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Title: GitHub - AdaptInfer/ReadingList: Our reading list

Open Graph Title: GitHub - AdaptInfer/ReadingList: Our reading list

X Title: GitHub - AdaptInfer/ReadingList: Our reading list

Description: Our reading list. Contribute to AdaptInfer/ReadingList development by creating an account on GitHub.

Open Graph Description: Our reading list. Contribute to AdaptInfer/ReadingList development by creating an account on GitHub.

X Description: Our reading list. Contribute to AdaptInfer/ReadingList development by creating an account on GitHub.

Opengraph URL: https://github.com/AdaptInfer/ReadingList

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https://patch-diff.githubusercontent.com/AdaptInfer/ReadingList#lengerich-lab-reading-list
https://patch-diff.githubusercontent.com/AdaptInfer/ReadingList#productivity
Getting Things Donehttps://amzn.to/3UohLug
https://patch-diff.githubusercontent.com/AdaptInfer/ReadingList#communication
How to email busy peoplehttps://simplystatistics.org/2011/09/23/getting-email-responses-from-busy-people/
Grice's Maximshttps://www.sas.upenn.edu/~haroldfs/dravling/grice.html
Guide for Interacting With Facultyhttps://shomir.net/teaching_faq.html
Guide to Professorspeakhttps://shomir.net/professorspeak.html
https://patch-diff.githubusercontent.com/AdaptInfer/ReadingList#research-wisdom
Taste comes before skillhttps://jamesclear.com/ira-glass-failure
Ego and Mathhttps://www.youtube.com/watch?v=z7GVHB2wiyg
Heckerthoughtshttps://arxiv.org/pdf/2302.05449
How to do researchhttps://pengsida.net/files/Bill_Freeman_How_to_do_research.pdf
Principles of Effective Researchhttps://pengsida.net/files/Michael_Nielsen_How_to_do_research.pdf
Hanging on to the Edges: Staying in the Gamehttp://www.danielnettle.org.uk/wp-content/uploads/2017/09/Staying-in-the-game.pdf
You and Your Researchhttp://www.cs.cmu.edu/~15712/papers//hamming86.pdf
The Structure of Scientific Revolutionshttp://projektintegracija.pravo.hr/_download/repository/Kuhn_Structure_of_Scientific_Revolutions.pdf
What are Worthwhile Problems?http://scienceblogs.com/thescian/2008/03/11/what-are-worthwhile-problems-f/
A Mathematician's Apologyhttps://www.math.ualberta.ca/mss/misc/A%20Mathematician%27s%20Apology.pdf
The importance of stupidity in scientific researchhttps://journals.biologists.com/jcs/article/121/11/1771/30038/The-importance-of-stupidity-in-scientific-research
https://patch-diff.githubusercontent.com/AdaptInfer/ReadingList#the-craft-of-research
Blog post on how we organize computational projects in the labhttp://rajlaboratory.blogspot.com/2017/08/figure-scripting-and-how-we-organize.html
Example project organizationhttps://github.com/arjunrajlaboratory/example_project
Staying on top of literaturehttps://docs.google.com/document/d/1QrDpIoOlQaUVjDnRCYqi_2IYYeWWz6OxC1w4pY5sIQs/edit
Writing for Computer Sciencehttps://amzn.to/44HN73P
Guide for Scholarly Writinghttps://shomir.net/scholarly_writing.html
Guide for Citations and Referenceshttps://shomir.net/citations_and_references.html
Guide for Research Conferenceshttps://shomir.net/scholarly_publishing.html
