Robbi Nespu
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## Affective Computing
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* :scroll: [Affective Computing](http://affect.media.mit.edu/pdfs/95.picard.pdf)
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* :scroll: [Theories, Methods and Current Research on Emotions](https://irenelopatovska.files.wordpress.com/2012/10/lopatovska_arapakis_2011_theories.pdf)
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Bioinformatics
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===========
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## Sequence Analysis
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* [SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs (2019)](https://arxiv.org/abs/1910.09020v2)
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* [Shouji: a fast and efficient pre-alignment filter for sequence alignment (2019)](https://arxiv.org/ftp/arxiv/papers/1809/1809.07858.pdf)
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* [Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping (2015)](https://doi.org/10.1093/bioinformatics/btu856)
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## Clustering Algorithms
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[On the resemblance and containment of documents](http://gatekeeper.dec.com/ftp/pub/dec/SRC/publications/broder/positano-final-wpnums.pdf) (Andrei Z. Broder)
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# Combinatory Logic
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* [Flattening Combinators: Surviving Without Parentheses]
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by Chris Okasaki (2003)
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by Chris Okasaki (2003) ([DOI])
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* [Combinatorial Analysis and Computers]
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by Marshall Hall Jr. and Donald E. Knuth (1965)
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by Marshall Hall Jr. and Donald E. Knuth (1965)
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[Flattening Combinators: Surviving Without Parentheses]:
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http://www.westpoint.edu/eecs/SiteAssets/SitePages/Faculty%20Publication%20Documents/Okasaki/jfp03flat.pdf
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https://web.archive.org/web/20170828181221/http://www.westpoint.edu:80/eecs/SiteAssets/SitePages/Faculty%20Publication%20Documents/Okasaki/jfp03flat.pdf
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[DOI]:
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https://doi.org/10.1017/S0956796802004483
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[Combinatorial Analysis and Computers]:
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http://poncelet.math.nthu.edu.tw/disk5/js/computer/hall-knuth.pdf
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https://web.archive.org/web/20170904072400/http://poncelet.math.nthu.edu.tw/disk5/js/computer/hall-knuth.pdf
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## Computer Science Fundamentals and History
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* "Turing, On computable numbers, with an application to the Entscheidungsproblem" by Alan Turing
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* As a PDF: [Turing, On computable numbers, with an application to the Entscheidungsproblem](https://www.cs.virginia.edu/~robins/Turing_Paper_1936.pdf)
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* As a PDF: [Turing, On computable numbers, with an application to the Entscheidungsproblem](https://www.cs.virginia.edu/~robins/Turing_Paper_1936.pdf)
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* As a collection of single images: [Turing, On computable numbers, with an application to the Entscheidungsproblem](http://www.turingarchive.org/browse.php/B/12) by Alan Turing
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* [Mealy, A Method for Synthesizing Sequential Circuits] (http://www3.alcatel-lucent.com/bstj/vol34-1955/articles/bstj34-5-1045.pdf) by George H. Mealy
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* [Mealy, A Method for Synthesizing Sequential Circuits](http://www3.alcatel-lucent.com/bstj/vol34-1955/articles/bstj34-5-1045.pdf) by George H. Mealy
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* :scroll: [Back to the Future - The Story of Squeak, A Practical Smalltalk Written in Itself](story-of-squeak-a-practical-smalltalk-written-in-itself.pdf) by Dan Ingalls, Ted Kaehler, John Maloney, Scott Wallace & Alan Kay
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* :scroll: [Recursive Functions of Symbolic Expressions and Their Computation by Machine, Part I](recursive-functions-of-symbolic-expressions-and-their-computation-by-machine-parti.pdf) by John McCarthy
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* :scroll: [An Axiomatic Basis for Computer Programming](axiomatic-basis-computer-programming.pdf) by C. A. R. HOARE
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* :scroll: [An Axiomatic Basis for Computer Programming](axiomatic-basis-computer-programming.pdf) by C. A. R. HOARE
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* [On the Computational Complexity of Algorithims](http://www.ams.org/journals/tran/1965-117-00/S0002-9947-1965-0170805-7/S0002-9947-1965-0170805-7.pdf) by J. HARTMANIS AND R. E. STEARNS
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* :scroll: [Hints for Computer System Design](hints-for-computer-system-design.pdf)
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* :scroll: [Early Lisp History: 1956-1959](early-lisp-history-1956-1959-herbert-stoyan-html-rendering.pdf) by Herbert Stoyan. This is a pdf rendering of the HTML page available at Archive.org.
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* :scroll: [Why Programming is a good medium for expressing poorly understood and sloppily-formulated ideas](http://web.media.mit.edu/~minsky/papers/Why%20programming%20is--.html) by Marvin Minsky
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# Data Compression
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* :scroll: [Data Compression](data-compression.pdf)
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> This paper surveys a variety of data compression methods spanning almost 40 years of research, from the work of Shannon, Fano and Huffman in the 40's, to a technique developed in 1986.
