh-miccai2007.pdf}} ==== Fall 2007 ==== === Jan 22 (Tuesday) === Shaohua Kevin Zhou and Dorin Comaniciu. Shape Regression Machine. IPMI 2007. {{wiki:zhou-ipmi2007.pdf}} === Jan 15 (Tuesday) === We will discuss the two simple examples defined in last meeting: a closed curve and an open curve. Please work through the examples and come with beatiful matlab figures of the embedding. We will also talk about wavelets. The first paper is what we already looked at; the other two are longer, more detailed versions. R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker. Geometric diffusions as a tool for harmonic analysis and structure definition of data: Multiscale methods. PNAS, 2005. {{wiki:geometric_diffusion2.pdf}} Additional papers on the topic: Diffusion wavelets and their use in spectral clustering: {{wiki:Nadler06.pdf}} {{wiki:CoifmanMaggoni06.pdf}} === Dec 10 (Mon, 9-10am) === Laplacian-Eigenmaps by Belkin and Niyogi{{wiki:laplacianeigenmaps.pdf}} Further papers on discrete Laplace-Beltrami Operators (overview): {{wiki:xu-04-discretelaplace.pdf}} {{wiki:wardetzky-07-discreteLBO.pdf}} === Dec 5 (Wed, 2:30-3:30 since Polina is away at NIPS on Monday) === We will finish the diffusion map discussion and will talk about the second paper. The week after that, we will come back to the operators in the first paper. === Nov 26 === We will start by discussing the first paper and go on to the second one. You only need to read the first paper for this meeting, but we will end up reading both by the end of this series. R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker. Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps. PNAS, 2005. {{wiki:geometric-diffusion1.pdf}} R. R. Coifman, S. Lafon, A. B. Lee, M. Maggioni, B. Nadler, F. Warner, and S. W. Zucker. Geometric diffusions as a tool for harmonic analysis and structure definition of data: Multiscale methods. PNAS, 2005. {{wiki:geometric_diffusion2.pdf}} Additional papers on the topic: Diffusion wavelets and their use in spectral clustering: {{wiki:Nadler06.pdf}} {{wiki:CoifmanMaggoni06.pdf}} === Nov 19 === We will finish the fast diff. paper. Mert and Thomas will lead. === Nov 14 (Wednesday, since Monday is Veterans Day) === Fast diffeomorphic registration. Thomas will lead the discussion. {{wiki:fastdiffeomorphicimageregistration.pdf}} === Oct 17 (Wednesday, to work around MMBIA) === We will finish Mahony's paper. === Oct 10 (Wednesday since Monday, Oct 8 is Columbus Day) === Lie groups tutorial. === Oct 1 === Continuing on the basic differential geometric notions required for understanding Mahony's paper, we will review 5th chapter of: Wolfgang Kuhnel and Bruce Hunt, //Differential Geometry: Curves - Surfaces - Manifolds//, AMS, Second Edition, 2005. Please check the discussion for mote details. [[discussion:Oct_1_2007|Discussion]] === Sep 24 === Danial will present: Mahony, R. Manton, J. H., ``The Geometry of the Newton Method on Non-Compact Lie Groups,'' JOURNAL OF GLOBAL OPTIMIZATION, 2002, VOL 23; NUMBER 3, pages 309--327. {{mahony.pdf}} [[discussion:Sep_24_2007|Discussion]] === Sep 17 === J.-P. Thirion, Image matching as a diffusion process: an analogy with Maxwell's demons. Medical Image Analysis (1998), volume 2, number 3. Biz will present. {{thirion98.pdf}} === Sep 12 === Tom Vercauteren, Xavier Pennec, Aymeric Perchant, Nicholas Ayache. Non-parametric Diffeomorphic Image Registration with the Demons Algorithm. MICCAI 2007. {{wiki:diffeodemons-miccai07-vercauteren.pdf}} ==== Summer 2007 ==== ===Aug 29 (Wed)=== Min Cut Max Flow and the Ford-Fulkerson method. Introduction to Algorithms, Second Edition Thomas H. Cormen, Charles E. Leiserson, Ronald L. Rivest and Clifford Stein. {{minmax.pdf}} ===Aug 16 (Thu)=== Graph cuts for energy