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
Textual case-based reasoning
Textual case-based reasoning (TCBR) is a subtopic of case-based reasoning, in short CBR, a popular area in artificial intelligence. CBR suggests the ways to use past experiences to solve future similar problems, requiring that past experiences be structured in a form similar to attribute-value pairs. This leads to the investigation of textual descriptions for knowledge exploration whose output will be, in turn, used to solve similar problems. == Subareas == Textual case-base reasoning research has focused on: measuring similarity between textual cases mapping texts into structured case representations adapting textual cases for reuse automatically generating representations.
The Quantum Thief
The Quantum Thief is the debut science fiction novel by Finnish writer Hannu Rajaniemi and the first novel in a trilogy featuring the character of Jean le Flambeur; the sequels are The Fractal Prince (2012) and The Causal Angel (2014). The novel was published in Britain by Gollancz in 2010, and by Tor in 2011 in the US. It is a heist story, set in a futuristic Solar System, that features a protagonist modeled on Arsène Lupin, the gentleman thief of Maurice Leblanc. The novel was nominated for the 2011 Locus Award for Best First Novel, and was second runner-up for the 2011 Campbell Memorial Award. == Setting == Several centuries after the technological singularity largely destroyed Earth, various posthuman factions compete for dominance in the Solar System. Though sentient superintelligent AGI has never been successfully developed, civilization has been greatly transformed by the proliferation of Hansonian brain emulations (termed "gogols" in reference to Nikolai Gogol, and in particular his novel Dead Souls). An alliance of powerful gogol copies rule the inner system from computronium megastructures housing trillions of virtual minds, laboring to resurrect the dead in religious devotion to the philosophy of Nikolai Fedorov. This alliance, the Sobornost, has been in conflict with a community of quantum entangled minds who adhere to the "no-cloning" principle of quantum information theory, and so do not see the Sobornost's ultimate goal as resurrection, but death. Most of this community, the Zoku, was devastated when Jupiter was destroyed with a weaponized gravitational singularity. Among the last remnants of near-baseline humanity exist on the mobile cities of Mars, where advanced cryptography and an obsessive privacy culture ensure that the Sobornost cannot upload their citizens' minds. The most notable of these cities is the Oubliette, where time is used as a currency. When a citizen's balance reaches zero their mind is transferred to a robotic body to serve the needs of the city for a set period, before being returned to their original body with a restored balance of time. == Plot summary == Countless gogols of the legendary gentleman thief Jean Le Flambeur are trapped in a virtual Sobornost prison in orbit around Neptune, playing an iterated prisoner's dilemma until his mind learns to cooperate. A warrior from the Oort Cloud, which has been settled by Finnish colonists, successfully retrieves one of the Le Flambeur gogols and uploads it into a real-space body. Acting on behalf of a competing Sobornost authority, this Oortian, Mieli, ferries the thief to the Martian city known as The Oubliette, where he has stored his memories for later recovery. The two intend to recover his memories so that he may return to an operating capacity sufficient to serve his Sobornost benefactor in a theft and repay his liberation. On the Oubliette, the young detective Isidore Beautrelet helps vigilantes catch Sobornost agents illicitly uploading human minds. These vigilantes are revealed to be in the service of a local colony of Zoku. Beautrelet is employed to investigate the arrival of Le Flambeur, and in the process becomes aware that the Oubliette's cryptographic security was always compromised. The memories of its citizens are fabrications, and the "King of Mars" long believed ousted in a revolution, still reigns behind the scenes. This King, who is another copy of Jean Le Flambeur, is defeated in the ensuing conflict. Le Flambeur fails to recover all of his memories, which he had locked with a quantum entangled revolver that required him to kill several of his old friends to open his stored memory. He and Mieli escape a liberated Mars having recovered only a mysterious "Schrödinger’s Box" from the Memory Palace. == Themes == Themes central to The Quantum Thief are the unreliability and malleability of memory and the effects of extreme longevity on an individual's perspective and personality. Prisons, surveillance and control in society are also major themes. In the book, the people living in the Oubliette society on Mars have two types of memory; in addition to a traditional, personal memory, there is the exomemory, which can be