Theaitre (stylized as THEaiTRE) is an interdisciplinary research project investigating to what extent artificial intelligence is able to generate theatre play scripts. The first theatre play produced within the project, AI: When a Robot Writes a Play, premiered online on February 26, 2021. == Goal == Following similar previous projects such as Sunspring, a short sci-fi movie with an automatically generated script, the THEaiTRE project investigates whether current language generation approaches are mature enough to generate a theatre play script that could be successfully performed in front of an audience. The project falls within the area of generative art, famously represented e.g. by the portrait of Edmond de Belamy which was generated by an artificial neural network. In this field, artists are trying to use automated techniques to create "art", questioning the modern definition of art itself. More broadly, the project aims at promoting cooperation rather than competition of humans and artificial intelligence as the more beneficial approach for both. The first theatre play created within the project, titled AI: When a Robot Writes a Play, was presented in February 2021 at the 100th anniversary of the premiere of the R.U.R. theatre play by the Czech author Karel Čapek to celebrate the invention of the word "robot". While R.U.R. was a play written by a human about robots (and humans), THEaiTRE tried to reverse this idea by presenting a play written by a "robot" (artificial intelligence) about humans (and robots). The script of the play was published online, with marked parts of the text which were written manually or manually post-edited. The analysis shows that 90% of the script is automatically generated, with 10% manually written or manually post-edited. The project also plans to produce a second play in 2022, addressing some of the many shortcomings of the approach used to generate the first play, as well as attempting to further minimize the amount of human influence on the script. == Approach == At the core of the project is the GPT-2 language model by OpenAI with various adjustments motivated by the task of generating theatre play scripts, for which the model is not particularly trained. The GPT-2 model is used in the usual way, providing it with a start of a document and prompting it to generate a continuation of the document. Specifically, the input for GPT-2 in this project is typically a short description of the scene setting, followed by a few lines to introduce the characters and start the dialogue. The model then generates 10 continuation lines, and hands control to the user, who can then either ask the model to continue generating, or make various edits before letting the model to generate further, deleting some parts of the script or adding new lines into the script. The adjustments include restricting the generator to only produce lines pertaining to characters appearing in the input prompt, limiting the repetitiveness of the generated text, and employing automatic summarization of the input prompt and the generated text to overcome the limitation of the GPT-2 model which only attends to the last 1,024 subword tokens. The limitations of the model include, among other, a lack of distinctiveness and self-consistency of the characters, an inability to generate the script for the whole play (scripts for individual scenes are generated independently), and errors due to the employment of automated machine translation, as GPT-2 generates English texts but the final play script is being produced in Czech language. The source codes of the project are available under the MIT licence. The project has also published some sample outputs. == Team == The project is a cooperation of the following experts, all based in Prague, Czech Republic: computational linguists from the Faculty of Mathematics and Physics, Charles University theatre experts from the Švanda Theatre and from the Theatre Faculty of the Academy of Performing Arts in Prague hackers from CEE Hacks The project is financially supported by the Technology Agency of the Czech Republic.
Automatic scorer
An automatic scorer is the computerized scoring system to keep track of scoring in ten-pin bowling. It was introduced en masse in bowling alleys in the 1970s and combined with mechanical pinsetters to detect overturned pins. By eliminating the need for manual score-keeping, these systems have introduced new bowlers into the game who otherwise would not participate because they had to count the score themselves, as many do not understand the mathematical formula involved in bowler scoring. At first, people were skeptical about whether a computer could keep an accurate score. In the twenty-first century, automatic scorers are used in most bowling centers around the world. The three manufacturers of these specialty computers have been Brunswick Bowling, AMF Bowling (later QubicaAMF), and RCA. == History == Automatic equipment is considered a cornerstone of the modern bowling center. The traditional bowling center of the early 20th century was advanced in automation when the pinsetter person ("pin boy"), who set back up by hand the bowled down pins, was replaced by a machine that automatically