SabLab Journal Club

This is the wiki for the Sabuncu Lab's journal club (or paper reading group). You can find information on the meeting format, schedule, papers and presenters.
We have an email list: moc.spuorgelgoog|bulc-balbas#moc.spuorgelgoog|bulc-balbas
If you want to be added to this list, ask someone who you know is a member.

SCHEDULE (Fall 2018)

Wednesdays 12 Noon at Rhodes 380.

Machine learning, computer vision, image processing, statistical modeling and inference, biomedical image/data analysis, …


At each meeting, there will be a presenter who will be responsible for leading the discussion of a paper. The paper will be chosen by the presenter (possibly from paper stack below) and posted here about a week before the corresponding meeting. The presenter will not use any slides but can rely on the whiteboard to illustrate ideas, equations, etc. Participants should come to the meeting with the paper either printed out (double-sided!) or available on a portable device (laptop, iPad, etc). Participants are strongly encouraged to read the paper beforehand (they should have spent at least 1-2 hours to gain a basic understanding).

Here are some guidelines for the presenter, who should come to the meeting with answers to each of these questions.

1) What problem is the paper addressing? Is this an interesting mathematical problem? At a very high level, is this a classical mathematical problem? Are there classical solutions (e.g., something you can find on wikipedia) that you can think of?
2) What other state-of-the-art methods/algorithms (say published in last 3-5 years) are out there that address the same/similar problem? Do authors run benchmarking experiments (i.e. empirical comparisons)?
3) What is the application the authors choose (if any)? Is this an interesting application? What was lacking for existing solutions? Were they too slow? Maybe they didn’t really solve the problem exactly?
4) What’s wrong with the proposed method? What are the acknowledged/unacknowledged weaknesses?
5) How can the proposed method be improved? What are the natural future directions of research? Are there new applications you can think of?
6) What would you do differently if you approached this problem?
7) What is the core innovation and contribution of this paper? Is it a mathematical derivation? If so, can you point to it and understand the steps? Was there a far-reaching theoretical result/insight? If so, can you summarize? Was there a novel empirical finding? Is there an accompanying open software package that others can pick up and use on their own data/problem?


Oct 16, 2018
Mohammad will lead the discussion
Shah, Meet P., S. N. Merchant, and Suyash P. Awate. "MS-Net: Mixed-Supervision Fully-Convolutional Networks for Full-Resolution Segmentation." International Conference on Medical Image Computing and Computer-Assisted Intervention (2018). link


M. Johnson, D. K. Duvenaud, A. Wiltschko, R. P. Adams, S. R. Datta. "Composing graphical models with neural networks for structured representations and fast inference" Advances in Neural Information Processing Systems 2016. link

S. Pereira, R. Meier, R. McKinley, R. Wiest, V. Alves, C. A. Silva, M. Reyes. "Enhancing interpretability of automatically extracted machine learning features: application to a RBM-Random Forest system on brain lesion segmentation" Medical Image Analysis 2018 Feb; vol. 44, 228-244. link

C. Sripada, M. Angstadt, S. Rutherford, D. Kessler, Y. Kim, M. Yee, L. Levina. "Fundamental Units of Inter-Individual Variation in Resting State Connectomes" bioRxiv. 2018 May 24; 326082. link

B. S. Veeling, J. Linmans, J. Winkens, T. Cohen, M. Welling. "Rotation Equivariant CNNs for Digital Pathology" arXiv preprint arXiv:1806.03962 (2018) link

S. Farquhar, Y. Gal. "Towards Robust Evaluations of Continual Learning" arXiv preprint arXiv:1805.09733 (2018) link

H. Hassani, M. Soltanolkotabi, A. Karbasi. "Gradient Methods for Submodular Maximization" arXiv preprint arXiv:1708.03949 (2017) link

R. Kondor, S. Trivedi. "On the Generalization of Equivariance and Convolution in Neural Networks to the Action of Compact Groups" arXiv preprint arXiv:1802.03690 (2018) link

E. R. Elenberg, A. G. Dimakis, M. Feldman, A. Karbasi. "Streaming Weak Submodularity: Interpreting Neural Networks on the Fly" arXiv preprint arXiv:1703.02647 (2017) link

R. R. Selvaraju, M. Cogswell, A. Das, R. Vedantam, D. Parikh, D. Batra. "Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization" arXiv preprint arXiv:1610.02391 (2017) link