example 1https://docs.google.com/document/d/1nqVYRTql1sgUNxT9RfE0SX0RiyH3QlgUZgX_Jg6fsos/edit?usp=sharing
example 2https://docs.google.com/document/d/1lGpMFtW4x4GOx-TUmVD_iguM-vh3nvdjNhN-R2PyXt8/edit?usp=sharing
example 3https://docs.google.com/document/d/1TEFLJpjwRiSM2E0gmiUg98sZFEigg_8Pj4vblEh39xI/edit?usp=sharing
Words to avoid when writinghttps://docs.google.com/document/d/1r6nDcF43esu3xBjmk3ERAmaEHKEB75_HflSkk3zZhBk/edit
Writing checklist (incomplete)https://docs.google.com/document/d/1DmoBuFUK6bJG9C5AM5B7i12GI2ew8egg2b-50DdgRFI/edit
Paper submission checklisthttps://docs.google.com/document/d/1_5R2c6WVjV5qi5profAlMHQd2LHhhXgzmYn_htsJl4Q/edit?usp=sharing
General how tohttps://docs.google.com/document/d/1fIpY8d90g0BrTCc0AAxr3PCZHhdVZUYPDxiPqSVkKOk/edit
Annotated examplehttps://docs.google.com/document/d/17f4pyQ1kowgTOIM7mazbXV8uzp2Ev8jaDOYp7MPnYF8/edit
Another examplehttps://drive.google.com/file/d/13d9x4V_RowStgSjDMm8MpiKx_xtlj5pV/view?usp=sharing
Quick guidelineshttps://jef.works/blog/2020/06/17/responding-to-scientific-peer-review/
Illustrator guidehttps://docs.google.com/document/d/1psC5olObkGHDfw3c7am9jpD2OdCN4lnCU_QF26MAQmQ/edit#heading=h.or1to9c1y8il
Blog post about figure makinghttp://rajlaboratory.blogspot.com/2019/08/i-adobe-illustrator-for-scientific.html
Labeling small multipleshttp://rajlaboratory.blogspot.com/2016/01/a-proposal-for-how-to-label-small.html
Incomplete blog post about figure design principleshttps://docs.google.com/document/d/1RozjPwJO57FndomEKUEkG9XwDNeXWj1X24TKq5CMNa0/edit
How to write a figure legendhttps://blog.bioturing.com/2018/05/10/how-to-craft-a-figure-legend-for-scientific-papers/
How to present - Writing, Figures, Talks (MIT Deep Learning Genomics Lecture 22)https://www.youtube.com/watch?v=KzyvIBjBkuc
RajLab: “Refusing the call” and presenting a scientific storyhttps://rajlaboratory.blogspot.com/2023/09/refusing-call-and-presenting-scientific.html
RajLab: Some thoughts on how to structure a talkhttps://rajlaboratory.blogspot.com/2016/09/some-thoughts-on-how-to-structure-talk.html
How To Give a Talkhttps://www.howtogiveatalk.com/
RajLab: Simple tips to improve your presentationshttps://rajlaboratory.blogspot.com/2014/01/simple-tips-to-improve-your.html
Designing Effective Scientific Presentations • iBiologyhttps://www.ibiology.org/professional-development/scientific-presentations/
How to review a paperhttp://rajlaboratory.blogspot.com/2014/04/how-to-review-paper.html
Another perspective on how to review a paperhttps://github.com/jtleek/reviews
How to re-review a paperhttp://rajlaboratory.blogspot.com/2014/04/how-to-re-review-paper.html
Annotated example review of science paperhttps://docs.google.com/document/d/1unO4J36sfmfynFNjBbjkjIiwrdAh0rg9BAB7TKF0R_M/edit
Annotated example review of tech paperhttps://docs.google.com/document/d/1k-DCuiR0cDM4h04AQXFjViNF2A0V0MLtA9zu9e-JmcU/edit
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RajLab: Dear me, I am awesome. Sincerely, me… aka How to write a letter of rec for yourselfhttps://rajlaboratory.blogspot.com/2019/02/dear-me-i-am-awesome-sincerely-me-aka.html
Choosing your dissertation committeehttps://www.dropbox.com/s/rj0yedv0v55n5nl/ChoosingyourDissertationCommittee.doc?dl=0