replaced the pins in their proper play positions. This machine came out in the 1950s. A detection system was developed from the pinsetter mechanism in the 1960s that could tell which pins had been knocked down, and that information could be transferred to a digital computer. Automatic electronic scoring was first conceived by Robert Reynolds, who was described by a newspaper story at the time as "a West Coast electronics calculator expert." He worked with the technical staff of Brunswick Bowling to develop it. The goal was realized in the late 1960s when a specialized computer was designed for the purpose of automatic scorekeeping for bowling. The field test for the automatic scorer took place at Village Lanes bowling center, Chicago in 1967. The scoring machine received approval for official use by the American Bowling Congress in August of that year. They were first used in national official league gaming on October 10, 1967. In November, Brunswick announced that they were accepting orders for the new digital computer, which cost around $3,000 per bowling lane. Bowling centers that installed these new automatic scoring devices in the 1970s charged a ten cents extra per line of scoring for the convenience. == Description == Each Automatic Scorer computer unit kept score for four lanes. It had two bowler identification panels serving two lanes each. The bowler pushed it into his named position when his turn came up so the computer knew who was bowling and score accordingly. After the bowler rolled the bowling ball down the lane and knocked down pins, the pinsetter detected which pins were down and relayed this information back to the computer for scoring. The result was then printed on a scoresheet and projected overhead onto a large screen for all to see. The Automatic Scorer digital computer was mathematically accurate, however the detection system at the pinsetter mechanism sometimes reported the wrong number of pins knocked down. The computer could be corrected manually for any errors in the system; similarly, human errors, such as neglecting to move the bowler identification mechanism, could be corrected for by manual action. The scorer could take into account bowlers' handicaps and could adjust for late-arriving bowlers. The automatic scorer is directly connected to the foul detection unit. As a result, foul line violations are automatically scored. Brunswick had put ten years of research and development into the Automatic Scorer, and by 1972 there were over 500 of these computers installed in bowling centers around the world. AMF Bowling, competitor to Brunswick, entered into the automatic scorer computer field during the 1970s and their systems were installed into their brand of bowling centers. By 1974, RCA was also making these computers for automatic scoring. == Reception and further developments == The purposes of the computerized scoring were to avoid errors by human scorers and to prevent cheating. It had the side benefit of speeding up the progress of the game and introducing new bowlers to the game. Score-keeping for bowling is based on a formula that many new to bowling were not familiar with and thought difficult to learn. These casual bowlers unfamiliar with the formula thought the scores given by the computers were confusing. Some bowlers were not comfortable with automatic scorers when they were introduced in the 1970s, so kept score using the traditional method on paper score sheets. The introduction of this device increased the popularity of the sport. Automatic scorers came to be considered a normal part of modern bowling installations worldwide, with owners and managers saying that bowlers expect such equipment to be present in bowling establishments and that business increased following their introduction. Brunswick introduced a color television style automatic scorer in 1983. Bowling center owners could use these style automatic scorers for advertising, management, videos, and live television. By the 2010s, these types of electronic visual displays could show bowler avatars and social media connections to publicize the bowlers' scores. Some are capable of being extended entertainment systems of games for children and adults. Some scoring systems support variations on traditional bowling, such as different kinds of bingo games where certain pins have to be knocked down at certain times or practice regimes where certain spares have to be accomplished. By this point, QubicaAMF Worldwide, an outgrowth of AMF, was one of the leading providers of bowling scoring equipment.
Defeasible logic
Defeasible logic is a non-monotonic logic proposed by Donald Nute to formalize defeasible reasoning. In defeasible logic, there are three different types of propositions: strict rules specify that a fact is always a consequence of another; defeasible rules specify that a fact is typically a consequence of another; undercutting defeaters specify exceptions to defeasible rules. A priority ordering over the defeasible rules and the defeaters can be given. During the process of deduction, the strict rules are always applied, while a defeasible rule can be applied only if no defeater of a higher priority specifies that it should not.