B. Zhu, J. Z. Liu, S. F. Cauley, B. R. Rosen, and M. S. Rosen. "Image reconstruction by domain-transform manifold learning." Nature. Mar 555(2018); 487-492 link

Z. C. Lipton, Y.-X. Wang, A. Smola. "Detecting and Correcting for Label Shift with Black Box Predictors" arXiv preprint arXiv:1802.03916 (2018) link

M. Johnson, D. K. Duvenaud, A. Wiltschko, R. P. Adams, and S. R. Datta. "Composing graphical models with neural networks for structured representations and fast inference." In Advances in neural information processing systems, pp. 2946-2954. (2016) link

C. Li, M. Z. Zia, Q.-H. Tran, X. Yu, G. D.Hager, M. Chandraker. "Deep Supervision with Intermediate Concepts" arXiv preprint arXiv:1711.11386 (2017) link

H. S. Seung "Learning in spiking neural networks by reinforcement of stochastic synaptic transmission" Neuron, Vol. 40, no. 6, pp. 1063-1073, (2003) link

W. Wang, Y. Pu, V.K. Verma, K. Fan, Y. Zhang, C. Chen, P. Rai, and L. Carin. "Zero-Shot Learning via Class-Conditioned Deep Generative Models" arXiv preprint arXiv:1711.05820 (2017) link

D. P. King, and M. Welling. "Auto-Encoding Variational Bayes" arXiv preprint arXiv:1312.6114 (2013) link

K. Kawaguchi, L. P. Kaelbling, Y. Bengio. "Generalization in Deep Learning" arXiv preprint arXiv:1710.05468 (2017) link

M. Fortunato, C. Blundell, and O. Vinyals. "Bayesian Recurrent Neural Networks" arXiv preprint arXiv:1704.02798 (2017) link

A. N. Gomez, M. Ren, R. Urtasun, and R. B. Grosse. "The Reversible Residual Network: Backpropagation Without Storing Activations" arXiv preprint arXiv:1707.04585 (2017) link

R. Shwartz-Ziv, and N. Tishby. "Opening the Black Box of Deep Neural Networks via Information" arXiv preprint arXiv:1703.00810 (2017) link

A. Mousavi, G. Dasarathy, and R. Baraniuk. "DeepCodec: Adaptive Sensing and Recovery via Deep Convolutional Neural Networks." arXiv preprint arXiv:1707.03386 (2017) link

Shah and Koltun - "Robust continuous clustering", PNAS 2017 link

Zhou, Yichen, and Giles Hooker. "Interpreting Models via Single Tree Approximation." arXiv preprint arXiv:1610.09036 (2016). link

Johansson, Fredrik D., Uri Shalit, and David Sontag. "Learning representations for counterfactual inference." arXiv preprint arXiv:1605.03661 (2016).

Friedman, Jerome H. "Greedy function approximation: a gradient boosting machine." Annals of Statistics (2001): 1189–1232.

H Mhaskar, Q Liao, T Poggio "When and Why Are Deep Networks Better than Shallow Ones?" 2017 pdf link

"Gradient Descent Learns Linear Dynamical Systems" M Hardt, T Ma, B Recht - arXiv preprint arXiv:1609.05191, 2016

"Image-to-image translation with conditional adversarial networks." Isola, P., Zhu, J.Y., Zhou, T. and Efros, A.A., 2016. arXiv preprint arXiv:1611.07004.

"Dropout as a Bayesian approximation: Representing model uncertainty in deep learning." Gal, Yarin, and Zoubin Ghahramani. arXiv preprint arXiv:1506.02142 2 (2015).

Zhou, Jian, and Olga G. Troyanskaya. "Predicting effects of noncoding variants with deep learning-based sequence model." Nature methods 12.10 (2015): 931-934.
g-drive copy


March 29, 2017
Zhilu will lead the discussion.
Gal, Yarin, Riashat Islam, and Zoubin Ghahramani. "Deep Bayesian Active Learning with Image Data." arXiv preprint arXiv:1703.02910 (2017). arxiv link

April 5, 2017
No meeting as it's spring break.