minimization. Koen will lead the discussion. Yuri Boykov, Olga Veksler, and Ramin Zabih. Fast Approximate Energy Minimization via Graph Cuts. IEEE PAMI 23(11), 2001. {{wiki:boykov2001.pdf}} ===July 25 (Wed)=== Finish the BP paper. ===July 19 (Thu)=== Belief propagation Our main reference is: Constructing free-energy approximations and generalized belief propagation algorithms: J. Yedidia, et al. {{wiki:yedidiafreemanweiss2005.pdf}} The basic mathematical motivation of belief propagation: A. M. Aji and J. McEliece {{wiki:gendislaw.pdf}} BP is used for learning problems on different types of graphs: Bayesian Networks, Markov Random Fields, Junction graphs, and Factor graphs. To see examples: Y. Weiss and W. T. Freeman {{wiki:max-product_optimality.pdf}} and F. R. Kschischang, et al. {{wiki:sum-product.pdf}} And a couple of other popular review papers by the same authors as of our main paper: {{wiki:genbp.pdf}} and {{wiki:understandingbp.pdf}}. ===June 27 (Wed)=== William T. Freeman, Thouis R. Jones, and Egon C. Pasztor, Example-based super-resolution, IEEE Computer Graphics and Applications, March/April, 2002. {{wiki:cgasres.pdf}} W. T. Freeman, E. C. Pasztor, O. T. Carmichael Learning Low-Level Vision International Journal of Computer Vision, 40(1), pp. 25-47, 2000. MERL-TR2000-05. {{wiki:TR2000-05.pdf}} ===June 20 (Wed)=== We will continue our discussion on projection pursuit and its connection to Infomax ICA. Original Infomax paper: InfoMax ICA algorithm and its connection to projection pursuit. An information-maximization approach to blind separation and blind deconvolution. Bell and Sejnowski, Neural Computation, 1995. {{wiki:infomax.pdf}} ICA Tutorial (with sections devoted to Infomax ICA): Independent Component Analysis: Algorithms and Applications, Aapo Hyvärinen and Erkki Oja, 2000. {{wiki:icatutorial.pdf}} ===June 6 (Wed)=== Projection Pursuit: Please read the first 17 pages of the following paper. M. C. Jones; Robin Sibson, //What is Projection Pursuit?,// Journal of the Royal Statistical Society. Series A (General), Vol. 150, No. 1. (1987), pp. 1-37. {{wiki:jones87.pdf}} A much longer, more detailed review paper is the below. Peter Huber,//Projection Pursuit,//The annals of Statistics, Vol 13, No2 (June 1985), pp. 435-475. {{wiki:Huber-1.pdf}} ==== Spring 2007 ==== === May 11 === MM algorithms: Hunter and Lange, //A Tutorial on MM Algorithms,// Am. Stat. 58(1):30-7, Feb. 2004. Clear Version {{wiki:mm_tutorial.pdf}} Hunter and Lange, //A Tutorial on MM Algorithms,// Am. Stat. 58(1):30-7, Feb. 2004. {{lange_04_amstat.pdf}} Jacobson and Fessler, //An Expanded Theoretical Treatment of Iteration-Dependent Majorize-Minimize Algorithms,// preprint. [[http://www.eecs.umich.edu/~fessler/papers/files/preprint/jacobson,tip.pdf|jacobson,tip.pdf]] === May 4 === "Information Theoretic Coclustering," by Inderjit S. Dhillon, Subramanyam Mallela, and Dharmendra S. Modha {{wiki:p89-dhillon.pdf}} === Apr 27 === "A Log-Euclidean Polyaffine Framework for Locally Rigid or Affine Registration" by Vincent Arsigny, Olivier Commowick, Xavier Pennec, and Nicholas Ayache {{logeuclidean_wbir.pdf}} === Apr 20 === Finish the CG. === Apr 13 === Conjugate gradient algorithm. Jonathan Richard Shewchuk. An Introduction to the Conjugate Gradient Method Without the Agonizing Pain. This is a nice (although long) tutorial paper: {{wiki:painless-conjugate-gradient.pdf}} A (shorter) section from the numerical recipes book: {{wiki:c10-6.pdf}} === Mar 2 === We will finish the paper. === Feb 23 === We will continue with the same paper. Please read Section 4 and the appendices. It's heavy reading; you might want to start early. === Feb 16 === Danial: The following paper makes a nice connection between exponential-family-mixture-model and