No Fakes Act
The NO FAKES Act or the Nurture Originals, Foster Art, and Keep Entertainment Safe Act, is proposed United States federal legislation concerning digital replicas. The bill was first introduced in 2023 as a discussion draft, formally introduced in 2024, and reintroduced in 2025. If enacted, the bill would establish a federal right of publicity, giving public figures and private individuals greater control over the creation and use of digital replicas of their likenesses, including artificial intelligence (AI)-generated content. If passed, the NO FAKES Act would create a legal framework for licensing digital replicas, including provisions for liability, safe harbors, and statutory exceptions. The proposal has received broad support from the entertainment and technology industries. However, digital rights organizations have raised concerns that the Act risks chilling protected speech. == Background == === Entertainment industry concerns === Actors’ concerns over studios' use of their digital likeness were one of the primary drivers of the Screen Actors Guild–American Federation of Television and Radio Artists (SAG-AFTRA) strike in 2023. Negotiators for SAG-AFTRA alleged that the Alliance of Motion Picture and Television Producers (AMPTP) sought to use the digital likenesses of actors in perpetuity and would try to replace union members, especially background actors. The AMPTP denied SAG-AFTRA's interpretation of its proposal. In November 2023, AMPTP and SAG-AFTRA reached an agreement on the use of actors’ digital replicas, which included requirements for consent and compensation. Recording labels have also expressed concerns over unauthorized digital replicas of their performers' likeness. In 2023, TikTok user Ghostwriter977 released "Heart on My Sleeve," an AI-produced song in the styles of Drake and the Weeknd. After the song received millions of streams, the Universal Music Group (UMG) initiated takedown requests to TikTok and YouTube, which removed the song from their platforms. The legal arguments attorneys made were not disclosed; however, commentators noted that they likely used the Digital Millennium Copyright Act (DMCA). This presented a novel scenario, since UMG did not have licensing rights to "Heart on My Sleeve." According to The Verge, UMG based its DMCA takedown request on an unauthorized sample used at the start of the song for the producer tag. While legal commentators noted that UMG could have asserted a violation of the artists’ rights of publicity, existing state right of publicity laws do not provide notice-and-takedown mechanisms comparable to those under the DMCA. === Legal landscape === Legal scholars have observed that AI-generated digital replicas raise questions under existing copyright and intellectual property law. U.S. copyright law generally requires that original authorship be attributable to a human; however, the extent of human intervention needed to satisfy this requirement is not clear. Copyright holders have filed lawsuits against AI companies alleging unauthorized usage of copyrighted material to train their models, though many of these cases remain pending. In terms of outputs, record labels often hold rights to artists’ musical works but do not necessarily control the artists’ voice, appearance, or likeness in the same way. As a result, AI-generated recordings such as "Heart on My Sleeve" may fall outside the scope of certain traditional copyright protections. Individuals' likenesses have historically been governed under the Lanham Act, the Federal Trade Commission Act, and right of publicity laws. The right of publicity, recognized in many state-level statutes and common law, allows individuals to bring legal claims against unauthorized commercial use of their identities. It has often, but not exclusively, been applied to celebrities or other recognizable individuals. There is no federal-level right to publicity, and state-level protections vary, especially on issues relating to digital replicas and posthumous rights, which makes it difficult for creators or other individuals to prevent unauthorized use of their likenesses. In July 2024, the U.S. Copyright Office released a report on digital replicas and recommended that Congress create a federal law to protect individuals from unauthorized uses of their digital replicas, noting the inadequacy, narrowness, and inconsistency of existing laws. == Provisions == Under the NO FAKES Act of 2025, a digital replica is defined as "a newly created, computer-generated, highly realistic electronic representation that is readily identifiable as the voice or visual likeness of an individual," living or dead. A digital replica can be embodied in sound recordings, images, or audiovisual works in which the individual did not perform or in which the individual did perform but the "fundamental character of the performance or appearance has been materially altered." The Act specifies that digital replicas do not include reproduced samples of works authorized by the copyright holder. The Act defines a "right holder" as either the individual who is the subject of a digital replica or an entity that has acquired the rights to that individual’s likeness. The Act grants right holders the exclusive right to authorize the use of an individual’s likeness in a digital replica. This right is