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clemgoub / DnaPipeTEdnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).
Aryia-Behroziuan / ReferencesPoole, Mackworth & Goebel 1998, p. 1. Russell & Norvig 2003, p. 55. Definition of AI as the study of intelligent agents: Poole, Mackworth & Goebel (1998), which provides the version that is used in this article. These authors use the term "computational intelligence" as a synonym for artificial intelligence.[1] Russell & Norvig (2003) (who prefer the term "rational agent") and write "The whole-agent view is now widely accepted in the field".[2] Nilsson 1998 Legg & Hutter 2007 Russell & Norvig 2009, p. 2. McCorduck 2004, p. 204 Maloof, Mark. "Artificial Intelligence: An Introduction, p. 37" (PDF). georgetown.edu. Archived (PDF) from the original on 25 August 2018. "How AI Is Getting Groundbreaking Changes In Talent Management And HR Tech". Hackernoon. Archived from the original on 11 September 2019. Retrieved 14 February 2020. Schank, Roger C. (1991). "Where's the AI". AI magazine. Vol. 12 no. 4. p. 38. Russell & Norvig 2009. "AlphaGo – Google DeepMind". Archived from the original on 10 March 2016. Allen, Gregory (April 2020). "Department of Defense Joint AI Center - Understanding AI Technology" (PDF). AI.mil - The official site of the Department of Defense Joint Artificial Intelligence Center. Archived (PDF) from the original on 21 April 2020. Retrieved 25 April 2020. Optimism of early AI: * Herbert Simon quote: Simon 1965, p. 96 quoted in Crevier 1993, p. 109. * Marvin Minsky quote: Minsky 1967, p. 2 quoted in Crevier 1993, p. 109. Boom of the 1980s: rise of expert systems, Fifth Generation Project, Alvey, MCC, SCI: * McCorduck 2004, pp. 426–441 * Crevier 1993, pp. 161–162,197–203, 211, 240 * Russell & Norvig 2003, p. 24 * NRC 1999, pp. 210–211 * Newquist 1994, pp. 235–248 First AI Winter, Mansfield Amendment, Lighthill report * Crevier 1993, pp. 115–117 * Russell & Norvig 2003, p. 22 * NRC 1999, pp. 212–213 * Howe 1994 * Newquist 1994, pp. 189–201 Second AI winter: * McCorduck 2004, pp. 430–435 * Crevier 1993, pp. 209–210 * NRC 1999, pp. 214–216 * Newquist 1994, pp. 301–318 AI becomes hugely successful in the early 21st century * Clark 2015 Pamela McCorduck (2004, p. 424) writes of "the rough shattering of AI in subfields—vision, natural language, decision theory, genetic algorithms, robotics ... and these with own sub-subfield—that would hardly have anything to say to each other." This list of intelligent traits is based on the topics covered by the major AI textbooks, including: * Russell & Norvig 2003 * Luger & Stubblefield 2004 * Poole, Mackworth & Goebel 1998 * Nilsson 1998 Kolata 1982. Maker 2006. Biological intelligence vs. intelligence in general: Russell & Norvig 2003, pp. 2–3, who make the analogy with aeronautical engineering. McCorduck 2004, pp. 100–101, who writes that there are "two major branches of artificial intelligence: one aimed at producing intelligent behavior regardless of how it was accomplished, and the other aimed at modeling intelligent processes found in nature, particularly human ones." Kolata 1982, a paper in Science, which describes McCarthy's indifference to biological models. Kolata quotes McCarthy as writing: "This is AI, so we don't care if it's psychologically real".[19] McCarthy recently reiterated his position at the AI@50 conference where he said "Artificial intelligence is not, by definition, simulation of human intelligence".[20]. Neats vs. scruffies: * McCorduck 2004, pp. 421–424, 486–489 * Crevier 1993, p. 168 * Nilsson 1983, pp. 10–11 Symbolic vs. sub-symbolic AI: * Nilsson (1998, p. 7), who uses the term "sub-symbolic". General intelligence (strong AI) is discussed in popular introductions to AI: * Kurzweil 1999 and Kurzweil 2005 See the Dartmouth proposal, under Philosophy, below. McCorduck 2004, p. 34. McCorduck 2004, p. xviii. McCorduck 2004, p. 3. McCorduck 2004, pp. 340–400. This is a central idea of Pamela McCorduck's Machines Who Think. She writes: "I like to think of artificial intelligence as the scientific apotheosis of a venerable cultural tradition."[26] "Artificial intelligence in one form or another is an idea that has pervaded Western intellectual history, a dream in urgent need of being realized."[27] "Our history is full of attempts—nutty, eerie, comical, earnest, legendary and real—to make artificial intelligences, to reproduce what is the essential us—bypassing the ordinary means. Back and forth between myth and reality, our imaginations supplying what our workshops couldn't, we have engaged for a long time in this odd form of self-reproduction."[28] She traces the desire back to its Hellenistic roots and calls it the urge to "forge the Gods."[29] "Stephen Hawking believes AI could be mankind's last accomplishment". BetaNews. 21 October 2016. Archived from the original on 28 August 2017. Lombardo P, Boehm I, Nairz K (2020). "RadioComics – Santa Claus and the future of radiology". Eur J Radiol. 122 (1): 108771. doi:10.1016/j.ejrad.2019.108771. PMID 31835078. Ford, Martin; Colvin, Geoff (6 September 2015). "Will robots create more jobs than they destroy?". The Guardian. Archived from the original on 16 June 2018. Retrieved 13 January 2018. AI applications widely used behind the scenes: * Russell & Norvig 2003, p. 28 * Kurzweil 2005, p. 265 * NRC 1999, pp. 216–222 * Newquist 1994, pp. 189–201 AI in myth: * McCorduck 2004, pp. 4–5 * Russell & Norvig 2003, p. 939 AI in early science fiction. * McCorduck 2004, pp. 17–25 Formal reasoning: * Berlinski, David (2000). The Advent of the Algorithm. Harcourt Books. ISBN 978-0-15-601391-8. OCLC 46890682. Archived from the original on 26 July 2020. Retrieved 22 August 2020. Turing, Alan (1948), "Machine Intelligence", in Copeland, B. Jack (ed.), The Essential Turing: The ideas that gave birth to the computer age, Oxford: Oxford University Press, p. 412, ISBN 978-0-19-825080-7 Russell & Norvig 2009, p. 16. Dartmouth conference: * McCorduck 2004, pp. 111–136 * Crevier 1993, pp. 47–49, who writes "the conference is generally recognized as the official birthdate of the new science." * Russell & Norvig 2003, p. 17, who call the conference "the birth of artificial intelligence." * NRC 1999, pp. 200–201 McCarthy, John (1988). "Review of The Question of Artificial Intelligence". Annals of the History of Computing. 