distance-measure-based clustering methods. A. Banerjee et al. Clustering with Bregman Divergence. J Mach Learn Res 6 (2005). Please read the first three sections for the first meeting. We will go through the key concepts: Bregman divergence, and information in more detail and try to understand the Bregman hard clustering algorithm. {{wiki:banerjee05b.pdf}} ==== Fall 2006 ==== === December 12 === Mert will lead the discussion on registration of fMRI. B. Thirion et al. Improving Sensitivity and Reliability of fMRI Group Studies through High Level Combination of Individual Subjects Results. MMBIA 2006. {{wiki:thirionmmbia06.pdf}} === December 5 === Serdar will lead the discussion on the multi-modal (not in a classical sense) nature of atlases: Daniel J. Blezek and James V. Miller. Atlas Stratification. MICCAI 2006. {{wiki:atlasstratification.pdf}} === November 21 === More Sobolev Active Contours this week... ===November 14=== Sobolev Active Contours: {{wiki:sobolevactivecontours.pdf}} --Thomas === November 7 === We will continue our asymptotic quest. Let's hope this process converges to the true value of the parameters! Here is my last version of summary: Reading: {{wiki:summaryDoob.pdf}} === October 31 === We will continue the discussion of Wilks' paper on the asymptotics of LR. In order to make sense of the main assumption of equation (3), we have to go through the reference to Doob's paper which is a seminal derivation of many basic theorems. Reading: {{wiki:doob1948.pdf}} Danial === October 24 === Reading: {{wiki:leemput_miccai2006.pdf}} --Thomas === October 16 === Papoulis (pp. 275--278) is a good introductory note on asymptotics of hypothesis testing (photocopies outside Polina's office). See also his statistics chapter (pp. 241--282) for hypothesis testing in general. The original papers for the asymptotics of the likelihood ratio are: {{wilks1938.pdf}} {{wald1943.pdf}} {{chernoff1954.pdf}} === September 19 === We will continue the paper from last week. We also made a note that we need to look into asympotic statistics results (mentioned in the paper) in the future. Kinh might take a lead on that. Here's the original DCM paper, for people who want more detail: {{wiki:Friston2003.pdf}} === September 12 === Note the special time: 10:00am Penny W.D. et al. (2004). Modelling functional integration: a comparison of structural equation and dynamic causal models. {{wiki:Modelling_Penny.pdf}} We will focus on the structural equation model this week. === September 5 === Note the special time: 4pm We will continue our discussion on effective connectivity in neuroimaging. We will focus on the second half of the first paper from last time (Friston 1994). If time is allowed, we will discuss the third paper from last time as well (Friston 1997). === August 29 === We will discuss functional and effective connectivity in neuroimaging. The first paper is the most general paper. The second paper is a book chapter version of the first paper on functional connectivity and goes a bit deeper. The third paper deals with more exotic topic in effective connectivity. We will mainly discuss the first paper, so if you have limited time, the first one is the paper to read. Friston, K.J. (1994). Functional and effective connectivity in neuroimaging: A synthesis. Human Brain Mapping, 2, 56-78. {{wiki:friston94.pdf}} Friston, K.J, Büchel, C (1993). Functional Connectivity: Eigenimages and multivariate analyses. {{wiki:friston93.pdf}} Friston, K.J., Buchel, C., Fink, G.R., Morris, J., Rolls, E., and Dolan, R. (1997). Psychophysiological and modulatory interactions in Neuroimaging. NeuroImage, 6, 218-229. {{wiki:friston97.pdf}} === August 22 === We will start the meetings with two papers that Wanmei claims use the same model in