not assignable during the individual’s lifetime; however, it can be licensed to a living individual for up to 10 years under certain conditions. Postmortem rights The Act provides that the right does not automatically expire upon an individual’s death. It may be transferred to executors, heirs, or other parties designated by the individual. The right is held by the right holder for 10 years following the individual’s death. If the right holder demonstrates active use of the digital replica within the 2 years preceding the end of the 10-year term, the right may be extended for an additional 5-year period. These five-year extensions may be renewed for up to 70 years after the individual’s death. Liability The Act establishes liability for individuals who knowingly distribute a digital replica without authorization from the right holder, as well as for entities that make available a service primarily designed to produce unlawful digital replicas. Safe harbor provisions Similar to the Communications Decency Act and the DMCA, the Act establishes safe harbor provisions for online service providers. Providers are shielded from liability if they adopt and inform users of a policy for terminating accounts that repeatedly violate the Act. The NO FAKES Act does not require online services to proactively monitor content. Instead, it creates a notice-and-takedown mechanism under which providers must promptly respond to notifications seeking the removal of unauthorized digital replicas. These safe harbor protections apply only if the online service provider designates an agent with the U.S. Copyright Office to receive notifications of alleged violations. Remedies The NO FAKES Act provides remedies that are similar to those available under U.S. copyright law. Under the Act, individuals may be held liable for either statutory damages of $5,000 or actual damages for creating or distributing an unauthorized digital replica. The legislation also establishes a tiered liability framework for online service providers. Those that make good faith efforts to comply with the Act may face statutory damages of up to $25,000 per work for violations or actual damages. Providers that do not undertake such compliance efforts may be liable for $5,000 per unauthorized display or transmission of a digital replica, with damages capped at $750,000 per work. Exclusions The Act includes several exceptions to liability that are modeled in part on fair use principles. Digital replicas are excluded from liability when "used in a bona fide news, public affairs, or sports broadcast or account;" in a documentary or historical context; or in a way that is "consistent with the public interest." These exclusions do not apply to de minimis uses or to digital replicas that are sexually explicit in nature. The Act further states that licensing requirements do not apply to licenses established through collective bargaining agreements that contain provisions governing the use of digital replicas. The Act does not impose secondary liability on providers of generative artificial intelligence tools or services whose primary purpose is not the creation of unauthorized digital replicas. Preemption The NO FAKES Act preempts laws that protect "an individual's voice and visual likeness rights in connection with a digital replica, as defined in this Act, in an expressive work." However, the Act preserves state laws governing digital replicas enacted before January 2, 2025, as well as state laws addressing digital replicas that portray sexually explicit conduct. == History == In 2023, Senators Marsha Blackburn, Chris Coons, Amy Klobuchar, and Th
AlphaGo
AlphaGo is a computer program that plays the board game Go. It was developed by the London-based DeepMind Technologies, an acquired subsidiary of Google. Subsequent versions of AlphaGo became increasingly powerful, including a version that competed under the name Master. After retiring from competitive play, AlphaGo Master was succeeded by an even more powerful version known as AlphaGo Zero, which was completely self-taught without learning from human games. AlphaGo Zero was then generalized into a program known as AlphaZero, which played additional games, including chess and shogi. AlphaZero has in turn been succeeded by a program known as MuZero which learns without being taught the rules. AlphaGo and its successors use a Monte Carlo tree search algorithm to find its moves based on knowledge previously acquired by machine learning, specifically by an artificial neural network (a deep learning method) by extensive training, both from human and computer play. A neural network is trained to identify the best moves and the winning percentages of these moves. This neural network improves the strength of the tree search, resulting in stronger move selection in the next iteration. In October 2015, in a match against Fan Hui, the original AlphaGo became the first computer Go program to beat a human professional Go player without handicap on a full-sized 19×19 board. In March 2016, it beat Lee Sedol in a five-game match, the first time a computer Go program has beaten a 9-dan professional without handicap. Although it lost to Lee Sedol in the fourth game, Lee resigned in the final game, giving a final score of 4 games to 1 in favour of AlphaGo. In recognition of the victory, AlphaGo