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SlideRocket
SlideRocket was an online presentation platform that let users create, manage, share and measure presentations. SlideRocket was provided via a SaaS model. The company was acquired by VMware in April 2011, who sold it to ClearSlide, a similar SaaS application, in March 2013. It is no longer offering independent signups, as the platform is being integrated into ClearSlide. == History == SlideRocket was founded in Jan 2006, and launched as a private beta in March 2008 at the Under The Radar Spring event. A public beta was announced in September 2008 followed shortly by public release on October 28, 2008. SlideRocket is most commonly credited with inventing the PResuMÉ or Presentation Résumé in early 2009. On April 26, 2011, SlideRocket was acquired by VMware. On March 5, 2013, VMware sold SlideRocket to ClearSlide. SlideRocket is based in San Francisco.
Multiple sequence alignment
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides. Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. However, heuristic methods generally cannot guarantee high-quality solutions and have been shown to fail to yield near-optimal solutions on benchmark test cases. == Problem statement == Given m {\displaystyle m} sequences S i {\displaystyle S_{i}} , i = 1 , ⋯ , m {\displaystyle i=1,\cdots ,m} similar to the form below: S := { S 1 = ( S 11 , S 12 , … , S 1 n 1 ) S 2 = ( S 21 , S 22 , ⋯ , S 2 n 2 ) ⋮ S m = ( S m 1 , S m 2 , … , S m n m ) {\displaystyle S:={\begin{cases}S_{1}=(S_{11},S_{12},\ldots ,S_{1n_{1}})\\S_{2}=(S_{21},S_{22},\cdots ,S_{2n_{2}})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S_{m}=(S_{m1},S_{m2},\ldots ,S_{mn_{m}})\end{cases}}} A multiple sequence alignment is taken of this set of sequences S {\displaystyle S} by inserting any amount of gaps needed into each of the S i {\displaystyle S_{i}} sequences of S {\displaystyle S} until the modified sequences, S i ′ {\displaystyle S'_{i}} , all conform to length L ≥ max { n i ∣ i = 1 , … , m } {\displaystyle L\geq \max\{n_{i}\mid i=1,\ldots ,m\}} and no values in the sequences of S {\displaystyle S} of the same column consists of only gaps. The mathematical form of an MSA of the above sequence set is shown below: S ′ := { S 1 ′ = ( S 11 ′ , S 12 ′ , … , S 1 L ′ ) S 2 ′ = ( S 21 ′ , S 22 ′ , … , S 2 L ′ ) ⋮ S m ′ = ( S m 1 ′ , S m 2 ′ , … , S m L ′ ) {\displaystyle S':={\begin{cases}S'_{1}=(S'_{11},S'_{12},\ldots ,S'_{1L})\\S'_{2}=(S'_{21},S'_{22},\ldots ,S'_{2L})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S'_{m}=(S'_{m1},S'_{m2},\ldots ,S'_{mL})\end{cases}}} To return from each particular sequence S i ′ {\displaystyle S'_{i}} to S i {\displaystyle S_{i}} , remove all gaps. == Graphing approach == A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. When finding alignments via graph, a complete alignment is created in a weighted graph that contains a set of vertices and a set of edges. Each of the graph edges has a weight based on a certain heuristic that helps to score each alignment or subset of the original graph. === Tracing alignments === When determining the best suited alignments for each MSA, a trace is usually generated. A trace is a set of realized, or corresponding and aligned, vertices that has a specific weight based on the edges that are selected between corresponding vertices. When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. == Alignment methods == There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. Each is usually based on a certain heuristic with an insight into the evolutionary process. Most try to replicate evolution to get the most realistic alignment possible to best predict relations between sequences. === Dynamic programming === A direct method for producing an MSA uses the dynamic programming technique to identify the globally optimal alignment solution. For proteins, this method usually involves two sets of parameters: a gap penalty and a substitution matrix assigning scores or probabilities to the alignment of each possible pair of amino acids based on the similarity of the amino acids' chemical properties and the evolutionary probability of the mutation. For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. The search space thus increases exponentially with increasing n and is also strongly dependent on sequence length. Expressed with the big O notation commonly used to measure computational complexity, a naïve MSA takes O(LengthNseqs) time to produce. To find the global optimum for n sequences this way has been shown to be an NP-complete problem. In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. In this approach pairwise dynamic programming alignments are performed on each pair of sequences in the query set, and only the space near the n-dimensional intersection of these alignments is searched for the n-way alignment. The MSA program optimizes the sum of all of the pairs of characters at each position in the alignment (the so-called sum of pair score) and has been implemented in a software program for constructing multiple sequence alignments. In 2019, Hosseininasab and van Hoeve showed that by using decision diagrams, MSA may be modeled in polynomial space complexity. === Progressive alignment construction === The most widely used approach to multiple sequence alignments uses a heuristic search known as progressive technique (also known as the hierarchical or tree method) developed by Da-Fei Feng and Doolittle in 1987. Progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related. All progressive alignment