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> This paper surveys a variety of data compression methods spanning almost 40 years of research, from the work of Shannon, Fano and Huffman in the 40's, to a technique developed in 1986.
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## Scientific Data Compression
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* :scroll: [Fast Error-bounded Lossy HPC Data Compression with SZ](fast_error_bounded_Lossy_hpc_data_compression_with_sz.pdf)
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> This is the first version of SZ. In this paper, SZ is introduced to achieve data reduction using regression-based data point prediction.
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* :scroll: [Significantly Improving Lossy Compression for Scientific Data Sets Based on Multidimensional Prediction and Error-Controlled Quantization](Significantly_Improving_Lossy_Compression_for_Scientific_Data_Sets_Based_on_Multidimensional_Prediction_and_Error-Controlled_Quantization.pdf)
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> This work is known as SZ-1.4. In this work, SZ employs multi-dimensional data prediction so that data with dimension larger than 1 is no longer linearized into single dimension before compression. In this way, more data locality is preserved thus compression ratio is improved.
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* :scroll: [Error-Controlled Lossy Compression Optimized for High Compression Ratios of Scientific Datasets](Error-Controlled_Lossy_Compression_Optimized_for_High_Compression_Ratios_of_Scientific_Datasets.pdf)
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> This work is known as SZ-2.0. In this work, authors proposed an online selection tool between 2 predictors, the mean-integrated Lorenzo predictor and linear regression-based predictor. Users can choose the predictor that yields larger compression ratio with higher prediction accuracy.
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* :scroll: [Fixed-Rate Compressed Floating-Point Arrays](fixed-rate_compressed_floating_point_arrays.pdf)
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* :scroll: [FPC: A High-Speed Compressor for Double-Precision Floating-Point Data](fpc_a_high_speed_compressor_for_double_precision_floating_point_data.pdf)
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# Data Replication
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* :scroll: [A comprehensive study of
Convergent and Commutative Replicated Data Types](a-comprehensive-study-of-convergent-and-communative-replicated-data-types.pdf)
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* :scroll: [Immutability Changes Everything](http://cidrdb.org/cidr2015/Papers/CIDR15_Paper16.pdf)
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> An overview on the patterns in computing leveraging immutability.
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Nowadays, keeping immutable copies of data is almost inexpensive. One of the advantages of this fact is that it
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can alleviate the burden of coordinated accesses to the data in the different layers of the SW/HW stack.
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* :scroll: [A comprehensive study of Convergent and Commutative Replicated Data Types](a-comprehensive-study-of-convergent-and-communative-replicated-data-types.pdf)
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> Eventual consistency aims to ensure that replicas of some mutable shared object converge without foreground synchronisation. We study a principled approach: to base the design of shared data types on some simple formal conditions that are sufficient to guarantee even- tual consistency. We call these types Convergent or Commutative Replicated Data Types (CRDTs).
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# Design
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* [No Silver Bullet — Essence and Accidents of Software Engineering](http://faculty.salisbury.edu/~xswang/Research/Papers/SERelated/no-silver-bullet.pdf)
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* [Traits: A Mechanism for Fine-Grained Reuse](http://scg.unibe.ch/archive/papers/Duca06bTOPLASTraits.pdf)
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* [THING-MODEL-VIEW-EDITOR an Example from a planningsystem](http://heim.ifi.uio.no/~trygver/1979/mvc-1/1979-05-MVC.pdf)
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* :scroll: [Out of the Tar Pit](out-of-the-tar-pit.pdf)
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> We identify common causes of complexity and discuss general approaches which can be taken to eliminate them where they are accidental in nature.
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# Digital Currency
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* :scroll: [Bitcoin](bitcoin.pdf)
* :scroll: [PeerCoin](peercoin.pdf)
* :scroll: [PrimeCoin](primecoin.pdf)
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## External Papers
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* [Ethereum: a secure decentralized generalized transaction ledger](https://ethereum.github.io/yellowpaper/paper.pdf)
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## Hosted Papers
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* :scroll: [Bitcoin](bitcoin.pdf)
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* :scroll: [PeerCoin](peercoin.pdf)
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* :scroll: [PrimeCoin](primecoin.pdf)
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# Distributed File Systems
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* [Sun NFS](http://www.cs.ucf.edu/~eurip/papers/sandbergnfs.pdf)
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* [Google (GFS)](https://static.googleusercontent.com/media/research.google.com/en//archive/gfs-sosp2003.pdf)
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* [Hadoop (HDFS)](https://storageconference.us/2010/Papers/MSST/Shvachko.pdf)
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* [Ceph](https://www.ssrc.ucsc.edu/Papers/weil-osdi06.pdf)
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* [Coda](http://www.coda.cs.cmu.edu/ljpaper/lj.html)
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* [Frangipani](https://pdos.csail.mit.edu/6.824/papers/thekkath-frangipani.pdf)
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## Information Retrieval
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Information retrieval is the activity of obtaining information resources relevant to an information need from a collection of information resources. (Says Wikipedia).