was awarded an honorary 9-dan by the Korea Baduk Association. The lead up and the challenge match with Lee Sedol were documented in a documentary film also titled AlphaGo, directed by Greg Kohs. The win by AlphaGo was chosen by Science as one of the Breakthrough of the Year runners-up on 22 December 2016. At the 2017 Future of Go Summit, the Master version of AlphaGo beat Ke Jie, the number one ranked player in the world at the time, in a three-game match, after which AlphaGo was awarded professional 9-dan by the Chinese Weiqi Association. After the match between AlphaGo and Ke Jie, DeepMind retired AlphaGo, while continuing AI research in other areas. The self-taught AlphaGo Zero achieved a 100–0 victory against the early competitive version of AlphaGo, and its successor AlphaZero was perceived as the world's top player in Go by the end of the 2010s. == History == Go is considered much more difficult for computers to win than other games such as chess, because its strategic and aesthetic nature makes it hard to directly construct an evaluation function, and its much larger branching factor makes it prohibitively difficult to use traditional AI methods such as alpha–beta pruning, tree traversal and heuristic search. Almost two decades after IBM's computer Deep Blue beat world chess champion Garry Kasparov in the 1997 match, the strongest Go programs using artificial intelligence techniques only reached about amateur 5-dan level, and still could not beat a professional Go player without a handicap. In 2012, the software program Zen, running on a four PC cluster, beat Masaki Takemiya (9p) twice at five- and four-stone handicaps. In 2013, Crazy Stone beat Yoshio Ishida (9p) at a four-stone handicap. According to DeepMind's David Silver, the AlphaGo research project was formed around 2014 to test how well a neural network using deep learning can compete at Go. AlphaGo represents a significant improvement over previous Go programs. In 500 games against other available Go programs, including Crazy Stone and Zen, AlphaGo running on a single computer won all but one. In a similar matchup, AlphaGo running on multiple computers won all 500 games played against other Go programs, and 77% of games played against AlphaGo running on a single computer. The distributed version in October 2015 was using 1,202 CPUs and 176 GPUs. === Match against Fan Hui === In October 2015, the distributed version of AlphaGo defeated the European Go champion Fan Hui, a 2-dan (out of 9 dan possible) professional, five to zero. This was the first time a computer Go program had beaten a professional human player on a full-sized board without handicap. The announcement of the news was delayed until 27 January 2016 to coincide with the publication of a paper in the journal Nature describing the algorithms used. === Match against Lee Sedol === AlphaGo played South Korean professional Go player Lee Sedol, ranked 9-dan, one of the best players at Go, with five games taking place at the Four Seasons Hotel in Seoul, South Korea on 9, 10, 12, 13, and 15 March 2016, which were video-streamed live. Out of five games, AlphaGo won four games and Lee won the fourth game which made him recorded as the only human player who beat AlphaGo in all of its 74 official games. AlphaGo ran on Google's cloud computing with its servers located in the United States. The match used Chinese rules with a 7.5-point komi, and each side had two hours of thinking time plus three 60-second byoyomi periods. The version of AlphaGo playing against Lee used a similar amount of computing power as was used in the Fan Hui match. The Economist reported that it used 1,920 CPUs and 280 GPUs. At the time of play, Lee Sedol had the second-highest number of Go international championship victories in the world after South Korean player Lee Chang-ho who kept the world championship title for 16 years. Since there is no single official method of ranking in international Go, the rankings may vary among the sources. While he was ranked top sometimes, some sources ranked Lee Sedol as the fourth-best player in the world at the time. AlphaGo was not specifically trained to face Lee nor was designed to compete with any specific human players. The first three games were won by AlphaGo following resignations by Lee. However, Lee beat AlphaGo in the fourth game, winning by resignation at move 180. AlphaGo then continued to achieve a fourth win, winning the fifth game by resignation. The prize was US$1 million. Since AlphaGo won four out of five and thus the series, the prize will be donated to charities, including UNICEF. Lee Sedol received $150,000 for participating in all five games and an additional $20,000 for his win in Game 4. In June 2016, at a presentation held at a university in the Netherlands, Aja Huang, one of the Deep Mind team, revealed that they had patched the logical weakness that occurred during the 4th game of the match between AlphaGo and Lee, and that after move 78 (which was dubbed the "divine move" by many professionals), it would play as intended and maintain Black's advantage. Before move 78, AlphaGo was leading throughout the game, but Lee's move caused the program's computing powers to be diverted and confused. Huang explained that AlphaGo's policy network of finding the most accurate move order and continuation did not precisely guide