10 (3): 224–229., collected in McCarthy, John (1996). "10. Review of The Question of Artificial Intelligence". Defending AI Research: A Collection of Essays and Reviews. CSLI., p. 73, "[O]ne of the reasons for inventing the term "artificial intelligence" was to escape association with "cybernetics". Its concentration on analog feedback seemed misguided, and I wished to avoid having either to accept Norbert (not Robert) Wiener as a guru or having to argue with him." Hegemony of the Dartmouth conference attendees: * Russell & Norvig 2003, p. 17, who write "for the next 20 years the field would be dominated by these people and their students." * McCorduck 2004, pp. 129–130 Russell & Norvig 2003, p. 18. Schaeffer J. (2009) Didn't Samuel Solve That Game?. In: One Jump Ahead. Springer, Boston, MA Samuel, A. L. (July 1959). "Some Studies in Machine Learning Using the Game of Checkers". IBM Journal of Research and Development. 3 (3): 210–229. CiteSeerX 10.1.1.368.2254. doi:10.1147/rd.33.0210. "Golden years" of AI (successful symbolic reasoning programs 1956–1973): * McCorduck 2004, pp. 243–252 * Crevier 1993, pp. 52–107 * Moravec 1988, p. 9 * Russell & Norvig 2003, pp. 18–21 The programs described are Arthur Samuel's checkers program for the IBM 701, Daniel Bobrow's STUDENT, Newell and Simon's Logic Theorist and Terry Winograd's SHRDLU. DARPA pours money into undirected pure research into AI during the 1960s: * McCorduck 2004, p. 131 * Crevier 1993, pp. 51, 64–65 * NRC 1999, pp. 204–205 AI in England: * Howe 1994 Lighthill 1973. Expert systems: * ACM 1998, I.2.1 * Russell & Norvig 2003, pp. 22–24 * Luger & Stubblefield 2004, pp. 227–331 * Nilsson 1998, chpt. 17.4 * McCorduck 2004, pp. 327–335, 434–435 * Crevier 1993, pp. 145–62, 197–203 * Newquist 1994, pp. 155–183 Mead, Carver A.; Ismail, Mohammed (8 May 1989). Analog VLSI Implementation of Neural Systems (PDF). The Kluwer International Series in Engineering and Computer Science. 80. Norwell, MA: Kluwer Academic Publishers. doi:10.1007/978-1-4613-1639-8. ISBN 978-1-4613-1639-8. Archived from the original (PDF) on 6 November 2019. Retrieved 24 January 2020. Formal methods are now preferred ("Victory of the neats"): * Russell & Norvig 2003, pp. 25–26 * McCorduck 2004, pp. 486–487 McCorduck 2004, pp. 480–483. Markoff 2011. 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Cognitive Systems Research. 48: 39–55. doi:10.1016/j.cogsys.2017.05.001. hdl:2318/1665207. S2CID 206868967. Problem solving, puzzle solving, game playing and deduction: * Russell & Norvig 2003, chpt. 3–9, * Poole, Mackworth & Goebel 1998, chpt. 2,3,7,9, * Luger & Stubblefield 2004, chpt. 3,4,6,8, * Nilsson 1998, chpt. 7–12 Uncertain reasoning: * Russell & Norvig 2003, pp. 452–644, * Poole, Mackworth & Goebel 1998, pp. 345–395, * Luger & Stubblefield 2004, pp. 333–381, * Nilsson 1998, chpt. 19 Psychological evidence of sub-symbolic reasoning: * Wason & Shapiro (1966) showed that people do poorly on completely abstract problems, but if the problem is restated to allow the use of intuitive social intelligence, performance dramatically improves. (See Wason selection task) * Kahneman, Slovic & Tversky (1982) have shown that people are terrible at elementary problems that involve uncertain reasoning. (See list of cognitive biases for several examples). * Lakoff & Núñez (2000) have controversially argued that even our skills at mathematics depend on knowledge and skills that come from "the body", i.e. sensorimotor and perceptual skills. (See Where Mathematics Comes From) Knowledge representation: * ACM 1998, I.2.4, * Russell & Norvig 2003, pp. 320–363, * Poole, Mackworth & Goebel 1998, pp. 23–46, 69–81, 169–196, 235–277, 281–298, 319–345, * Luger & Stubblefield 2004, pp. 227–243, * Nilsson 1998, chpt. 18 Knowledge engineering: * Russell & Norvig 2003, pp. 260–266, * Poole, Mackworth & Goebel 1998, pp. 199–233, * Nilsson 1998, chpt. ≈17.1–17.4 Representing categories and relations: Semantic networks, description logics, inheritance (including frames and scripts): * Russell & Norvig 2003, pp. 349–354, * Poole, Mackworth & Goebel 1998, pp. 174–177, * Luger & Stubblefield 2004, pp. 248–258, * Nilsson 1998, chpt. 18.3 Representing events and time:Situation calculus, event calculus, fluent calculus (including solving the frame problem): * Russell & Norvig 2003, pp. 328–341, * Poole, Mackworth & Goebel 1998, pp. 281–298, * Nilsson 1998, chpt. 18.2 Causal calculus: * Poole, Mackworth & Goebel 1998, pp. 335–337 Representing knowledge about knowledge: Belief calculus, modal logics: * Russell & Norvig 2003, pp. 341–344, * Poole, Mackworth & Goebel 1998, pp. 275–277 Sikos, Leslie F. (June 2017). Description Logics in Multimedia Reasoning. Cham: Springer. doi:10.1007/978-3-319-54066-5. ISBN 978-3-319-54066-5. S2CID 3180114. Archived from the original on 29 August 2017. Ontology: * Russell & Norvig 2003, pp. 320–328 Smoliar, Stephen W.; Zhang, HongJiang (1994). "Content based video indexing and retrieval". IEEE Multimedia. 1 (2): 62–72. doi:10.1109/93.311653. S2CID 32710913. Neumann, Bernd; Möller, Ralf (January 2008). "On scene interpretation with description logics". Image and Vision Computing. 