accessed by other people, from anywhere in the city. Memories about personal experiences can be stored in the exomemory and partitioned, with different levels of access granted to different people. These memories can be used, among other things, as an expedient form of communication. The Oubliette society has an economy where time is used as currency. When an individual's time is expended, their consciousness is uploaded into a "Quiet". The Quiet are mute machine servants who maintain and protect the city. Although the quiet seem to have little interest in the world outside their occupations, they do seem to retain some traces of their former personalities and memories. The conspiracy central to the plot involves the hidden rulers, called the "cryptarchs", manipulating and abusing the exomemory and through the citizens' transformations to quiet and back, the traditional memory as well. In the book, the Oubliette society is compared to a panopticon; a prison, where every action of the dwellers can be scrutinized. == History and influences == The first chapter of The Quantum Thief was presented by Rajaniemi's literary agent, John Jarrold, to Gollancz as the basis for the three-book deal that was eventually secured. Rajaniemi has stated that he had "come up with an outline that had every single idea I could cram into it, because I wanted to be worthy of what had happened." The outline eventually expanded into three parts, and the first part became The Quantum Thief. The novel's plot was inspired by one of Rajaniemi's favorite characters in fiction, Maurice Leblanc's gentleman thief Arsène Lupin, who operates on both sides of the law. What intrigued Rajaniemi were the cycles of redemption and relapse Lupin goes through as he tries to go straight, always falling short. Besides LeBlanc, Rajaniemi mentioned Roger Zelazny as a strong influence. Ian McDonald was the other science fiction author he mentioned as influential, plus Frances A.Yates's book The Art of Memory, for memory palaces. In an interview, Rajaniemi said he wasn't trying to write the novel as hard science fiction: "For me, the more important consequence of having a scientific background is a degree of speculative rigour: trying hard to work out the consequences of the assumptions one begins with." == Reception == The novel has received generally positive reviews. Gary K. Wolfe writes in his Locus review that Rajaniemi has "spectacularly delivered on the promise that this is likely the most important debut SF novel we'll see this year". James Lovegrove, reviewing the book in his Financial Times column, notes that "many an anglophone author would kill to turn out prose half as good as this, especially on their maiden effort." Eric Brown, reviewing for The Guardian, finds the novel to be "a brilliant debut", while alluding to the "apocryphal" (and incorrect) myth that "this novel sold on the strength of its first line." Sam Bandah, at SciFiNow, praises the novel for "its engaging narrative and characters backed by often almost intimidatingly good sci-fi concepts." Criticism for the novel has generally centred on Rajaniemi's sparse "show, don't tell" writing style. Brown notes that "the author makes no concessions to the lazy reader with info-dumps or convenient explanations." Niall Alexander, of the Speculative Scotsman, states that "had there been some sort of index, [he] would have gladly (and repeatedly) referred to it during the mind-boggling first third of The Quantum Thief", while proclaiming the novel to be "the sci-fi debut of 2010." == Awards == Nominee for the 2011 Locus Award for Best First Novel. Third place for the 2011 John W. Campbell Memorial Award for Best Science Fiction Novel
Transhuman Space
Transhuman Space (THS) is a role-playing game by David Pulver, published by Steve Jackson Games as part of the "Powered by GURPS" (Generic Universal Role-Playing System) line. Set in the year 2100, humanity has begun to colonize the Solar System. The pursuit of transhumanism is now in full swing, as more and more people reach fully posthuman states. In 2002, the Transhuman Space adventure "Orbital Decay" received an Origins Award nomination for Best Role-Playing Game Adventure. Transhuman Space won the 2003 Grog d'Or Award for Best Role-playing Game, Game Line or RPG Setting. == Setting == The game assumes that no cataclysm — natural or human-induced — swept Earth in the 21st century. Instead, constant developments in information technology, genetic engineering, nanotechnology and nuclear physics generally improved condition of the average human life. Plagues of the 20th century (like cancer or AIDS) have been suppressed, the ozone layer is being restored and Earth's ecosystems are recovering (although thermal emission by fusion power plants poses an environmental threat—albeit a much lesser one than previous sources of energy). Thanks to modern medicine humans live biblical timespans surrounded by various artificially intelligent