two somewhat unrelated applications. Both papers consider the fundamental problem of evidence integration from independent sources. We will discuss the details of the models and the relationship between them. If you have time to read just one paper, the first one is lighter. Genovese, C. R., Noll, D. C. and Eddy, W. F. (1997). Estimating Test-Retest Reliability in fMRI I: Statistical Methodology, Magnetic Resonance in Medicine, 38, 497--507. {{wiki:Genovese97.pdf}} Simultaneous Truth and Performance Level Estimation (STAPLE): An Algorithm for the Validation of Image Segmentation. Warfield S, Zou KH, Wells WM. IEEE Trans Med Imag 2004; 23:903-921. {{wiki:Warfield04.pdf}} ==== Spring 2006 ==== === May 10 === We will discuss ICA for fMRI time series analysis. The longer paper discusses the method in details, and will be the basis for our discussion. The shorter one is a nice overview. {{wiki:ISC.pdf}} {{wiki:ICA.pdf}} === May 3 === We will discuss the Dirichlet process mixture model, as presented in Teh 04, , which develops a variant of the DP mixture for grouped data. Other papers (all cited by Teh) are provided here for those interested in a deeper theoretical background: Ferguson 73 and Antoniak 74 are the seminal papers (with fairly technical measure-theoretic proofs), while Sethuraman 94, followed by Ishwaran and James 01 and Ishwaran and Zarepour 02, are more constructive. Of these, I'd recommend Sethuraman for clarity and brevity. -- John Yee Whye Teh //et al.// \\ Hierarchical Dirichlet Processes \\ {{wiki:teh04hdp.pdf}} Thomas Ferguson \\ A Bayesian Analysis of Some Nonparametric Problems \\ {{wiki:ferguson.ps.gz}} Charles Antoniak \\ Mixtures of Dirichlet Processes with Applications to Bayesian Nonparametric Problems \\ {{wiki:antoniak74mixtures.ps}} Jayaram Sethuraman \\ A Constructive Definition of Dirichlet Priors \\ {{wiki:sethuraman94constructive.pdf}} Hemant Ishwaran and Lancelot James \\ Gibbs Sampling Methods for Stick-Breaking Priors \\ {{wiki:ishwaran01gibbs.pdf}} Hemant Ishwaran and Mahmoud Zarepour \\ Exact and approximate sum-representations for the Dirichlet process \\ {{wiki:ishwaran02exact.pdf}} === April 26 === We will continue the discussion from the last time. I posted some questions in the Discussion section. Feel free to add comments and more questions. -- Polina [[discussion:April_26_2006|Discussion]] === April 19 === We will discuss the Information Bottleneck Method and its uses in determining the number of clusters in fMRI data. The second paper describes the information bottleneck approach and is a background reading for the first paper. Bertrand Thirion, Olivier Faugeras. Feature Detection in fMRI Data: The Information Bottleneck Approach. {{wiki:thirionmedia.pdf}} Naftali Tishby, Fernando C. Pereira, William Bialek. The Information Bottleneck Method \\ {{wiki:tishby99information.pdf}}\\ Uncut Version:\\ {{wiki:allertoninfobottleneck.pdf}} === April 13 === I (Thomas) am posting the writeups for Apr 12. Gheorghe has also kindly provided his short writeup on EM. Happy Reading!! {{wiki:spectralclustering.pdf}}\\ {{wiki:MixtureFitting.pdf}}\\ {{wiki:emtut.pdf}}\\ === April 12 === I (Thomas) will be presenting the papers for this week. Andrew Ng Michael Jordan and Yair Weiss\\ On Spectral Clustering: An analysis and an algorithm\\ {{wiki:Ng-SpectralClustering.pdf}} Optional Papers: I will talk about mixture fitting, but I will not be completely following Michael Collins' derivations. However, the tutorial is still nice if you have no experience with mixture fitting or EM. We will NOT go over the theorems about convergence, i.e. we will not go beyond section 3.3. The idea is to give everyone an intuitive feel about the concept of mixture fitting, not limiting oneself to using only gaussians or the EM technique. Michael Collins\\ {{wiki:MichaelCollinsTutorialOnEM.ps}} More Variants of Spectral Clustering:\\ Jianbo Shi and Jitendra Malik\\ {{wiki: ShiMalik-NormalizedCuts.pdf}}\\ Mikhail Belkin and Partha Niyogi\\ {{wiki: Belkin-LaplacianEigenmaps.pdf}}\\ Marina Meila and Jianbo Shi\\ {{wiki: randomwalkspectralclustering.ps}}\\ === April 5 === We will take a two week break and resume our discussion of FDR at the next meeting. We'll start with Efron, B. and Tibshirani, R.