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The included documents are
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* [:scroll:](graph_of_word_and_tw_idf.pdf) [Graph of Word and TW-IDF](http://www.lix.polytechnique.fr/~rousseau/papers/rousseau-cikm2013.pdf) - Francois Rousseau & Michalis Vazirgiannis
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The traditional IR system stores term-specific statistics (typically
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a term's frequency in each document - which we call TF) in an index.
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Such a model ignores dependencies between terms and considers a
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document's terms to occur independently of each other (and is aptly
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called the bag-of-words model). In this paper the authors use a
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statistic that uses a graph representation of a document to encode
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dependencies between terms and replace the TF statistic with a new
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TW statistic based on the graph constructed and achieve
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significantly better results that popular existing models. This
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paper won a honorable mention at CIKM 2013.
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* [:scroll:](pagerank.pdf) [Pagerank Algorithm](http://ilpubs.stanford.edu:8090/422/1/1999-66.pdf) - Lawrence Page, Sergey Brin, Rajeev Motwani and Terry Winograd
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This paper introduces the PageRank algorithm, which forms the backbone of
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the present day google search engine. Pagerank operates by assessing the
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number of incoming and outgoing hyper links to a given web page and ranks the
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pages based on the link structure of a page. The authors also implemented
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PageRank on the backrub system (now called the Google Search
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Engine) in the [Anatomy of a Large-Scale Hypertextual Web Search Engine]
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http://infolab.stanford.edu/~backrub/google.html which assigned page ranks to
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every webpage in the world wide web. Google is currently the most commercially
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sucessful generic search engine in the world.
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* [:scroll:](ocapi-trec3.pdf) [Okapi System](http://trec.nist.gov/pubs/trec3/papers/city.ps.gz) - Stephen E. Robertson, Steve Walker, Susan Jones, Micheline Hancock-Beaulieu, and Mike Gatford
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This paper introduces the now famous Okapi information retrieval
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framework which introduces the BM25 ranking function for ranked
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retrieval. It is one of the first implementations of the probabilistic
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retrieval frameworks in literature. BM25 is a bag of words retrieval
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function. The IDF(Inverse document frequency) term can be interpreted
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via information theory. If a query q appears in n(q) docs the probability
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of picking a doc randomly and it containing that term :p(q) = n(q) / D,
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where D is the number of documents. The information content based on
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shannon's noisy channel model is = -log(p(q)) = log (D / n(q)). Smoothing
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by adding a constant to both numberator and demoninator leads to IDF term
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used in BM25. BM25 has been shown to be one of the best probabilistic
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weighting schemes. While the paper was in postscript form, the committer has
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changed the format to pdf as per guidelines of papers we love via ps2pdf.
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* [:scroll:](hits.pdf) [Hits Algorithm](https://www.cs.cornell.edu/home/kleinber/auth.pdf) - Jon M. Kleinberg
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This paper introduces the HITS algorithm, a link analysis algorithm that rates webpages. Unlike the more famous page rank algorithm, the hits algorithm makes a distinction between webpage behavior classifies them as hubs and autho rities. A page is authoratitative (in the sense the page has a large number of incoming links) or acts as a hub (a directory of sort, which can be measured by the number of outgoing link). The hits algorithm computes two scores for a page (authority and hub score) where the algorithm iteratively computes the hub score as sum of authority scores of outgoing links and authority scores as sum of hub scores of incoming links until a convergence is attained. These scores can then be used to rank documents. While this algorithm is famous in academia, its not very widely used in the industry (a variant of this algorithm was used by a company called Teoma which was acquired by AskJeeves)
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# C++
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* [Why C++ is not just an Object-Oriented Programming Language-Original](http://www.stroustrup.com/oopsla.pdf)
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# C
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* [The Development of the C Language-Original](https://www.bell-labs.com/usr/dmr/www/chist.pdf)
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# Go
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* [Go Lang Original Paper](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.138.6297&rep=rep1&type=pdf)
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# Java
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* [Java Original Paper](https://pdfs.semanticscholar.org/ee07/8894734c70589cb9653e2169a4342ae02355.pdf)
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* [Java Whitepaper](http://www.stroustrup.com/1995_Java_whitepaper.pdf)
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# Programming Language Theory
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Programming language theory (PLT) is a branch of computer science that deals with the design, implementation, analysis, characterization, and classification of programming languages and their individual features.
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## Included Papers
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* :scroll: [On the Expressive Power of Programming Languages](scp91-felleisen.ps.gz) [sciencedirect](https://www.sciencedirect.com/science/article/pii/016764239190036W)(Matthias Felleisen): "The literature on programming languages contains an abundance of informal claims on the relative expressive power of programming languages, but there is no framework for formalizing such statements nor for deriving interesting consequences. As a first step in this direction, we develop a formal notion of expressiveness and investigate its properties. To demonstrate the theory's closeness to published intuitions on expressiveness, we analyze the expressive power of several extensions of functional languages. Based on these results, we believe that our system correctly captures many of the informal ideas on expressiveness, and that it constitutes a good basis for further research in this direction. " (abstract)
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