helper applications and robots (cybershells), sensory experience broadcasts (future TV) and cyberspace telepresence. Thanks to cheap and clean fusion energy humanity has power to fuel all these wonders, restore and transform its home planet and finally settle on other heavenly bodies. Human genetic engineering has advanced to the point that anyone—single individuals, same-sex couples, groups of three or more—can reproduce. The embryos can be allowed to be developed naturally, or they can undergo three levels of tinkering: 1. Genefixing, which corrects defects; 2. Upgrades, which boost natural abilities (Ishtar Upgrades are slightly more attractive than usual, Metanoia Upgrades are more intelligent, etc.); and... 3. Full transition to parahuman status (Nyx Parahumans only need a few hours of sleep per week, Aquamorphs can live underwater, etc.) Another type of human genetic engineering, far more controversial, is the creation of bioroids, fully sentient slave races. People can "upload" by recording the simulation of their brains on computer disks. The emulated individual then becomes a ghost, an infomorph very easily confused with "sapient artificial intelligence". However, this technology has several problems as the solely available "brainpeeling" technique is fatal to the original biological lifeform being simulated, has a significant failure rate and the philosophical questions regarding personal identity remain equivocal. Any infomorph, regardless of its origin, can be plugged into a "cybershell" (robotic or cybernetic body), or a biological body, or "bioshell". Or, the individual can illegally make multiple "xoxes", or copies of themselves, and scatter them throughout the system, exponentially increasing the odds that at least one of them will live for centuries more, if not forever. This is also a time of space colonization. First, humanity (specifically China, followed by the United States and others) colonized Mars in a fashion resembling that outlined in the Mars Direct project. The Moon, Lagrangian points, inner planets and asteroids soon followed. In the late 21st century even some of Saturn's moons have been settled as a base for that planet's Helium-3 scooping operations. Transhuman Space's setting is neither utopia nor dystopia, however: several problems have arisen from these otherwise beneficial developments. The generation gap has become a chasm as lifespans increase. No longer do the elite fear death, and no longer can the young hope to replace them. While it seemed that outworld colonies would offer accommodation and work for those young ones, they are being replaced by genetically tailored bioroids and AI-powered cybershells. The concept of humanity is no longer clear in a world where even some animals speak of their rights and the dead haunt both cyberspace and reality (in form of infomorph-controlled bioshells or cybershells). And the wonders of high science are not universally shared — some countries merely struggle with informatization while others suffer from nanoplagues, defective drugs, implants and software tested on their populace. In some poor countries high-tech tyrants oppress their backward people. And in outer space all sort of modern crime thrives, barely suppressed by military forces. == Publication history == After the initial set of GURPS books that were published using the GURPS Lite, later publications such as Transhuman Space by David Pulver were labelled simply "Powered by GURPS" without using the name "GURPS" in the book title. Transhuman Space received a significant amount of supporting publications, and was the largest original background setting that Steve Jackson Games produced in 15 years. Shannon Appelcline noted that by its inclusion of posthuman characters, the book began to show the limits of the GURPS system as it was, which is something that Pulver would address soon thereafter. Steve Jackson Games has not updated the core book (GURPS Transhuman Space) to 4th edition, although the supplement Transhuman Space: Changing Times provides a path for migrating to 4th edition. It has produced several 4th edition supplements for the setting: Transhuman Space: Bioroid Bazaar, Transhuman Space: Cities on the Edge, Transhuman Space: Martial Arts 2100, Transhuman Space: Personnel Files 2-5, Transhuman Space: Shell-Tech, GURPS Spaceships 8: Transhuman Spacecraft, Transhuman Space: Transhuman Mysteries, and Transhuman Space: Wings of the Rising Sun. == Reception == In a review of Transhuman Space in Black Gate, William Stoddard said "Transhuman Space was a richly detailed setting; if it had imperfections, it had enough depth to make up for them. I think it has the potential to become a classic in its field. Perhaps a campaign set in its default start year of 2100 could leave the early twenty-first century blurry enough to avoid obvious incongruities." == Reviews == Review in Vol. 20, No. 1 of Prometheus, the journal of the Libertarian Futurist Society.