26 (1): 82–101. doi:10.1016/j.imavis.2007.08.013. Kuperman, G. J.; Reichley, R. M.; Bailey, T. C. (1 July 2006). "Using Commercial Knowledge Bases for Clinical Decision Support: Opportunities, Hurdles, and Recommendations". Journal of the American Medical Informatics Association. 13 (4): 369–371. doi:10.1197/jamia.M2055. PMC 1513681. PMID 16622160. MCGARRY, KEN (1 December 2005). "A survey of interestingness measures for knowledge discovery". The Knowledge Engineering Review. 20 (1): 39–61. doi:10.1017/S0269888905000408. S2CID 14987656. Bertini, M; Del Bimbo, A; Torniai, C (2006). "Automatic annotation and semantic retrieval of video sequences using multimedia ontologies". MM '06 Proceedings of the 14th ACM international conference on Multimedia. 14th ACM international conference on Multimedia. Santa Barbara: ACM. pp. 679–682. Qualification problem: * McCarthy & Hayes 1969 * Russell & Norvig 2003[page needed] While McCarthy was primarily concerned with issues in the logical representation of actions, Russell & Norvig 2003 apply the term to the more general issue of default reasoning in the vast network of assumptions underlying all our commonsense knowledge. Default reasoning and default logic, non-monotonic logics, circumscription, closed world assumption, abduction (Poole et al. places abduction under "default reasoning". Luger et al. places this under "uncertain reasoning"): * Russell & Norvig 2003, pp. 354–360, * Poole, Mackworth & Goebel 1998, pp. 248–256, 323–335, * Luger & Stubblefield 2004, pp. 335–363, * Nilsson 1998, ~18.3.3 Breadth of commonsense knowledge: * Russell & Norvig 2003, p. 21, * Crevier 1993, pp. 113–114, * Moravec 1988, p. 13, * Lenat & Guha 1989 (Introduction) Dreyfus & Dreyfus 1986. Gladwell 2005. Expert knowledge as embodied intuition: * Dreyfus & Dreyfus 1986 (Hubert Dreyfus is a philosopher and critic of AI who was among the first to argue that most useful human knowledge was encoded sub-symbolically. See Dreyfus' critique of AI) * Gladwell 2005 (Gladwell's Blink is a popular introduction to sub-symbolic reasoning and knowledge.) * Hawkins & Blakeslee 2005 (Hawkins argues that sub-symbolic knowledge should be the primary focus of AI research.) Planning: * ACM 1998, ~I.2.8, * Russell & Norvig 2003, pp. 375–459, * Poole, Mackworth & Goebel 1998, pp. 281–316, * Luger & Stubblefield 2004, pp. 314–329, * Nilsson 1998, chpt. 10.1–2, 22 Information value theory: * Russell & Norvig 2003, pp. 600–604 Classical planning: * Russell & Norvig 2003, pp. 375–430, * Poole, Mackworth & Goebel 1998, pp. 281–315, * Luger & Stubblefield 2004, pp. 314–329, * Nilsson 1998, chpt. 10.1–2, 22 Planning and acting in non-deterministic domains: conditional planning, execution monitoring, replanning and continuous planning: * Russell & Norvig 2003, pp. 430–449 Multi-agent planning and emergent behavior: * Russell & Norvig 2003, pp. 449–455 Turing 1950. Solomonoff 1956. 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Archived from the original on 11 June 2020. Retrieved 11 June 2020. Machine perception: * Russell & Norvig 2003, pp. 537–581, 863–898 * Nilsson 1998, ~chpt. 6 Speech recognition: * ACM 1998, ~I.2.7 * Russell & Norvig 2003, pp. 568–578 Object recognition: * Russell & Norvig 2003, pp. 885–892 Computer vision: * ACM 1998, I.2.10 * Russell & Norvig 2003, pp. 863–898 * Nilsson 1998, chpt. 6 Robotics: * ACM 1998, I.2.9, * Russell & Norvig 2003, pp. 901–942, * Poole, Mackworth & Goebel 1998, pp. 443–460 Moving and configuration space: * Russell & Norvig 2003, pp. 916–932 Tecuci 2012. Robotic mapping (localization, etc): * Russell & Norvig 2003, pp. 908–915 Cadena, Cesar; Carlone, Luca; Carrillo, Henry; Latif, Yasir; Scaramuzza, Davide; Neira, Jose; Reid, Ian; Leonard, John J. (December 2016). "Past, Present, and Future of Simultaneous Localization and Mapping: Toward the Robust-Perception Age". IEEE Transactions on Robotics. 32 (6): 1309–1332. arXiv:1606.05830. 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Retrieved 26 April 2018. Domingos 2015. Artificial brain arguments: AI requires a simulation of the operation of the human brain * Russell & Norvig 2003, p. 957 * Crevier 1993, pp. 271 and 279 A few of the people who make some form of the argument: * Moravec 1988 * Kurzweil 2005, p. 262 * Hawkins & Blakeslee 2005 The most extreme form of this argument (the brain replacement scenario) was put forward by Clark Glymour in the mid-1970s and was touched on by Zenon Pylyshyn and John Searle in 1980. Goertzel, Ben; Lian, Ruiting; Arel, Itamar; de Garis, Hugo; Chen, Shuo (December 2010). "A world survey of artificial brain projects, Part II: Biologically inspired cognitive architectures". Neurocomputing. 74 (1–3): 30–49. doi:10.1016/j.neucom.2010.08.012. Nilsson 1983, p. 10. Nils Nilsson writes: "Simply put, there is wide disagreement in the field about what AI is all about."[163] AI's immediate precursors: * McCorduck 2004, pp. 51–107 * Crevier 1993, pp. 27–32 * Russell & Norvig 2003, pp. 15, 940 * Moravec 1988, p. 3 Haugeland 1985, pp. 112–117 The most dramatic case of sub-symbolic AI being pushed into the background was the devastating critique of perceptrons by Marvin Minsky and Seymour Papert in 1969. See History of AI, AI winter, or Frank Rosenblatt. Cognitive simulation, Newell and Simon, AI at CMU (then called Carnegie Tech): * McCorduck 2004, pp. 139–179, 245–250, 322–323 (EPAM) * Crevier 1993, pp. 145–149 Soar (history): * McCorduck 2004, pp. 450–451 * Crevier 1993, pp. 258–263 McCarthy and AI research at SAIL and SRI International: * McCorduck 2004, pp. 251–259 * Crevier 1993 AI research at Edinburgh and in France, birth of Prolog: * Crevier 1993, pp. 193–196 * Howe 1994 AI at MIT under Marvin Minsky in the 1960s : * McCorduck 2004, pp. 259–305 * Crevier 1993, pp. 83–102, 163–176 * Russell & Norvig 2003, p. 19 Cyc: * McCorduck 2004, p. 489, who calls it "a determinedly scruffy enterprise" * Crevier 1993, pp. 239–243 * Russell & Norvig 2003, p. 363−365 * Lenat & Guha 1989 Knowledge revolution: * McCorduck 2004, pp. 266–276, 298–300, 314, 421 * Russell & Norvig 2003, pp. 22–23 Frederick, Hayes-Roth; William, Murray; Leonard, Adelman. "Expert systems". AccessScience. doi:10.1036/1097-8542.248550. Embodied approaches to AI: * McCorduck 2004, pp. 454–462 * Brooks 1990 * Moravec 1988 Weng et al. 2001. Lungarella et al. 2003. Asada et al. 2009. Oudeyer 2010. Revival of connectionism: * Crevier 1993, pp. 214–215 * Russell & Norvig 2003, p. 25 Computational intelligence * IEEE Computational Intelligence Society Archived 9 May 2008 at the Wayback Machine Hutson, Matthew (16 February 2018). "Artificial intelligence faces reproducibility crisis". Science. pp. 725–726. Bibcode:2018Sci...359..725H. doi:10.1126/science.359.6377.725. Archived from the original on 29 April 2018. Retrieved 28 April 2018. Norvig 2012. Langley 2011. Katz 2012. The intelligent agent paradigm: * Russell & Norvig 2003, pp. 27, 32–58, 968–972 * Poole, Mackworth & Goebel 1998, pp. 7–21 * Luger & Stubblefield 2004, pp. 235–240 * Hutter 2005, pp. 125–126 The definition used in this article, in terms of goals, actions, perception and environment, is due to Russell & Norvig (2003). Other definitions also include knowledge and learning as additional criteria. Agent architectures, hybrid intelligent systems: * Russell & Norvig (2003, pp. 27, 932, 970–972) * Nilsson (1998, chpt. 25) Hierarchical control system: * Albus 2002 Lieto, Antonio; Lebiere, Christian; Oltramari, Alessandro (May 2018). "The knowledge level in cognitive architectures: Current limitations and possibile developments". Cognitive Systems Research. 48: 39–55. doi:10.1016/j.cogsys.2017.05.001. hdl:2318/1665207. S2CID 206868967. Lieto, Antonio; Bhatt, Mehul; Oltramari, Alessandro; Vernon, David (May 2018). "The role of cognitive architectures in general artificial intelligence". Cognitive Systems Research. 48: 1–3. doi:10.1016/j.cogsys.2017.08.003. hdl:2318/1665249. S2CID 36189683. Russell & Norvig 2009, p. 1. White Paper: On Artificial Intelligence - A European approach to excellence and trust (PDF). Brussels: European Commission. 2020. p. 1. Archived (PDF) from the original on 20 February 2020. Retrieved 20 February 2020. CNN 2006. Using AI to predict flight delays Archived 20 November 2018 at the Wayback Machine, Ishti.org. N. Aletras; D. Tsarapatsanis; D. Preotiuc-Pietro; V. Lampos (2016). "Predicting judicial decisions of the European Court of Human Rights: a Natural Language Processing perspective". PeerJ Computer Science. 2: e93. doi:10.7717/peerj-cs.93. "The Economist Explains: Why firms are piling into artificial intelligence". The Economist. 31 March 2016. Archived from the original on 8 May 2016. Retrieved 19 May 2016. Lohr, Steve (28 February 2016). "The Promise of Artificial Intelligence Unfolds in Small Steps". The New York Times. Archived from the original on 29 February 2016. Retrieved 29 February 2016. Frangoul, Anmar (14 June 2019). "A Californian business is using A.I. to change the way we think about energy storage". CNBC. Archived from the original on 25 July 2020. Retrieved 5 November 2019. Wakefield, Jane (15 June 2016). "Social media 'outstrips TV' as news source for young people". BBC News. Archived from the original on 24 June 2016. Smith, Mark (22 July 2016). "So you think you chose to read this article?". BBC News. Archived from the original on 25 July 2016. Brown, Eileen. "Half of Americans do not believe deepfake news could target them online". ZDNet. Archived from the original on 6 November 2019. Retrieved 3 December 2019. The Turing test: Turing's original publication: * Turing 1950 Historical influence and philosophical implications: * Haugeland 1985, pp. 6–9 * Crevier 1993, p. 24 * McCorduck 2004, pp. 70–71 * Russell & Norvig 2003, pp. 2–3 and 948 Dartmouth proposal: * McCarthy et al. 1955 (the original proposal) * Crevier 1993, p. 49 (historical significance) The physical symbol systems hypothesis: * Newell & Simon 1976, p. 116 * McCorduck 2004, p. 153 * Russell & Norvig 2003, p. 18 Dreyfus 1992, p. 156. Dreyfus criticized the necessary condition of the physical symbol system hypothesis, which he called the "psychological assumption": "The mind can be viewed as a device operating on bits of information according to formal rules."[206] Dreyfus' critique of artificial intelligence: * Dreyfus 1972, Dreyfus & Dreyfus 1986 * Crevier 1993, pp. 120–132 * McCorduck 2004, pp. 211–239 * Russell & Norvig 2003, pp. 950–952, Gödel 1951: in this lecture, Kurt Gödel uses the incompleteness theorem to arrive at the following disjunction: (a) the human mind is not a consistent finite machine, or (b) there exist Diophantine equations for which it cannot decide whether solutions exist. Gödel finds (b) implausible, and thus seems to have believed the human mind was not equivalent to a finite machine, i.e., its power exceeded that of any finite machine. He recognized that this was only a conjecture, since one could never disprove (b). Yet he considered the disjunctive conclusion to be a "certain fact". The Mathematical Objection: * Russell & Norvig 2003, p. 949 * McCorduck 2004, pp. 448–449 Making the Mathematical Objection: * Lucas 1961 * Penrose 1989 Refuting Mathematical Objection: * Turing 1950 under "(2) The Mathematical Objection" * Hofstadter 1979 Background: * Gödel 1931, Church 1936, Kleene 1935, Turing 1937 Graham Oppy (20 January 2015). "Gödel's Incompleteness Theorems". Stanford Encyclopedia of Philosophy. Archived from the original on 22 April 2016. Retrieved 27 April 2016. These Gödelian anti-mechanist arguments are, however, problematic, and there is wide consensus that they fail. Stuart J. Russell; Peter Norvig (2010). "26.1.2: Philosophical Foundations/Weak AI: Can Machines Act Intelligently?