\\ Empirical Bayes Methods and False Discovery Rates for Microarrays\\ Genetic Epidemiology 23:70-86, 2002.\\ {{wiki:EfronTibshirani_FDR.pdf}} And then move onto the Genovese et al. paper on thresholding maps in neuroimaging using FDR {{wiki:NicholsFDR.pdf}} (listed below). A comparison of several similar methods (FDR, pFDR, PER, PFP) can be found in\\ K. Manly, D. Nettleton, and J.T.G. Hwang\\ Genomics, Prior Probability, and Statistical Tests of Multiple Hypotheses\\ Genome Research 14: 997-1001, 2004 {{wiki:Manlyetal.pdf}}\\ I might touch on some of these different options during the discussion. > The PFP paper was \\ Controlling the Proportion of False Positives in Multiple Dependent Tests\\ R. L. Fernando, D. Nettletonb, B. R. Southey, J. C. M. Dekkers, M. F. Rothschild, and M. Soller\\ Genetics, Vol. 166, 611-619, January 2004 [[discussion:April_5_2006|Discussion]] === March 15 === Benjamini, Y. and Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57 289-300, 1995. {{wiki:benjaminiFDR.pdf}} Christopher R. Genovese, Nicole A. Lazar, Thomas Nichols. Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate. NeuroImage 15:870-878, 2002. {{wiki:NicholsFDR.pdf}} Yoav Benjamini and Daniel Yekutieli. THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY. The Annals of Statistics 2001, Vol. 29, No. 4, 1165-1188. {{wiki:benjaminiANNSTAT2001.pdf}} > I think it might be worth switching to one of the pFDR papers for the extensions of the FDR. I'm reading through some of them, and will post suggestions if one of them strikes me. In particular, I think they have a nicer treatment of independence, and it will be nice to see some other approaches to FDR. -Ray [[discussion:March_15_2006|Discussion]] === March 8 === We will continue with the permutation testing. We also finshed the proof that the sample mean and the sample variance are independent for Gaussian iid case. See Discussion for additional notes. [[discussion:March_1_2006|Discussion]] === March 1 === Thomas E. Nichols and Andrew P. Holmes.\\ Nonparametric Permutation Tests For Functional Neuroimaging: A Primer with Examples.\\ Human Brain Mapping 15:1-25(2001). \\ {{wiki:nichols-perm.pdf}} === February 22 === Wanmei Ou will define the general setup of the fMRI detection problem, preparing us for the series of papers in fMRI analysis. Notes for the group meeting. {{wiki:fMRI_intro.pdf}} [[discussion:Feb_22_2006|Discussion]] === February 15 === Michael Siracusa will lead a discussion on a classical hypothesis testing, in preparation for some papers in fMRI and DTI statistics. Notes for the group meeting. {{wiki:hyptest-faq.pdf}} [[discussion:Feb_14_2006|Discussion]] ==== Fall 2005 ==== === December 13 === Duygu Tosun and Jerry L. Prince. \\ Cortical Surface Alignment Using Geometry Driven Multispectral Optical Flow, \\ Information Processing in Medical Imaging (IPMI), Colorado, USA, July 11-15, 2005. \\ {{wiki:tosun2005.pdf.gz}} **Additional papers:** Duygu Tosun, Maryam E. Rettmann, Jerry L. Prince. \\ Mapping techniques for aligning sulci across multiple brains. \\ Medical Image Analysis 8 (2004) 295-309. \\ {{wiki:tosun2004a.pdf.gz}} Xiao Han, Dzung L. Pham, Duygu Tosun, Maryam E. Rettmann, Chenyang Xu, and Jerry L. Prince. \\ CRUISE: Cortical reconstruction using implicit surface evolution. \\ NeuroImage 23 (2004) 997-1012.