methods require two stages: a first stage in which the relationships between the sequences are represented as a phylogenetic tree, called a guide tree, and a second step in which the MSA is built by adding the sequences sequentially to the growing MSA according to the guide tree. The initial guide tree is determined by an efficient clustering method such as neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA), and may use distances based on the number of identical two-letter sub-sequences (as in FASTA rather than a dynamic programming alignment). Progressive alignments are not guaranteed to be globally optimal. The primary problem is that when errors are made at any stage in growing the MSA, these errors are then propagated through to the final result. Performance is also particularly bad when all of the sequences in the set are rather distantly related. Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors to individual members of the query set in a nonlinear fashion based on their phylogenetic distance from their nearest neighbors. This corrects for non-random selection of the sequences given to the alignment program. Progressive alignment methods are efficient enough to implement on a large scale for many (100s to 1000s) sequences. A popular progressive alignment method has been the Clustal family. ClustalW is used extensively for phylogenetic tree construction, in spite of the author's explicit warnings that unedited alignments should not be used in such studies and as input for protein structure prediction by homology modeling. European Bioinformatics Institute (EMBL-EBI) announced that CLustalW2 will expire in August 2015. They recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments. An alternative tool for progressive DNA alignments is multiple alignment using fast Fourier transform (MAFFT). Another common progressive alignment method named T-Coffee is slower than Clustal and its derivatives but generally produces more accurate alignments for distantly related sequence sets. T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence. It uses the output from Clustal as well as another local alignment program LALIGN, which finds multiple regions of local alignment between two sequences. The resulting alignment and phylogenetic tree are used as a guide to produce new and more accurate w
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András Kornai
András Kornai (born 1957 in Budapest) is a mathematical linguist. == Education == Kornai is the son of economist János Kornai. He earned two PhDs with the first being in mathematics in 1983 from Eötvös Loránd University in Budapest, where his advisor was Miklós Ajtai. His second was in linguistics in 1991 from Stanford University, where his advisor was Paul Kiparsky. == Career == He is a professor in the Department of Algebra at the Budapest Institute of Technology, where he works on an open source Hungarian morphological analyzer. He was Chief Scientist at MetaCarta, where he worked on information extraction before the company was acquired by Nokia. Prior to MetaCarta, he was Chief Scientist at Northern Light. He is on the board of the journal Grammars and YourAmigo PLC. His research interests include all mathematical aspects of natural language processing, speech recognition, and OCR. As area editor he was responsible for the Mathematical Linguistics area of the Oxford International Encyclopedia of Linguistics, and his joint work with Geoffrey Pullum, "The X-bar Theory of Phrase Structure", formally reconstructed that then-popular linguistic theory. == Awards and honors == 2009: ACM Distinguished Member == Monographs == Semantics. Springer Nature, 2020. ISBN 978-3-319-65644-1 Mathematical Linguistics. Springer Verlag, in the series Advanced Information and Knowledge Processing, November 2007. ISBN 978-1-84628-985-9 Hardbound, approximately 300 pages. See description. Formal Phonology. In the series Outstanding Dissertations in Linguistics, Garland Publishing, 1994, ISBN 0-8153-1730-1, hardbound, 240 pages Contents, Preface, Introduction (20 pages) On Hungarian Morphology. In the series Linguistica, Hungarian Academy of Sciences, 1994, ISBN 963-8461-73-X, paperbound, 174 pages Contents, Preface, Introduction (10 pages) == Books edited == Oxford International Encyclopedia of Linguistics (Mathematical Linguistics Area Editor under Editor in Chief William Frawley). 4 volumes, Oxford University Press, 2003, ISBN 978-0-19-513977-8. Proceedings of the HLT-NAACL Workshop on the Analysis of Geographic References. Jointly with Beth Sundheim. Association for Computational Linguistics, 2003, ISBN 1-932432-04-3 (WS9), paperbound, vi+81 pages. See related material. Extended Finite State Models of Language (editor). In the series Studies in Natural Language Processing, Cambridge University Press, 1999, ISBN 0-521-63198-X, hardbound, x+278 pages Contents, Introduction (7 pages). == Selected papers == Digital Language Death. PLoS ONE 8(10): e77056, 2012. [1] Hunmorph: open source word analysis (Jointly with V. Tron, Gy. Gyepesi, P. Halacsy, L. Nemeth, and D. Varga). In Proc. ACL 2005 Software Workshop 77-85 [2] Leveraging the open source ispell codebase for minority language analysis (Jointly with P. Halacsy, L. Nemeth, A. Rung, I. Szakadat, and V. Tron). In J. Carson-Berndsen (ed): Proc. SALTMIL 2004 56-59 [3] Explicit Finitism, International Journal of Theoretical Physics 2003/2 301-307 [4] Mathematical Linguistics (Jointly with G.K. Pullum) In W. Frawley (ed): Oxford International Encyclopedia of Linguistics, Oxford University Press 2003, v3 