/The mathematical objection". Artificial Intelligence: A Modern Approach (3rd ed.). Upper Saddle River, NJ: Prentice Hall. ISBN 978-0-13-604259-4. even if we grant that computers have limitations on what they can prove, there is no evidence that humans are immune from those limitations. Mark Colyvan. An introduction to the philosophy of mathematics. Cambridge University Press, 2012. From 2.2.2, 'Philosophical significance of Gödel's incompleteness results': "The accepted wisdom (with which I concur) is that the Lucas-Penrose arguments fail." Iphofen, Ron; Kritikos, Mihalis (3 January 2019). "Regulating artificial intelligence and robotics: ethics by design in a digital society". Contemporary Social Science: 1–15. doi:10.1080/21582041.2018.1563803. ISSN 2158-2041. "Ethical AI Learns Human Rights Framework". Voice of America. Archived from the original on 11 November 2019. Retrieved 10 November 2019. Crevier 1993, pp. 132–144. In the early 1970s, Kenneth Colby presented a version of Weizenbaum's ELIZA known as DOCTOR which he promoted as a serious therapeutic tool.[216] Joseph Weizenbaum's critique of AI: * Weizenbaum 1976 * Crevier 1993, pp. 132–144 * McCorduck 2004, pp. 356–373 * Russell & Norvig 2003, p. 961 Weizenbaum (the AI researcher who developed the first chatterbot program, ELIZA) argued in 1976 that the misuse of artificial intelligence has the potential to devalue human life. Wendell Wallach (2010). Moral Machines, Oxford University Press. Wallach, pp 37–54. Wallach, pp 55–73. Wallach, Introduction chapter. Michael Anderson and Susan Leigh Anderson (2011), Machine Ethics, Cambridge University Press. "Machine Ethics". aaai.org. Archived from the original on 29 November 2014. Rubin, Charles (Spring 2003). "Artificial Intelligence and Human Nature". The New Atlantis. 1: 88–100. Archived from the original on 11 June 2012. Brooks, Rodney (10 November 2014). "artificial intelligence is a tool, not a threat". Archived from the original on 12 November 2014. "Stephen Hawking, Elon Musk, and Bill Gates Warn About Artificial Intelligence". Observer. 19 August 2015. Archived from the original on 30 October 2015. Retrieved 30 October 2015. Chalmers, David (1995). "Facing up to the problem of consciousness". Journal of Consciousness Studies. 2 (3): 200–219. Archived from the original on 8 March 2005. Retrieved 11 October 2018. See also this link Archived 8 April 2011 at the Wayback Machine Horst, Steven, (2005) "The Computational Theory of Mind" Archived 11 September 2018 at the Wayback Machine in The Stanford Encyclopedia of Philosophy Searle 1980, p. 1. This version is from Searle (1999), and is also quoted in Dennett 1991, p. 435. Searle's original formulation was "The appropriately programmed computer really is a mind, in the sense that computers given the right programs can be literally said to understand and have other cognitive states." [230] Strong AI is defined similarly by Russell & Norvig (2003, p. 947): "The assertion that machines could possibly act intelligently
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SOYJUN / Application With Raw IP SocketsOverview For this assignment you will be developing an application that uses raw IP sockets to ‘walk’ around an ordered list of nodes (given as a command line argument at the ‘source’ node, which is the node at which the tour was initiated), in a manner similar to the IP SSRR (Strict Source and Record Route) option. At each node, the application pings the preceding node in the tour. However, unlike the ping code in Stevens, you will be sending the ping ICMP echo request messages through a SOCK_RAW-type PF_PACKET socket and implementing ARP functionality to find the Ethernet address of the target node. Finally, when the ‘walk’ is completed, the group of nodes visited on the tour will exchange multicast messages. Your code will consist of two process modules, a ‘Tour’ application module (which will implement all the functionality outlined above, except for ARP activity) and an ARP module. The following should prove to be useful reference material for the assignment: Sections 21.2, 21.3, 21.6 and 21.10, Chapter 21, on Multicasting. Sections 27.1 to 27.3, Chapter 27, on the IP SSRR option. Sections 28.1 to 28.5, Chapter 28, on raw sockets, the IP_HDRINCL socket option, and ping. Sections 15.5, Chapter 15, on Unix domain SOCK_STREAM sockets. Figure 29.14, p. 807, and the corresponding explanation on p. 806, on filling in an IP header when the IP_HDRINCL socket option is in effect. The Lecture Slides on ARP & RARP (especially Section 4.4, ARP Packet Format, and the Figure 4.3 it includes). The link http://www.pdbuchan.com/rawsock/rawsock.html contains useful code samples that use IP raw sockets and PF_PACKET sockets. Note, in partcular, the code “icmp4_ll.c” in Table 2 for building an echo request sent through a PF_PACKET SOCK_RAW socket. The VMware environment You will be using the same vm1 , . . . . . , vm10 nodes you used for Assignment 3. However, unlike Assignment 3, you should use only interfaces eth0 and their associated IP addresses and ignore the other Ethernet interfaces that nodes have (interfaces eth0 make vm1 , . . . . . , vm10 look as if they belong to the same Ethernet LAN segment IP network 130.245.156.0/24). Note that, apart from the primary IP addresses associated with interfaces eth0, some nodes might also have one or more alias IP addresses associated with their interface eth0. Tour application module specifications The application will create a total of four sockets: two IP raw sockets, a PF_PACKET socket and a UDP socket for multicasting. We shall call the two IP raw sockets the ‘rt ’ (‘route traversal’) and ‘pg ’ (‘ping’) sockets, respectively. The rt socket should have the IP_HDRINCL option set. You will only be receiving ICMP echo reply messages through the pg socket (and not sending echo requests), so it does not matter