AlphaGo to make the correct continuation after move 78, since its value network did not determine Lee's 78th move as being the most likely, and therefore when the move was made AlphaGo could not make the right adjustment to the logical continuation. === Sixty online games === On 29 December 2016, a new account on the Tygem server named "Magister" (shown as 'Magist' at the server's Chinese version) from South Korea began to play games with professional players. It changed its account name to "Master" on 30 December, then moved to the FoxGo server on 1 January 2017. On 4 January, DeepMind confirmed that the "Magister" and the "Master" were both played by an updated version of AlphaGo, called AlphaGo Master. As of 5 January 2017, AlphaGo Master's online record was 60 wins and 0 losses, including three victories over Go's top-ranked player, Ke Jie, who had been quietly briefed in advance that Master was a version of AlphaGo. After losing to Master, Gu Li offered a bounty of 100,000 yuan (US$14,400) to the first human player who could defeat Master. Master played at the pace of 10 games per day. Many quickly suspected it to be an AI player due to little or no resting between games. Its adversaries included many world champions such as Ke Jie, Park Jeong-hwan, Yuta Iyama, Tuo Jiaxi, Mi Yuting, Shi Yue, Chen Yaoye, Li Qincheng, Gu Li, Chang Hao, Tang Weixing, Fan Tingyu, Zhou Ruiyang, Jiang Weijie, Chou Chun-hsun, Kim Ji-seok, Kang Dong-yun, Park Yeong-hun, and Won Seong-jin; national champions or world championship runners-up such as Lian Xiao, Tan Xiao, Meng Tailing, Dang Yifei, Huang Yunsong, Yang Dingxin, Gu Zihao, Shin Jinseo, Cho Han-seung, and An Sungjoon. All 60 games except one were fast-paced games with three 20 or 30 seconds byo-yomi. Master offered to extend the byo-yomi to one minute when playing with Nie Weiping in consideration of his age. After winning its 59th game Master revealed itse
Empirical dynamic modeling
Empirical dynamic modeling (EDM) is a framework for analysis and prediction of nonlinear dynamical systems. Applications include population dynamics, ecosystem service, medicine, neuroscience, dynamical systems, geophysics, and human-computer interaction. EDM was originally developed by Robert May and George Sugihara. It can be considered a methodology for data modeling, predictive analytics, dynamical system analysis, machine learning and time series analysis. == Description == Mathematical models have tremendous power to describe observations of real-world systems. They are routinely used to test hypothesis, explain mechanisms and predict future outcomes. However, real-world systems are often nonlinear and multidimensional, in some instances rendering explicit equation-based modeling problematic. Empirical models, which infer patterns and associations from the data instead of using hypothesized equations, represent a natural and flexible framework for modeling complex dynamics. Donald DeAngelis and Simeon Yurek illustrated that canonical statistical models are ill-posed when applied to nonlinear dynamical systems. A hallmark of nonlinear dynamics is state-dependence: system states are related to previous states governing transition from one state to another. EDM operates in this space, the multidimensional state-space of system dynamics rather than on one-dimensional observational time series. EDM does not presume relationships among states, for example, a functional dependence, but projects future states from localised, neighboring states. EDM is thus a state-space, nearest-neighbors paradigm where system dynamics are inferred from states derived from observational time series. This provides a model-free representation of the system naturally encompassing nonlinear dynamics. A cornerstone of EDM is recognition that time series observed from a dynamical system can be transformed into higher-dimensional state-spaces by time-delay embedding with Takens's theorem. The state-space models are evaluated based on in-sample fidelity to observations, conventionally with Pearson correlation between predictions and observations. == Methods == Primary EDM algorithms include Simplex projection, Sequential locally weighted global linear maps (S-Map) projection, Multivariate embedding in Simplex or S-Map, Convergent cross mapping (CCM), and Multiview Embeding, described below. Nearest neighbors are found according to: NN ( y , X , k ) = ‖ X N i E − y ‖ ≤ ‖ X N j E − y ‖ if 1 ≤ i ≤ j ≤ k {\displaystyle {\text{NN}}(y,X,k)=\|X_{N_{i}}^{E}-y\|\leq \|X_{N_{j}}^{E}-y\|{\text{ if }}1\leq i\leq j\leq k} === Simplex === Simplex projection is a nearest neighbor projection. It locates the k {\displaystyle k} nearest neighbors to the location in the state-space from which a prediction is desired. To minimize the number of free parameters k {\displaystyle k} is typically set to E + 1 {\displaystyle E+1} defining an E + 1 {\displaystyle E+1} dimensional simplex in the state-space. The prediction is computed as the average of the weighted phase-space simplex projected T p {\displaystyle Tp} points ahead. Each neighbor is weighted proportional to their distance to the projection origin vector in the state-space. Find k {\displaystyle k} nearest neighbor: N k ← NN ( y , X , k ) {\displaystyle N_{k}\gets {\text{NN}}(y,X,k)} Define the distance scale: d ← ‖ X N 1 E − y ‖ {\displaystyle d\gets \|X_{N_{1}}^{E}-y\|} Compute weights: For{ i = 1 , … , k {\displaystyle i=1,\dots ,k} } : w i ← exp ( − ‖ X N i E − y ‖ / d ) {\displaystyle w_{i}\gets \exp(-\|X_{N_{i}}^{E}-y\|/d)} Average of state-space simplex: y ^ ← ∑ i = 1 k ( w i X N i + T p ) / ∑ i = 1 k w i {\displaystyle {\hat {y}}\gets \sum _{i=1}^{k}\left(w_{i}X_{N_{i}+T_{p}}\right)/\sum _{i=1}^{k}w_{i}} === S-Map === S-Map extends the state-space prediction in Simplex from an average of the E + 1 {\displaystyle E+1} nearest neighbors to a linear regression fit to all neighbors, but localised with an exponential decay kernel. The exponential localisation function is F ( θ ) = exp ( − θ d / D ) {\displaystyle F(\theta )={\text{exp}}(-\theta d/D)} , where d {\displaystyle d} is the neighbor distance and D {\displaystyle D} the mean distance. In this way, depending on the value of θ {\displaystyle \theta } , neighbors close to the prediction origin point have a higher weight than those further from it, such that a local linear approximation to the nonlinear system is reasonable. This localisation ability allows one to identify an optimal local scale, in-effect quantifying the degree of state dependence, and hence nonlinearity of the system. Another feature of S-Map is that for a properly fit model, the regression coefficients between variables have been shown to approximate the gradient (directional derivative) of variables along the manifold. These Jacobians represent the time-varying interaction strengths between system variables. Find k {\displaystyle k} nearest neighbor: N ← NN ( y , X , k ) {\displaystyle N\gets {\text{NN}}(y,X,k)} Sum of distances: D ← 1 k ∑ i = 1 k ‖ X N i E − y ‖ {\displaystyle D\gets {\frac {1}{k}}\sum _{i=1}^{k}\|X_{N_{i}}^{E}-y\|} Compute weights: For{ i = 1 , … , k {\displaystyle i=1,\dots ,k} } : w i ← exp ( − θ ‖ X N i E − y ‖ / D ) {\displaystyle w_{i}\gets \exp(-\theta \|X_{N_{i}}^{E}-y\|/D)} Reweighting matrix: W ← diag ( w i ) {\displaystyle W\gets {\text{diag}}(w_{i})} Design matrix: A ← [ 1 X N 1 X N 1 − 1 … X N 1 − E + 1 1 X N 2 X N 2 − 1 … X N 2 − E + 1 ⋮ ⋮ ⋮ ⋱ ⋮ 1 X N k X N k − 1 … X N k − E + 1 ] {\displaystyle A\gets {\begin{bmatrix}1&X_{N_{1}}&X_{N_{1}-1}&\dots &X_{N_{1}-E+1}\\1&X_{N_{2}}&X_{N_{2}-1}&\dots &X_{N_{2}-E+1}\\\vdots &\vdots &\vdots &\ddots &\vdots \\1&X_{N_{k}}&X_{N_{k}-1}&\dots &X_{N_{k}-E+1}\end{bmatrix}}} Weighted design matrix: A ← W A {\displaystyle A\gets WA} Response vector at T p {\displaystyle Tp} : b ← [ X N 1 + T p X N 2 + T p ⋮ X N k + T p ] {\displaystyle b\gets {\begin{bmatrix}X_{N_{1}+T_{p}}\\X_{N_{2}+T_{p}}\\\vdots \\X_{N_{k}+T_{p}}\end{bmatrix}}} Weighted response vector: b ← W b {\displaystyle b\gets Wb} Least squares solution (SVD): c ^ ← argmin c ‖ A c − b ‖ 2 2 {\displaystyle {\hat {c}}\gets {\text{argmin}}_{c}\|Ac-b\|_{2}^{2}} Local linear model c ^ {\displaystyle {\hat {c}}} is prediction: y ^ ← c ^ 0 + ∑ i = 1 E c ^ i y i {\displaystyle {\hat {y}}\gets {\hat {c}}_{0}+\sum _{i=1}^{E}{\hat {c}}_{i}y_{i}} === Multivariate Embedding === Multivariate Embedding recognizes that time-delay embeddings are not the only valid state-space construction. In Simplex and S-Map one can generate a state-space from observational vectors, or time-delay embeddings of a single observational time series, or both. === Convergent Cross Mapping === Convergent cross mapping (CCM) leverages a corollary to the Generalized Takens Theorem that it should be possible to cross predict or cross map between variables observed from the same system. Suppose that in some dynamical system involving variables X {\displaystyle X} and Y {\displaystyle Y} , X {\displaystyle X} causes Y {\displaystyle Y} . Since X {\displaystyle X} and Y {\displaystyle Y} belong to the same dynamical system, their reconstructions (via embeddings) M x {\displaystyle M_{x}} , and M y {\displaystyle M_{y}} , also map to the same system. The causal variable X {\displaystyle X} leaves a signature on the affected variable Y {\displaystyle Y} , and consequently, the reconstructed states based on Y {\displaystyle Y} can be used to cross predict values of X {\displaystyle X} . CCM leverages this property to infer causality by predicting X {\displaystyle X} using the M y {\displaystyle M_{y}} library of points (or vice versa for the other direction of causality), while assessing improvements in cross map predictability as larger and larger random samplings of M y {\displaystyle M_{y}} are used. If the prediction skill of X {\displaystyle X} increases and saturates as the entire M y {\displaystyle M_{y}} is used, this provides evidence that X {\displaystyle X} is casually influencing Y {\displaystyle Y} . === Multiview Embedding === Multiview Embedding is a Dimensionality reduction technique where a large number of state-space time series vectors are combitorially assessed towards maximal model predictability. == Extensions == Extensions to EDM techniques include: Generalized Theorems for Nonlinear State Space Reconstruction Extended Convergent Cross Mapping Dynamic stability S-Map regularization Visual analytics with EDM Convergent Cross Sorting Expert system with EDM hybrid Sliding windows based on the extended convergent cross-mapping Empirical Mode Modeling Accounting for missing data and variable step sizes Accounting for observation noise Hierarchical Bayesian EDM via Gaussian processes Intelligent and Adaptive Control Optimal control via Empirical dynamic programming Multiview distance regularised S-map