Megami Tensei
Megami Tensei, marketed internationally as Shin Megami Tensei (formerly Revelations), is a Japanese media franchise created by Aya Nishitani, Kouji "Cozy" Okada, Ginichiro Suzuki, and Kazunari Suzuki. Primarily developed and published by Atlus, the franchise consists of multiple subseries and covers multiple role-playing video game genres including tactical role-playing, action role-playing, and massively multiplayer online role-playing. The first two titles in the series were published by Namco (now Bandai Namco Entertainment), but have been almost always published by Atlus in Japan and North America since the release of Shin Megami Tensei. For Europe, Atlus publishes the games through third-party companies. The series was originally based on Digital Devil Story, a science fiction novel series by Aya Nishitani. The series takes its name from the first book's subtitle. Most Megami Tensei titles are stand-alone entries with their own stories and characters. Recurring elements include plot themes, a story shaped by the player's choices, and the ability to fight using and often recruit creatures (demons, Personas) to aid the player in battle. Elements of philosophy, religion, occultism, and science fiction have all been incorporated into the series at different times. While not maintaining as high a profile as series such as Final Fantasy and Dragon Quest, it is highly popular in Japan and maintains a strong cult following in the West, finding critical and commercial success. The series has become well known for its artistic direction, challenging gameplay, and music, but raised controversy over its mature content, dark themes, and use of Christian religious imagery. Additional media include manga adaptations, anime films, and television series. In Japan, some games in the series do not use the "Megami Tensei" title, such as the Persona sub-series. Many of the early games in the series were not localized due to potentially controversial content including religious references, and later due to their age. English localizations have used the "Shin Megami Tensei" moniker since the release of Shin Megami Tensei: Nocturne in 2004. == Titles == === Games === The first installment in the franchise, Digital Devil Story: Megami Tensei, was released on September 11, 1987. The following entries have nearly always been unrelated to each other except in carrying over thematic and gameplay elements. The Megami Tensei games, and the later Shin Megami Tensei titles form the core of the series, while other subseries such as Persona, Devil Children, and Devil Summoner are spin-offs marketed as part of the franchise. There are also stand-alone spin-off titles. ==== Main series ==== Two entries were released for the Famicom: Digital Devil Story: Megami Tensei in 1987, and Digital Devil Story: Megami Tensei II in 1990. The two titles are unrelated to each other in terms of story, and each introduced the basic gameplay and story mechanics that would come to define the series. Three entries were released for the Super Famicom: Shin Megami Tensei in 1992, followed byShin Megami Tensei II in 1994, and Shin Megami Tensei If..., released later in the same year. Shin Megami Tensei III: Nocturne was released in 2003 for the PlayStation 2. Its Maniax Edition director's cut was released in Japan and North America in 2004, and in Europe in 2005. The numeral was dropped for its North American release, and its title changed to Shin Megami Tensei: Lucifer's Call in Europe. Shin Megami Tensei IV for the Nintendo 3DS was released in 2013 in Japan and North America, and a year later in Europe as a digital-only release. Another game set in the same universe, Shin Megami Tensei IV: Apocalypse, was released for the 3DS in February 2016 in Japan. Shin Megami Tensei V was released on the Nintendo Switch in 2021. An enhanced version of the game titled Shin Megami Tensei V: Vengeance was released in June 2024 for Microsoft Windows, Nintendo Switch, PlayStation 4, PlayStation 5, Xbox One and Xbox Series X/S. In addition to the main series, there are also numerous spin-offs. Shin Megami Tensei: Nine, was released for the Xbox in 2002. Originally designed as a massively multiplayer online role-playing game (MMORPG), it was later split into a dual single-player and multiplayer package, and the single-player version released first. The online version was delayed and eventually cancelled as the developers could not manage the required online capacities using Xbox Live. Shin Megami Tensei: Imagine, a true MMOROG released for Microsoft Windows, was released in 2007 in Japan, 2008 in North America, and 2009 in Europe. Western service was terminated in 2014 when Marvelous USA, the game's then-handlers, shut down their PC Online game department. Shin Megami Tensei: Strange Journey was released for the Nintendo DS in 2009 in Japan and 2010 in North America. Its Japanese service ended in May 2016. A smartphone game, Shin Megami Tensei: Liberation Dx2, was released in 2018. ==== Persona ==== The Persona series is the largest and most popular spin-off from the Megami Tensei series. The first entry in the series, Megami Ibunroku Persona (originally released overseas as Revelations: Persona), was released in 1996 in Japan and North America. The first Persona 2 title, Innocent Sin, was released in 1999 in Japan. The second game, Eternal