whether it has the IP_HDRINCL option set or not. The pg socket should have protocol value (i.e., protocol demultiplexing key in the IP header) IPPROTO_ICMP. The rt socket should have a protocol value that identifies the application - i.e., some value other than the IPPROTO_XXXX values in /usr/include/netinet/in.h. However, remember that you will all be running your code using the same root account on the vm1 , . . . . . , vm10 nodes. So if two of you happen to choose the same protocol value and happen to be running on the same vm node at the same time, your applications will receive each other’s IP packets. For that reason, try to choose a protocol value for your rt socket that is likely to be unique to yourself. The PF_PACKET socket should be of type SOCK_RAW (not SOCK_DGRAM). This socket should have a protocol value of ETH_P_IP = 0x0800 (IPv4). The UDP socket for multicasting will be discussed below. Note that, depending on how you choose to bind that socket, you might actually need to have two UDP sockets for multicast communication – see bottom of p. 576, Section 21.10. Your application will, of course, have to be running on every vm node that is included in the tour. When evoking the application on the source node, the user supplies a sequence of vm node names (not IP addresses) to be visited in order. This command line sequence starts with the next node to be visited from the source node (i.e., it does not start with the source node itself). The sequence can include any number of repeated visits to the same node. For example, suppose that the source node is vm3 and the executable is called badr_tour : [root@vm3/root]# badr_tour vm2 vm10 vm4 vm7 vm5 vm2 vm6 vm2 vm9 vm4 vm7 vm2 vm6 vm5 vm1 vm10 vm8 (but note that the tour does not necessarily have to visit every vm node; and the same node should not appear consequentively in the tour list – i.e., the next node on the tour cannot be the current node itself). The application turns the sequence into a list of IP addresses for source routing. It also adds the IP address of the source node itself to the beginning of the list. The list thus produced will be carried as the payload of an IP packet, not as a SSRR option in the packet header. It is our application which will ensure that every node in the sequence is visited in order, not the IP SSRR capability. The source node should also add to the list an IP multicast address and a port number of its choice. It should also join the multicast group at that address and port number on its UDP socket. The TTL for outgoing multicasts should be set to 1. The application then fills in the header of an IP packet, designating itself as the IP source, and the next node to be visited as the IP destination. The packet is sent out on the rt socket. Note that on Linux, all the fields of the packet header must be in network byte order (Stevens, Section 28.3, p. 737, the fourth bullet point). When filling in the packet header, you should explicitly fill in the identification field (recall that, with the IP_HDRINCL socket option, if the identification field is given value 0, then the kernel will set its value). Try to make sure that the value you choose is likely to be unique to yourself (for reasons similar to those explained with respect to the IPPROTO_XXXX in 1. above). When a node receives an IP packet on its rt socket, it should first check that the identification field carries the right value (this implies that you will hard code your choice of identification field value determined in item 2 above in your code). If the identification field value does not check out, the packet is ignored. For a valid packet : Print out a message along the lines of: <time> received source routing packet from <hostname> <time> is the current time in human-readable format (see lines 19 & 20 in Figure 1.9, p. 14, and the corresponding explanation on p. 14f.), and <hostname> is the host name corresponding to the source IP address in the header of the received packet. If this is the first time the node is visited, the application should use the multicast address and port number in the packet received to join the multicast group on its UDP socket. The TTL for outgoing multicasts should be set to 1. The application updates the list in the payload, so that the next node in the tour can easily identify what the next hop from itself will be when it receives the packet. How you do this I leave up to you. You could, for example, include as part of the payload a pointer field into the list of nodes to be visited. This pointer would then be updated to the next entry in the list as the packet progresses hop by hop (see Figure 27.1 and the associated explanation on pp. 711-712). Other solutions are, of course, possible. The application then fills in a new IP header, designating itself as the IP source, and the next node to be visited as the IP destination. The identification field should be set to the same value as in the received packet. The packet is sent out on the rt socket. The node should also initiate pinging to the preceding node in the tour (the IP address of which it should pick up from the header of the received packet). However, unlike the Stevens ping code, it will be using the SOCK_RAW-type PF_PACKET socket of item 1 above to send the ICMP echo request messages. Before it can send echo request messages, the application has to call on the ARP module you will implement to get the Ethernet address of this preceding / ‘target’ node; this call is made using the API function areq which you will also implement (see sections ARP module specifications & API specifications below). Note that ARP has to be evoked every time the application wants to send out an echo request message, and not just the first time. An echo request message has to be encapsulated in a properly-formulated IP packet, which