PhD: An uncommon guide to research, writing & PhD lifehttps://www.dropbox.com/s/omgfbmklnudy1m2/PhD_an_uncommon_guide_to_research_writing_and_PhD_life_free_sample%20copy.pdf?dl=0
Phobidden FooDhttps://www.dropbox.com/s/o0y0oha9f8ylcjf/PhorbiDden_PhooD_1stEdition.pdf?dl=0
How to assemble and use a thesis committeehttps://docs.google.com/document/d/14w3XX1n8Ees2Wy_pIZFj3FN645Yr4mQX_Hyav7xneRw
Documenting your PhD — Keeping Track of Meetings, Experiments and Decisions • David Stutzhttps://davidstutz.de/documenting-your-phd/
So you want to apply for a PhD fellowship?https://docs.google.com/document/d/1WTMW3LZl1ifpFE1ddH1lvfijmmMsFwZggwsuQcotV_A/edit
Example F30 specific aimshttps://docs.google.com/document/d/1DPCGlyU6yoSPnnZH1EAtLmdPs8CRuF2CWoyw3JEoj84/edit#heading=h.kr6a3jnprsx7
Computer Science Graduate Job and Interview Guidehttps://web.eecs.umich.edu/~weimerw/grad-job-guide/guide/index.html
Example CV for PhD Studentshttps://shomir.net/wilhom_rosins.html
Thoughts from my faculty application experiencehttps://docs.google.com/document/d/1ucYHlFbIw87sTWKH3KfP78giPVQycc8R7O5--yxXw0U/edit
Academic Job Searchhttps://docs.google.com/document/u/1/d/e/2PACX-1vSeOnC_QdaJVc3OuuMfDHVlk3QotUxvghytRFaDsrdA0uovD5axQjp8kJCM4Evu1cCf9Hg_u_Stabu1/pub
Interview Questions for Computer Science Faculty Jobshttps://csfaculty.github.io/
https://sites.google.com/view/elizabethbondi/blog?pli=1https://sites.google.com/view/elizabethbondi/blog?pli=1
Faculty job talks: tips from the faculty – MIT EECShttps://www.eecs.mit.edu/career-opportunities-at-eecs/faculty-job-talks-tips-from-the-faculty/
Guide for the Tenure-Track Job Market in Computer/Information Scienceshttps://shomir.net/tt_job_guide.html
Faculty Application : EECS Communication Labhttps://mitcommlab.mit.edu/eecs/commkit/faculty-application/
https://rosecersonsky.com/assets/slides/2022-06-14-academic-jobs.pdfhttps://rosecersonsky.com/assets/slides/2022-06-14-academic-jobs.pdf
Virtual Workshops - YouTubehttps://www.youtube.com/playlist?list=PLAc3DH2raxwoljRhz0x8w8cXHSffewgd8
Tips for negotiating salary and startup for newly-hired tenure-track faculty | Dynamic Ecologyhttps://dynamicecology.wordpress.com/2017/03/01/tips-for-negotiating-salary-and-startup-for-newly-hired-tenure-track-faculty/
Thoughts on applying for faculty jobshttps://docs.google.com/document/d/1Yew6wb1PMDPanPyJIRspqFvYDcIe7FwwvmKheRy8XHI/edit#heading=h.mmvbe39ryleo
https://patch-diff.githubusercontent.com/AdaptInfer/ReadingList#fun
On the Turing Completeness of PowerPointhttps://www.youtube.com/watch?v=uNjxe8ShM-8
https://patch-diff.githubusercontent.com/AdaptInfer/ReadingList#classic-papers
Regression shrinkage and selection via the lassohttp://statweb.stanford.edu/~tibs/lasso/lasso.pdf
Model selection and estimation in models with grouped variableshttp://pages.stat.wisc.edu/~myuan/papers/glasso.final.pdf
Covariance regularized regression and classification for high-dimensional problemshttp://faculty.washington.edu/dwitten/Papers/WittenTibshiraniJune2010CorrectedForWebsite.pdf
High-dimensional support union recovery in multivariate regressionhttp://papers.nips.cc/paper/3432-high-dimensional-support-union-recovery-in-multivariate-regression.pdf