Punishment, was released in 2000 in Japan and North America. Persona 3 was released in 2006 in Japan, 2007 in North America, and 2008 in Europe. Its sequel, Persona 4, was released in 2008 in Japan and North America, and in 2009 in Europe. A sixth entry in the series, Persona 5, was released in Japan on September 15, 2016, and was released in North America and Europe on April 4, 2017, to critical acclaim. The series also features spin-offs, including Persona Q: Shadow of the Labyrinth and Persona Q2: New Cinema Labyrinth, two fighting games Persona 4 Arena and its sequel Arena Ultimax as well as the crossover fighting game BlazBlue: Cross Tag Battle, tactical role-playing game Persona 5 Tactica, action role-playing game Persona 5 Strikers and rhythm games Persona 4: Dancing All Night, Persona 3: Dancing in Moonlight, and Persona 5: Dancing in Starlight. While Persona 3 and 4 used the Shin Megami Tensei moniker in the West, it was dropped for the Persona 4 Arena duology and Persona 4 Golden as it would have made the titles too long to be practical. ==== Devil Summoner ==== The Devil Summoner subseries began in 1995 with the release of Shin Megami Tensei: Devil Summoner. It was followed by Devil Summoner: Soul Hackers in 1997, then followed by Soul Hackers 2, released in 2022. Two action role-playing prequels set in 1920s Tokyo were also developed, which revolve around demon summoner Raidou Kuzunoha: Raidou Kuzunoha vs. the Soulless Army was released in 2006, and Raidou Kuzunoha vs. King Abaddon was released in 2008. ==== Other spin-offs ==== Aside from Persona and Devil Summoner, there are other spin-off series covering multiple genres. After the release of Shin Megami Tensei II, Atlus began focusing work on building spin-offs and subseries that would form part of the Megami Tensei franchise. Shortly after Nocturne's release, a duology titled Digital Devil Saga (Digital Devil Saga: Avatar Tuner in Japan) was created based around similar systems to Nocturne, and was also intended as a more accessible gaming experience. Two tactical role-playing games have been developed by Atlus for the DS under the Devil Survivor moniker: the original Devil Survivor and Devil Survivor 2. Both have received expanded ports for the 3DS. Other subseries include Last Bible, a series aimed at a younger audience and using a pure fantasy setting; Devil Children, which was inspired by the popular Pokémon series; and Majin Tensei, a series of strategy games. Two notable stand-alone spin-offs are action spin-off Jack Bros. and Tokyo Mirage Sessions ♯FE, a crossover with Intelligent Systems' Fire Emblem series. === Related media === Several titles in the franchise have received anime and manga adaptations. Persona 3 received both a four-part theatrical adaptation (#1 Spring of Birth, #2 Midsummer Knight's Dream, #3 Falling Down, #4 Winter of Rebirth), and a spin-off series titled Persona: Trinity Soul. Persona 4 received two adaptations: Persona 4: The Animation, based on the original game, and Persona 4: The Golden Animation, based on its expanded PlayStation Vita port. A live-action television series based on the original Devil Summoner was broadcast between 1997 and 1998. Devil Survivor 2 also received an anime adaptation of the same name, and the Devil Children series received two anime adaptations. Multiple Shin Megami Tensei and Persona titles have received manga and CD drama adaptations. Action figures and merchandise related to Persona have also been produced. == Common elements == Despite most games in the series taking place in different continuities, they do share certain elements
Lexical choice
Lexical choice is the subtask of Natural language generation that involves choosing the content words (nouns, non-auxiliary verbs, adjectives, and adverbs) in a generated text. Function words (determiners, for example) are usually chosen during realisation. == Examples == The simplest type of lexical choice involves mapping a domain concept (perhaps represented in an ontology) to a word. For example, the concept Finger might be mapped to the word finger. A more complex situation is when a domain concept is expressed using different words in different situations. For example, the domain concept Value-Change can be expressed in many ways: The temperature rose: the verb rose is used for a Value-Change in temperature which increases the value. The temperature fell: the verb fell is used for a Value-Change in temperature which decreases the value. The rain got heavier: the phrase got heavier is used for a Value-Change in precipitation amount when the precipitation is rain. Sometimes words can communicate additional contextual information, for example: The temperature plummeted: the verb plummeted is used for a Value-Change in temperature which decreases the value, when the change is rapid and large. Contextual information is especially significant for vague terms such as tall. For example, a 2m tall man is tall, but a 2m tall horse is small. == Linguistic perspective == Lexical choice modules must be informed by linguistic knowledge of how the system's input data maps onto words. This is a question of semantics, but it is also influenced by syntactic factors (such as collocation effects) and pragmatic factors (such as context). Hence NLG systems need linguistic models of how meaning is mapped to words in the target domain (genre) of