is in turn encapsulated in a properly-formulated Ethernet frame transmitted out through the PF_PACKET socket ; otherwise, ICMP at the source node will not receive it. You will have to modify Stevens’ ping code accordingly, specifically, the send_v4 function. In particular, the Ethernet frame must have a value of ETH_P_IP = 0x0800 (IPv4 – see <linux/if_ether.h>) in the frame type / ‘length’ field ; and the encapsulated IP packet must have a value of IPPROTO_ICMP = 0x01 (ICMPv4 – see <netinet_in.h>) in its protocol field. You should also simplify the ping code in its entirety by stripping all the ‘indirection’ IPv4 / IPv6 dual-operability paraphernalia and making the code work just for IPv4. Also note that the functions host_serv and freeaddrinfo, together with the associated structure addrinfo (see Sections 11.6, 11.8 & 11.11), in Figures 27.3, 27.6 & 28.5 ( pp. 713, 716 & 744f., respectively) can be replaced by the function gethostbyname and associated structure hostent (see Section 11.3) where needed. Also, there is no ‘-v’ verbose option, so this too should be stripped from Stevens’ code. When a node is ready to start pinging, it first prints out a ‘PING’ message similar to lines 32-33 of Figure 28.5, p. 744. It then builds up ICMP echo request messages and sends them to the source node every 1 second through the PF_PACKET socket. It also reads incoming echo response messages off the pg socket, in response to which it prints out the same kind of output as the code of Figure 28.8, p. 748. If this node and its preceding node have been previously visited in that order during the tour, then pinging would have already been initiated from the one to the other in response to the first visit, and nothing further should nor need be done during second and subsequent visits. In light of the above, note that once a node initiates pinging, it needs to read from both its rt and pg sockets, necessitating the use of the select function. As will be clear from what follows below, the application will anyway be needing also to simultaneously monitor its UDP socket for incoming multicast datagrams. When the last node on the tour is reached, and if this is the first time it is visited, it joins the multicast group and starts pinging the preceding node (if it is not already doing so). After a few echo replies are received (five, say), it sends out the multicast message below on its UDP socket (i.e., the node should wait about five seconds before sending the multicast message) : <<<<< This is node vmi . Tour has ended . Group members please identify yourselves. >>>>> where vmi is the name (not IP address) of the node. The node should also print this message out on stdout preceded, on the same line, by the phrase: Node vmi . Sending: <then print out the message sent>. Each node vmj receiving this message should print out the message received preceded, on the same line, by the phrase: Node vmj . Received <then print out the message received>. Each such node in step a above should then immediately stop its pinging activity. The node should then send out the following multicast message: <<<<< Node vmj . I am a member of the group. >>>>> and print out this message preceded, on the same line, by the phrase: Node vmj . Sending: <then print out the message sent>. Each node receiving these second multicast messages (i.e., the messages that nodes – including itself – sent out in step c above) should print each such message out preceded, on the same line, by the phrase: Node vmk . Received: <then print out the message received>. Reading from the socket in step d above should be implemented with a 5-second timeout. When the timeout expires, the node should print out another message to the effect that it is terminating the Tour application, and gracefully exit its Tour process. Note that under Multicast specifications, the last node in the tour, which sends out the End of Tour message, should itself receive a copy of that message and, when it does, it should behave exactly as do the other nodes in steps a. – e. above. ARP module specifications Your executable is evoked with no command line arguments. Like the Tour module, it will be running on every vm node. It uses the get_hw_addrs function of Assignment 3 to explore its node’s interfaces and build a set of <IP address , HW address> matching pairs for all eth0 interface IP addresses (including alias IP addresses, if any). Write out to stdout in some appropriately clear format the address pairs found. The module creates two sockets: a PF_PACKET socket and a Unix domain socket. The PF_PACKET should be of type SOCK_RAW (not type SOCK_DGRAM) with a protocol value of your choice (but not one of the standard values defined in <linux/if_ether.h>) which is, hopefully, unique to yourself. This value effectively becomes the protocol value for your implementation of ARP. Because this protocol value will be carried in the frame type / ‘length’ field of the Ethernet frame header (see Figure 4.3 of the ARP & RARP handout), the value chosen should be not less than 1536 (0x600) so that it is not misinterpreted as the length of an Ethernet 802.3 frame. The Unix domain socket should be of type SOCK_STREAM (not SOCK_DGRAM). It is a listening socket bound to a ‘well-known’ sun_path file. This socket will be used to communicate with the function areq that is implemented in the Tour module (see the section API specifications below). In this context, areq will act as the client and the ARP module as the server. The ARP module then sits in an infinite loop, monitoring these two sockets. As ARP request messages arrive on the PF_PACKET socket, the module processes them, and responds with ARP reply messages as appropriate. The protocol builds a ‘cache’ of matching <IP address , HW address> pairs from the replies (and requests – see below) it