\\ {{wiki:han-2004.pdf.gz}} Xiao Han, Chenyang Xu, and Jerry L. Prince.\\ A Topology Preserving Level Set Method for Geometric Deformable Models.\\ PAMI, VOL. 25, NO. 6, JUNE 2003. \\ {{wiki:han-2003.pdf.gz}} **Also on the list for future reading:** Thompson, P. Toga, A.W. \\ A surface-based technique for warping three-dimensional images of the brain. \\ IEEE Transactions on Medical Imaging, Volume 15, Issue 4, 402 - 417, 1996. \\ {{wiki:thompson96.pdf.gz}} **Additional papers:** Xianfeng Gu; Yalin Wang; Chan, T.F.; Thompson, P.M.; Shing-Tung Yau; \\ Genus zero surface conformal mapping and its application to brain surface mapping. \\ IEEE Transactions on Medical Imaging, Volume 23, Issue 8, 949 - 958, 2004. \\ {{wiki:thompson2004.pdf.gz}} ---- === December 6 === Bruce Fischl, Martin I. Sereno and Anders M. Dale. \\ Cortical Surface-Based Analysis: II: Inflation, Flattening, and a Surface-Based Coordinate System. \\ Neuroimage. 9(2):195-207. 1999.\\ {{wiki:fischl99.pdf.gz}} Bruce Fischl, Martin I. Sereno, Roger B.H. Tootell, Anders M. Dale.\\ High-resolution inter-subject averaging and a coordinate system for the cortical surface. \\ Human Brain Mapping, Volume 8, Issue 4, Pages 272 - 284, 1999. {{wiki:fischl99a.pdf.gz}} **Additional papers:** Anders M. Dale, Bruce Fischl and Martin I. Sereno.\\ Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction. \\ Neuroimage, 9(2):179-194, 1999. {{wiki:dale99.pdf.gz}} ---- === November 29 === We will continue the discussion on the permutation tests. The future meetings will be shifted by one week. ---- === November 22 === Timothy B. Terriberry, Sarang C. Joshi, and Guido Gerig.\\ Hypothesis Testing with Nonlinear Shape Models.\\ IPMI 2005, LNCS 3565, pp. 15-26, 2005. \\ {{wiki:multperm2005.pdf.gz}} **Additional papers:** Blair, R.C., Higgins, J.J., Karniski, W., Kromrey, J.D.\\ A study of multivariate permutation tests which may replace Hotelling T2 test in prescribed circumstances.\\ Multivariate Behavioral Research 29 (1994) 141-164.\\ {{wiki:multperm94.pdf.gz}} Book:\\ Pesarin, Fortunato\\ Multivariate permutation tests : with applications in biostatistics.\\ I have the book. ---- === November 15 === GE Christensen, RD Rabbit, MI Miller. \\ Deformable Templates Using Large Deformation Kinematics. \\ IEEE Transactions on Image Processing, 5(10), 1996, pp. 1435-1447.\\ {{wiki:DeformableTemplatesUsingLargeDeformationKinematics.pdf.gz}} **Additional papers:** Ain A. Sonin.\\ Fundamental Laws of Motion for Particles, Material Volumes, and Control Volumes, 2001.\\ {{wiki:fundamental_laws.pdf.gz}} On Choosing and Using Control Volumes: Six Ways of Applying the Integral Mass Conservation Theorem to a Simple Problem.\\ {{wiki:choosingcontrolvolumes.pdf.gz}} ---- === November 8 === We will also finish the discussion on using prior examples to bias registration. D. M. Blei, A. Y. Ng, and M. I. Jordan. \\ Latent Dirichlet allocation. \\ Journal of Machine Learning Research, 3, 993-1022, 2003. \\ {{wiki:blei03a.pdf.gz}} **Additional papers:** Thomas Hofmann.\\ Probabilistic Latent Semantic Analysis.\\ UAI 1999.\\ http://www.cs.brown.edu/people/th/papers/Hofmann-UAI99.pdf.gz Josef Sivic, Bryan C. Russell, Alexei A. Efros, Andrew Zisserman, William T. Freeman.\\ Discovering objects and their location in images.\\ ICCV 2005. \\ http://people.csail.mit.edu/brussell/research/SREZF05.pdf.gz Brian Russell's RQE paper. http://www.csail.mit.edu/~brussell/research/rqe.pdf.gz ---- === November 1 === Mert R. Sabuncu and Peter J. Ramadge. \\ Gradient based optimization of an EMST registration function.\\ IEEE Conference on Acoustics, Speech and Signal Processing, Philadelphia, March 2005.