the NLG system. Genre tends to be very important; for example the verb veer has a very specific meaning in weather forecasts (wind direction is changing in a clockwise direction) which it does not have in general English, and a weather-forecast generator must be aware of this genre-specific meaning. In some cases there are major differences in how different people use the same word; for example, some people use by evening to mean 6PM and others use it to mean midnight. Psycholinguists have shown that when people speak to each other, they agree on a common interpretation via lexical alignment; this is not something which NLG systems can yet do. Ultimately, lexical choice must deal with the fundamental issue of how language relates to the non-linguistic world. For example, a system which chose colour terms such as red to describe objects in a digital image would need to know which RGB pixel values could generally be described as red; how this was influenced by visual (lighting, other objects in the scene) and linguistic (other objects being discussed) context; what pragmatic connotations were associated with red (for example, when an apple is called red, it is assumed to be ripe as well as have the colour red); and so forth. == Algorithms and models == A number of algorithms and models have been developed for lexical choice in the research community, for example Edmonds developed a model for choosing between near-synonyms (words with similar core meanings but different connotations). However such algorithms and models have not been widely used in applied NLG systems; such systems have instead often used quite simple computational models, and invested development effort in linguistic analysis instead of algorithm development.
Structure mapping engine
In artificial intelligence and cognitive science, the structure mapping engine (SME) is an implementation in software of an algorithm for analogical matching based on the psychological theory of Dedre Gentner. The basis of Gentner's structure-mapping idea is that an analogy is a mapping of knowledge from one domain (the base) into another (the target). The structure-mapping engine is a computer simulation of the analogy and similarity comparisons. The theory is useful because it ignores surface features and finds matches between potentially very different things if they have the same representational structure. For example, SME could determine that a pen is like a sponge because both are involved in dispensing liquid, even though they do this very differently. == Structure mapping theory == Structure mapping theory is based on the systematicity principle, which states that connected knowledge is preferred over independent facts. Therefore, the structure mapping engine should ignore isolated source-target mappings unless they are part of a bigger structure. The SME, the theory goes, should map objects that are related to knowledge that has already been mapped. The theory also requires that mappings be done one-to-one, which means that no part of the source description can map to more than one item in the target and no part of the target description can be mapped to more than one part of the source. The theory also requires that if a match maps subject to target, the arguments of subject and target must also be mapped. If both these conditions are met, the mapping is said to be "structurally consistent." == Concepts in SME == SME maps knowledge from a source into a target. SME calls each description a dgroup. Dgroups contain a list of entities and predicates. Entities represent the objects or concepts in a description — such as an input gear or a switch. Predicates are one of three types and are a general way to express knowledge for SME. Relation predicates contain multiple arguments, which can be other predicates or entities. An example relation is: (transmit (what from to)). This relation has a functor transmit and takes three arguments: what, from, and to. Attribute predicates are the properties of an entity. An example of an attribute is (red gear) which means that gear has the attribute red. Function predicates map an entity into another entity or constant. An example of a function is (joules power source) which maps the entity power source onto the numerical quantity joules. Functions and attributes have different meanings, and consequently SME processes them differently. For example, in SME's true analogy rule set, attributes differ from functions because they cannot match unless there is a higher-order match between them. The difference between attributes and functions will be explained further in this section's examples. All predicates have four parameters. They have (1) a functor, which identifies it, and (2) a type, which is either relation, attribute, or function. The other two parameters (3 and 4) are for determining how to process the arguments in the SME algorithm. If the arguments have to be matched in order, commutative is false. If the predicate can take any number of arguments, N-ary is false. An example of a predicate definition is: (sme:defPredicate behavior-set (predicate) relation :n-ary? t :commutative? t) The predicate's functor is “behavior-set,” its type is “relation,” and its n-ary and commutative parameters are both set to true. The “(predicate)” part of the definition specifies that there will be one or more