April 12, 2017
No meetings as Mert's in NYC

April 19, 2017
Evan will lead the discussion.
Rasmussen, Carl Edward. "Gaussian processes for machine learning." (2006). pdf link

April 26, 2017
Mert will lead the discussion.
Chapters 1 and 2 of Andrew Wilson's PhD thesis. link

May 3, 2017
Evan will lead the discussion.
"Generative adversarial nets." In Advances in neural information processing systems Goodfellow, I., Pouget-Abadie, J., Mirza, M., Xu, B., Warde-Farley, D., Ozair, S., Courville, A. and Bengio, Y., 2014 (pp. 2672-2680). pdf link

May 31, 2017
Zhilu will lead the discussion.
Doersch, Carl. "Tutorial on variational autoencoders." arXiv preprint arXiv:1606.05908 (2016).pdf link

June 7, 2017
Mohammad will lead the discussion.
"Spatial Transformer Networks." M Jaderberg, K Simonyan, A Zisserman, K Kavukcuoglu. NIPS 2015

June 14, 2017
Evan will lead the discussion.
"Understanding deep learning requires rethinking generalization" C Zhang, S Bengio, M Hardt, B Recht, O Vinyals - arXiv preprint arXiv:1611.03530, 2016

September 6, 2017
Mert will lead the discussion.
Zhu, Jun-Yan, et al. "Unpaired image-to-image translation using cycle-consistent adversarial networks." arXiv preprint arXiv:1703.10593 (2017). link

We will skip September 13 as Mert, Evan and Zhilu are at MICCAI.

September 20, 2017
Evan will lead the discussion.
Zhao, Mingmin, et al. "Learning Sleep Stages from Radio Signals: A Conditional Adversarial Architecture." International Conference on Machine Learning. 2017. link

We will skip September 27 as Mert is not here.

October 04, 2017
Yingying will lead the discussion.
P. Ji, T. Zhang, H. Li, M. Salzmann, and I. Reid. "Deep Subspace Clustering Networks." arXiv preprint arXiv:1709.02508 (2017) link

October 11, 2017
Cagla will lead the discussion.
D. Ma, V. Gulani, N. Sieberlich, K. Liu, J. L. Sunshine, J. L. Duerk, and M. A. Griswold. "Magnetic resonance fingerprinting." Nature. 2013 Mar 14; 495(7440): 187–192. link

October 18, 2017
Sundaresh will lead the discussion.
Stéphane Mallat. "Understanding deep convolutional networks." Phil. Trans. R. Soc. A 374.2065 (2016): 20150203. link

October 25, 2017
Jinwei will lead the discussion.
K. Kamnitsas, C. Ledig, V. F. J. Newcombe, J. P. Simpson, A. D. Kane, D. K. Menon, D. Reuckert, and B. Glocker. "Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation." Medical Image Analysis. Feb 36(2017); 61-78 link

P. Krahenbuhl and V. koltun. "Efficient Inference in Fully Connected CRFs with Gaussian Edge Potentials." arXiv preprint arXiv:1210.5644 (2012) link

We will skip November 1 as Mert is not here.

November 8, 2017
Meenakshi will lead the discussion.
S. Parisot, S. I. Ktena, E. Ferrante, M. Lee, R. M. Moreno, B. Glocker, and D. Rueckert. "Spectral Graph Convolutions for Population-based Disease Prediction" arXiv preprint arXiv:1703.03020 (2017) link

November 15, 2017
Evan and Sundaresh will lead the discussion.
Mescheder, Lars, Sebastian Nowozin, and Andreas Geiger. "Adversarial variational bayes: Unifying variational autoencoders and generative adversarial networks." arXiv preprint arXiv:1701.04722 (2017). link

Novermber 22, 2017
No journal club due to Thanksgiving break

We will skip November 29 as Mert is not here.

December 6, 2017
Yingying will lead the discussion.
K. He, G. Gkioxari, P. Dollár, R. Girshick. "Mask R-CNN." arXiv preprint arXiv:1703.06870 (2017). link

R. Girshick. "Fast R-CNN." arXiv preprint arXiv:1504.08083 (2015). link

December 13, 2017
James will lead the discussion.
S. Sabour, N. Frosst, G. E. Hinton. "Dynamic Routing Between Capsules" arXiv preprint arXiv:1710.09829 (2017). link

January 10, 2018
Mohammad will lead the discussion.
D. L. K. Yamins and J. D. DiCarlo "Using goal-driven deep learning models to understand sensory cortex" Nature Neuroscience 19, pp.356–365 (2016) link

We will skip January 17 as Mert is busy.