Latent Dirichlet Allocationhttps://www.jmlr.org/papers/volume3/blei03a/blei03a.pdf
On Discriminative vs. Generative classifiers: A comparison of logistic regression and naive Bayes Andrew Y. Ng Computer Sciencehttps://ai.stanford.edu/~ang/papers/nips01-discriminativegenerative.pdf
A Unifying Review of Linear Gaussian Modelshttps://cs.nyu.edu/~roweis/papers/NC110201.pdf
Information Theory and Statistical Mechanics - ET Jayneshttps://batistalab.com/classes/CHEM584/Jaynes.pdf
Best Paper Awards in Computer Sciencehttps://jeffhuang.com/best_paper_awards/
video lectureshttp://groups.csail.mit.edu/mac/classes/6.001/abelson-sussman-lectures/
Hints for Computer System Designhttp://www.cs.cmu.edu/~15712/papers//lampson83.pdf
End-to-End Arguments in Systems Designhttp://www.cs.cmu.edu/~15712/papers//saltzer84.pdf
Ilya Sutskever's "90% of Deep Learning in 30 papers"https://arc.net/folder/D0472A20-9C20-4D3F-B145-D2865C0A9FEE
Deep Learning book chapter on convolutional netshttp://www.iro.umontreal.ca/~bengioy/DLbook/convnets.html
Generalization and Network Design Strategieshttp://yann.lecun.com/exdb/publis/pdf/lecun-89.pdf
ImageNet Classification with Deep Convolutional Neural Networkshttp://books.nips.cc/papers/files/nips25/NIPS2012_0534.pdf
On Random Weights and Unsupervised Feature Learninghttp://www.stanford.edu/~asaxe/papers/Saxe%20et%20al.%20-%202010%20-%20On%20Random%20Weights%20and%20Unsupervised%20Feature%20Learning.pdf
Quoc Le's lectures on Deep Learninghttp://www.trivedigaurav.com/blog/quoc-les-lectures-on-deep-learning/?owa_referral=pitt&owa_source=~gtrivedi/blog/quoc-les-lectures-on-deep-learning/
Introduction to NN architectureshttp://culurciello.github.io/tech/2016/06/04/nets.html?utm_content=bufferbbc97&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer
Tree-guided group Lassohttp://www.cs.cmu.edu/~sssykim/papers/tlasso_final.pdf
Joint eQTL Mapping & Network Inferencehttp://www.cs.cmu.edu/~sssykim/papers/377_paper.pdf
Graphical Lassohttp://statweb.stanford.edu/~tibs/ftp/graph.pdf
Neighborhood Selectionhttps://projecteuclid.org/download/pdfview_1/euclid.aos/1152540754
KELLER: estimating time-varying interactions between geneshttp://bioinformatics.oxfordjournals.org/content/25/12/i128.full.pdf
TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineageshttps://www.cs.cmu.edu/~apparikh/papers/Parikh_Wu_Curtis_Xing_ISMB11.pdf
Structured learning of gaussian graphical modelshttp://papers.nips.cc/paper/4499-structured-learning-of-gaussian-graphical-models.pdf
Bayesian inference of multiple gaussian graphical modelshttp://www.stat.rice.edu/~marina/papers/JASA14.pdf
Learning graphical models with hubshttp://jmlr.org/papers/volume15/tan14b/tan14b.pdf
An Introduction to Graphical Modelshttp://www.cis.upenn.edu/~mkearns/papers/barbados/jordan-tut.pdf
A View of the EM Algorithm that Justifies Incremental, Sparse and Other Variantshttp://www.cs.toronto.edu/~radford/ftp/emk.pdf
A Unifying Review of Linear Gaussian Modelshttp://authors.library.caltech.edu/13697/1/ROWnc99.pdf
An Introduction to Variational Methods for Graphical Modelshttp://www.cs.berkeley.edu/~jordan/papers/variational-intro.pdf
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