predicates inside an instantiation of behavior-set. == Algorithm details == The algorithm has several steps. The first step of the algorithm is to create a set of match hypotheses between source and target dgroups. A match hypothesis represents a possible mapping between any part of the source and the target. This mapping is controlled by a set of match rules. By changing the match rules, one can change the type of reasoning SME does. For example, one set of match rules may perform a kind of analogy called literal similarity, and another performs a kind of analogy called true-analogy. These rules are not the place where domain-dependent information is added, but rather where the analogy process is tweaked, depending on the type of cognitive function the user is trying to emulate. For a given match rule, there are two types of rules that further define how it will be applied: filter rules and intern rules. Intern rules use only the arguments of the expressions in the match hypotheses that the filter rules identify. This limitation makes the processing more efficient by constraining the number of match hypotheses that are generated. At the same time, it also helps to build the structural consistencies that are needed later on in the algorithm. An example of a filter rule from the true-analogy rule set creates match hypotheses between predicates that have the same functor. The true-analogy rule set has an intern rule that iterates over the arguments of any match hypothesis, creating more match hypotheses if the arguments are entities or functions, or if the arguments are attributes and have the same functor. In order to illustrate how the match rules produce match hypotheses consider these two predicates: transmit torque inputgear secondgear (p1) transmit signal switch div10 (p2) Here we use true analogy for the type of reasoning. The filter match rule generates a match between p1 and p2 because they share the same functor, transmit. The intern rules then produce three more match hypotheses: torque to signal, inputgear to switch, and secondgear to div10. The intern rules created these match hypotheses because all the arguments were entities. If the arguments were functions or attributes instead of entities, the predicates would be expressed as: transmit torque (inputgear gear) (secondgear gear) (p3) transmit signal (switch circuit) (div10 circuit) (p4) These additional predicates make inputgear, secondgear, switch, and div10 functions or attributes depending on the value defined in the language input file. The representation also contains additional entities for gear and circuit. Depending on what type inputgear, secondgear, switch, and div10 are, their meanings change. As attributes, each one is a property of the gear or circuit. For example, the gear has two attributes, inputgear and secondgear. The circuit has two attributes, switch and circuit. As functions inputgear, secondgear, switch, and div10 become quantities of the gear and circuit. In this example, the functions inputgear and secondgear now map to the numerical quantities “torque from inputgear” and “torque from secondgear,” For the circuit the quantities map to logical quantity “switch engaged” and the numerical quantity “current count on the divide by 10 counter.” SME processes these differently. It does not allow attributes to match unless they are part of a higher-order relation, but it does allow functions to match, even if they are not part of such a relation. It allows functions to match because they indirectly refer to entities and thus should be treated like relations that involve no entities. However, as next section shows, the intern rules assign lower weights to matches between functions than to matches between relations. The reason SME does not match attributes is because it is trying to create connected knowledge based on relationships and thus satisfy the systematicity principle. For example, if both a clock and a car have inputgear attributes, SME will not mark them as similar. If it did, it would be making a match between the clock and car based on their appearance — not on the relationships between them. When the additional predicates in p3 and p4 are functions, the results from matching p3 and p4 are similar to the results from p1 and p2 except there is an additional match between gear and circuit and the values for the match hypotheses between (inputgear gear) and (switch circuit), and (secondgear gear) and (div10 circuit), are lower. The next section describes the reason for this in more detail. If the inputgear, secondgear, switch, and div10 are attributes instead of entities, SME does not find matches between any of the attributes. It finds matches only between the transmit predicates and between torque and signal. Additionally, the structural-evaluation scores for the remaining two matches decrease. In order to get the two predicates to match, p3 would need to be replaced by p5, which is demonstrated below. transmit torque (inputgear gear) (div10 gear) (p5) Since the true-analogy rule set identifies that the div10 attributes are the same between p5 and p4 and because the div10 attributes are both part of the higher-relation match between torque and signal, SME makes a match between (div10 gear) and (div10 circuit) — which leads to a match between gear and circuit. Being part of a higher-order match is a requiremen