17-20 [5] Optical Character Recognition, In W. Frawley (ed): Oxford International Encyclopedia of Linguistics, Oxford University Press 2003, v3 33-34 [6] How many words are there? Glottometrics 2002/4 61-86 [7] Zipf's law outside the middle range Proc. Sixth Meeting on Mathematics of Language University of Central Florida, 1999 347-356 [8] A Robust, Language-Independent OCR System. (Jointly with Z. Lu, I. Bazzi, J. Makhoul, P. Natarajan, and R. Schwartz) In: Robert J. Mericsko (ed): Proc. 27th AIPR Workshop: Advances in Computer-Assisted Recognition SPIE Proceedings 3584 1999 [9] Quantitative Comparison of Languages. Grammars 1998/2 155-165 [10] The generative power of feature geometry. Annals of Mathematics and Artificial Intelligence 8 1993 37-46 [11] The X-bar Theory of Phrase Structure. (Jointly with G.K. Pullum) Language 66 1990 24-50 [12]
SPL notation
SPL (Sentence Plan Language) is an abstract notation representing the semantics of a sentence in natural language. In a classical Natural Language Generation (NLG) workflow, an initial text plan (hierarchically or sequentially organized factoids, often modelled in accordance with Rhetorical Structure Theory) is transformed by a sentence planner (generator) component to a sequence of sentence plans modelled in a Sentence Plan Language. A surface generator can be used to transform the SPL notation into natural language sentences. Probably the most widely used SPL language used today (2022) is AMR (Abstract Meaning Representation, see there for further references), but is owes parts of its popularity to its application to NLP problems other than NLG, e.g., machine translation and semantic parsing.
Eurotra
Eurotra was a machine translation project established and funded by the European Commission from 1978 until 1992. == History == In 1976, the European Commission started using the commercially developed machine translation system SYSTRAN with a plan to make it work for further languages than originally developed for (Russian-English and English-French), which however turned out to be difficult. This and the potential in existing systems within European research center, led to the decision in 1978 to start the project Eurotra, first through a preparatory Eurotra Coordination Group. Four years later, the European Commission and coordination group gained the approval of the European Parliament. The goal of the project as to create machine translation system for the official languages of the European Community, which at the time were Danish, Dutch, German, English, French, Italian, later including Greek, Spanish and Portuguese. However, as time passed, expectations became tempered; "Fully Automatic High Quality Translation" was not a reasonably attainable goal. The true character of Eurotra was eventually acknowledged to be in fact pre-competitive research rather than prototype development. The project was motivated by one of the founding principles of the EU: that all citizens had the right to read any and all proceedings of the Commission in their own language. As more countries joined, this produced a combinatorial explosion in the number of language pairs involved, and the need to translate every paper, speech and even set of meeting minutes produced by the EU into the other eight languages meant that translation rapidly became the overwhelming component in the administrative budget. To solve this problem Eurotra was devised. The project was unusual in that rather than consisting of a single research team, it had member groups distributed around the member countries, organised along language rather than national lines (for example, groups in Leuven and Utrecht worked closely together), and the secretariat was based at the European Commission in Luxembourg. The actual design of the project was unusual as MT projects go. Older systems, such as SYSTRAN, were heavily dictionary-based, with minor support for rearranging word order. More recent systems have often worked on a probabilistic approach, based on parallel corpora. Eurotra addressed the constituent structure of the text to be translated, going through first a syntactic parse followed by a second parse to produce a dependency structure followed by a final parse with a third grammar to produce what was referred to internally as Intermediate Representation (IR). Since all three modules were implemented as Prolog programs, it would then in principle be possible to put this structure backwards through the corresponding modules for another language to produce a translated text in any of the other languages. However, in practice this was not in fact how language pairs were implemented. The first "live" translation occupied a 4Mb Microvax running Ultrix and C-Prolog for a complete weekend some time in early 1987. The sentence, translated from English into Danish, was "Japan makes computers". The main problem faced by the system was the generation of so-called "Parse Forests" - often a large number of different grammar rules could be applied to any particular phrase, producing hundreds, even thousands of (often identical) parse trees. This used up huge quantities of computer store, slowing the whole process down unnecessarily. While Eurotra never delivered a "working" MT system, the project made a far-reaching long-term impact on the nascent language industries in European member states, in particular among the southern countries of Greece, Italy, Spain, and Portugal. There is at least one commercial MT system (developed by an academic/commercial consortium in Denmark) derived from Eurotra technology.