January 24, 2018
Cagla will lead the discussion.
K. C. Tezcan, C. F. Baumgartner, and E. Konukoglu. "MR image reconstruction using the learned data distribution as prior" arXiv preprint arXiv:1801.03399 (2018) link

January 31, 2018
Adrian will lead the discussion.
W. Wang, R. Arora, K. Livescu, and J. Blimes "On Deep Multi-View Representation Learning" Proceedings of International Conference on Machine Learning (2015) link

We will skip February 7 due to snow storm

February 14, 2018
Zhilu will lead the discussion.
H. Noh, T. You, J. Mun, and B. Han. "Regularizing deep neural networks by noise: its interpretation and optimization" arXiv preprint arXiv:1710.05179 (2017) link

We will skip February 21 as Mert is busy.

February 28, 2018
Evan will lead the discussion.
X. Chen, D. P. Kingma, T. Salimans, Y. Duan, P. Dhariwal, J. Schulman, I. Sutskever, P. Abbeel. "Variational Lossy Autoencoder" arXiv preprint arXiv:1611.02731 (2016) link

We will skip March 7 as Mert is unavailable.

We will skip March 14 as Mert is busy.

March 21, 2018
Sundaresh will lead the discussion.
D. M. Pelt and J. A. Sethian "A mixed-scale dense convolutional neural network for image analysis" Proceedings of the National Academy of Sciences (2017): p.201715832 link

We will skip March 28 as Mert is out of town.

We will skip April 4 on account of spring break.

We will skip April 11 as Mert is out of town.

We will skip April 18 as Mert is busy.

April 25, 2018
Meenakshi will lead the discussion
L. M. Zintgarf, T. S. Cohen, T. Adel, M. Welling. "Visualizing Deep Neural Network Decisions: Prediction Difference Analysis" arXiv preprint arXiv:1702.04595 (2017) link

May 2, 2018
Adrian will lead the discussion
D. P. Kingma, J. Ba. "Adam: A Method for Stochastic Optimization" arXiv preprint arXiv:1412.6980 (2014) link

We will skip May 9 as Mert is out of town.

We will skip May 16 as Mert is busy.

We will skip May 23 as Mert is out of town.

May 30, 2018
Sundaresh will lead the discussion
H. Zhang, I. Goodfellow, D. Metaxas, A. Odena. "Self-Attention Generative Adversarial Networks" arXiv preprint arXiv:1805.08318 (2018) link

June 6, 2018
Cagla will lead the discussion
A. Loktyushin, H. Nickisch, R. Pohmann, B. Schölkopf. "Blind retrospective motion correction of MR images" Magnetic Resonance in Medicine. 2013 Dec 11; 70(6): 1608–1618. link

June 13, 2018
Artem and Jinwei will lead the discussion
J. P. Haldar, D. Kim. "OEDIPUS: An Experiment Design Framework for Sparsity-Constrained MRI" arXiv preprint arXiv:1805.00524 (2018) link

June 20, 2018
Sundaresh will lead the discussion.
H. K. Aggarwal, M. P. Mani, M. Jacob. "MoDL: Model Based Deep Learning Architecture for Inverse Problems" arXiv preprint arXiv:1712.02862 (2017) link

August 22, 2018
Artem will lead the discussion
D. P. Kingma, P. Dhariwal. "Glow: Generative Flow with 1x1 Convolutions" arXiv preprint arXiv:1807.03039 (2018) link

Background Reading which might be useful, which first introduced Flow-based density estimation:
Laurent Dinh, Jascha Sohl-Dickstein, Samy Bengio. "Density estimation using Real NVP" arXiv preprint arXiv:1605.08803 (2016) link

September 5, 2018
Gia will lead the disussion
A. Mensch, J. Mairal, D. Bzdok, B. Thirion, G. Varoquaux. "Learning Neural Representations of Human Cognition across Many fMRI Studies" arXiv preprint arXiv:1710.11438 link

September 12, 2018
Meenakshi will lead the discussion
A. Zhitnikov, R. Mulayoff, T. Michaeli. "Revealing common statistical behaviors in heterogeneous populations". Proceedings of the 35th International Conference on Machine Learning, PMLR 80:5950-5959, 2018. link

September 26, 2018
Evan will lead the discussion
Adebayo, Julius, et al. "Local explanation methods for deep neural networks lack sensitivity to parameter values." (2018). link

Oct 3, 2018
Zhilu will lead the discussion
Alemi, Alexander, et al. "Fixing a Broken ELBO." International Conference on Machine Learning. 2018. link

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