\\ {{wiki:Sabuncu_ICASSP05-1.pdf.gz}} Mert R. Sabuncu and Peter J. Ramadge.\\ Graph theoretic image registration using prior examples.\\ European Signal Processing Conference 2005, Antalya, Turkey, September 2005.\\ {{wiki:eusipco05_submit-1.pdf.gz}} **Additional papers:** B. Ma, A.O. Hero, J.D. Gorman and O. Michel. \\ Image Registration with Minimum Spanning Tree Algorithm. \\ IEEE International Conf. on Image Processing, vol.1, pp.481-484, Vancouver, BC, Canada, Sept. 2000.\\ {{wiki:ma_icip00.pdf.gz}} ---- === October 25 === A. O. Hero, B. Ma, O. Michel and J. Gorman. \\ Applications of entropic spanning graphs. \\ IEEE Signal Proc. Magazine (Special Issue on Mathematics in Imaging), Vol 19, No. 5, pp 85-95, Sept. 2002. \\ {{wiki:spmag_ma_01-1.pdf.gz}} **Additional papers:** Beirlant, J., Dudewicz, E. J., Gyorfi, L., and van der Meulen, E. C. \\ Nonparametric entropy estimation: An overview.\\ International Journal of the Mathematical Statistics Sciences, 6, 17-39, 2001.\\ {{wiki:beirlant.pdf.gz}} ---- === October 18 === No meeting, many of us are at ICCV. ---- === October 11 === P.D. Grünwald. \\ A Tutorial Introduction to the Minimum Description Principle. \\ {{wiki:grunwald-mdlintro.pdf.gz}} Also use material from Septermber 27 meeting. A minimum description length approach to statistical shape modeling.\\ Davies, R.H.; Twining, C.J.; Cootes, T.F.; Waterton, J.C.; Taylor, C.J.\\ IEEE Transactions on Medical Imaging, 21(5):525 - 537, 2002. \\ {{wiki:Shape-MDL.pdf.gz}} ---- === October 4 === Erik Learned-Miller. \\ Data Driven Image Models through Continuous Joint Alignment. \\ to appear in IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 2005. \\ {{wiki:PAMI_congeal.pdf.gz}} **Additional papers:** Lilla Zollei, Erik Learned-Miller, Eric Grimson and William Wells. \\ Efficient population registration of 3D data. \\ Workshop on Computer Vision for Biomedical Image Applications: Current Techniques and Future Trends, at the International Confernece of Computer Vision (ICCV), 2005. \\ {{wiki:congeal_3D.pdf.gz}} ---- === September 27 === Connection between the code length and entropy - Section 5.4 (and around) in Cover and Tomas. J. Rissanen. \\ An Introduction to the MDL Principle. \\ {{wiki:Rissanen-Intro.pdf.gz}} **Additional papers on MDL:** Rissanen, J. \\ Stochastic Complexity and Modeling. \\ Annals of Statistics, Vol 14, 1080-1100, 1986. \\ {{wiki:Rissanen86.pdf.gz}} P.D. Grünwald. \\ A Tutorial Introduction to the Minimum Description Principle. \\ {{wiki:grunwald-mdlintro.pdf.gz}} **Additional papers on BIC and AIC:** Schwarz, G. (1978). \\ Estimating the dimension of a model. Annals of Statistics, 6, 461-464.\\ {{wiki:ScwarzBIC.pdf.gz}} Akaike, H. (1974). \\ A new look at the statistical model identification. \\ IEEE Transactions on Automatic Control, AC-19, 716-723. {{wiki:Akaike74.pdf.gz}} ---- === September 20 === A Unified Information-Theoretic Approach to Groupwise Non-rigid Registration and Model Building. \\ Carole J. Twining, Tim Cootes, Stephen Marsland, Vladimir Petrovic, Roy Schestowitz and Chris J. Taylor.\\ Information Processing in Medical Imaging: 19th International Conference, IPMI 2005, Glenwood Springs, CO, USA, July 10-15, 2005.\\ {{wiki:twining-ipmi-2005.pdf.gz}} **Additional papers:** Carole J. Twining, Stephen Marsland, and Chris Taylor. \\ Groupwise Non-Rigid Registration: The Minimum Description Length Approach. \\ BMVC 2004.\\ {{wiki:twining-bmvc-2004.pdf.gz}} Carole Twining and Stephen Marsland. \\ A Unified Information-Theoretic Approach to the Correspondence Problem in Image Registration. \\ International Conference on Pattern Recognition, Cambridge, U.K. 2004. \\ {{wiki:twining-icpr-2004.pdf.gz}} ---- === September 13 === First meeting, general intros.[[Internal Link]]