receives. For simplicity, and unlike the real ARP, we shall not implement timing out mechanisms for these cache entries. A cache entry has five parts: (i) IP address ; (ii) HW address ; (iii) sll_ifindex (the interface to be used for reaching the matching pair <(i) , (ii)>) ; (iv) sll_hatype ; and (v) a Unix-domain connection-socket descriptor for a connected client (see the section API specifications below for the latter three). When an ARP reply is being entered in the cache, the ARP module uses the socket descriptor in (v) to send a reply to the client, closes the connection socket, and deletes the socket descriptor from the cache entry. Note that, like the real ARP, when an ARP request is received by a node, and if the request pertains to that receiving node, the sender’s (see Figure 4.3 of the ARP & RARP handout) <IP address, HW address> matching pair should be entered into the cache if it is not already there (together, of course, with (iii) sll_ifindex & (iv) sll_hatype), or updated if need be if such an entry already exists in the cache. If the ARP request received does not pertain to the node receiving it, but there is already an entry in that receiving node's cache for the sender’s <IP address, HW address> matching pair, that entry should be checked and updated if need be. If there is no such entry, no action is taken (in particular, and unlike the case above, no new entry should be made in the receiving node's cache of the sender’s <IP address, HW address> matching pair if such an entry does not already exist). ARP request and reply messages have the same format as Figure 4.3 of the ARP & RARP handout, but with an extra 2-byte identification field added at the beginning which you fill with a value chosen so that it has a high probability of being unique to yourself. This value is to be echoed in the reply message, and helps to act as a further filter in case some other student happens to have fortuitously chosen the same value as yourself for the protocol parameter of the ARP PF_PACKET. Values in the fields of our ARP messages must be in network byte order. You might find the system header file <linux/if_arp.h> useful for manipulating ARP request and reply messages, but remember that our version of these messages have an extra two-byte field as mentioned above. Your code should print out on stdout, in some appropriately clear format, the contents of the Ethernet frame header and ARP request message you send. As described in Section 4.4 of the ARP & RARP handout, the node that responds to the request should, in its reply message, swap the two sender addresses with the two target addresses, as well as, of course, echo back the extra identification field sent with the request. The protocol at this responding node should print out, in an appropriately clear format, both the request frame (header and ARP message) it receives and the reply frame it sends. Similarly, the node that sent the request should print out the reply frame it receives. Finally, recall that the node issuing the request sends out a broadcast Ethernet frame, but the responding node replies with a unicast frame. API specifications The API is for communication between the Tour process and the ARP process. It consists of a single function, areq, implemented in the Tour module. areq is called by send_v4 function of the application every time the latter want to send out an ICMP echo request message: int areq (struct sockaddr *IPaddr, socklen_t sockaddrlen, struct hwaddr *HWaddr); IPaddr contains the primary or alias IPaddress of a ‘target’ node on the LAN for which the corresponding hardware address is being requested. hwaddr is a new structure (and not a pre-existing type) modeled on the sockaddr_ll of PF_PACKET; you will have to declare it in your code. It is used to return the requested hardware address to the caller of areq : structure hwaddr { int sll_ifindex; /* Interface number */ unsigned short sll_hatype; /* Hardware type */ unsigned char sll_halen; /* Length of address */ unsigned char sll_addr[8]; /* Physical layer address */ }; areq creates a Unix domain socket of type SOCK_STREAM and connects to the ‘well-known’ sun_path file of the ARP listening socket. It sends the IP address from parameter IPaddr and the information in the three fields of parameter HWaddr to ARP. It then blocks on a read awaiting a reply from ARP. This read should be backed up by a timeout since it is possible that no reply is received for the request. If a timeout occurs, areq should close the socket and return to its caller indicating failure (through its int return value). Your application code should print out on stdout, in some appropriately clear format, a notification every time areq is called, giving the IP address for which a HW address is being sought. It should similarly print out the result when the call to areq returns (HW address returned, or failure). When the ARP module receives a request for a HW address from areq through its Unix domain listening socket, it first checks if the required HW address is already in the cache. If so, it can respond immediately to the areq and close the Unix domain connection socket. Else : it makes an ‘incomplete’ entry in the cache, consisting of parts (i), (iii), (iv) and (v) ; puts out an ARP request message on the network on its PF_PACKET socket; and starts monitoring the areq connection socket for readability – if the areq client closes the connection socket (this would occur in response to a timeout in areq), ARP deletes the corresponding incomplete entry from the cache (and ignores any subsequent ARP reply from the network if such is received). On the other hand, if ARP receives a reply from the network, it updates the incomplete cache entry, responds to areq, and closes the connection socket.
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