Minimum information standard
Minimum information standards are sets of guidelines and formats for reporting data derived by specific high-throughput methods. Their purpose is to ensure the data generated by these methods can be easily verified, analysed and interpreted by the wider scientific community. Ultimately, they facilitate the transfer of data from journal articles (unstructured data) into databases (structured data) in a form that enables data to be mined across multiple data sets. Minimal information standards are available for a vast variety of experiment types including microarray (MIAME), RNAseq (MINSEQE), metabolomics (MSI) and proteomics (MIAPE). Minimum information standards typically have two parts. Firstly, there is a set of reporting requirements – typically presented as a table or a checklist. Secondly, there is a data format. Information about an experiment needs to be converted into the appropriate data format for it to be submitted to the relevant database. In the case of MIAME, the data format is provided in spreadsheet format (MAGE-TAB). Some of the communities that maintain minimum information standards also provide tools to help experimental researchers to annotate their data. == MI Standards == The individual minimum information standards are brought by the communities of cross-disciplinary specialists focused on the problematic of the specific method used in experimental biology. The standards then provide specifications what information about the experiments (metadata) is crucial and important to be reported together with the resultant data to make it comprehensive. The need for this standardization is largely driven by the development of high-throughput experimental methods that provide tremendous amounts of data. The development of minimum information standards of different methods is since 2008 being harmonized by "Minimum Information about a Biomedical or Biological Investigation" (MIBBI) project. === MIAPPE, Minimum Information About a Plant Phenotyping Experiment === MIAPPE is an open, community driven project to harmonize data from plant phenotyping experiments. MIAPPE comprises both a conceptual checklist of metadata required to adequately describe a plant phenotyping experiment. === MIQE, Minimum Information for Publication of Quantitative Real-Time PCR Experiments === Published in 2009 these guidelines for the basis of requirements by many journals when submitting QPCR data, sadly they are not adhered to enough. === MIAME, gene expression microarray === Minimum Information About a Microarray Experiment (MIAME) describes the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment and is aimed at facilitating the dissemination of data from microarray experiments. It was published by the FGED Society in 2001 and was the first published minimum information standard for high-throughput experiments in the life sciences. MIAME contains a number of extensions to cover specific biological domains, including MIAME-env, MIAME-nut and MIAME-tox, covering environmental genomics, nutritional genomics and toxogenomics, respectively. === MINI: Minimum Information about a Neuroscience Investigation === ==== MINI: Electrophysiology ==== Electrophysiology is a technology used to study the electrical properties of biological cells and tissues. Electrophysiology typically involves the measurements of voltage change or electric current flow on a wide variety of scales from single ion channel proteins to whole tissues. This document is a single module, as part of the Minimum Information about a Neuroscience investigation (MINI) family of reporting guideline documents, produced by community consultation and continually available for public comment. A MINI module represents the minimum information that should be reported about a dataset to facilitate computational access and analysis to allow a reader to interpret and critically evaluate the processes performed and the conclusions reached, and to support their experimental corroboration. In practice a MINI module comprises a checklist of information that should be provided (for example about the protocols employed) when a data set is described for publication. The full specification of the MINI module can be found here. === MIARE, RNAi experiment === Minimum Information About an RNAi Experiment (MIARE) is a data reporting guideline which describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results. === MIACA, cell based assay === Advances in genomics and functional genomics have enabled large-scale analyses of gene and protein function by means of high-throughput cell biological analyses. Thereby, cells in culture can be perturbed in vitro and the induced effects recorded and analyzed. Perturbations can be triggered in several ways, for instance with molecules (siRNAs, expression constructs, small chemical compounds, ligands for receptors, etc.), through environmental stresses (such as temperature shift, serum starvation, oxygen deprivation, etc.), or combinations thereof. The cellular responses to such perturbations are analyzed in order to identify molecular events in the biological processes addressed and understand biological principles. We propose the Minimum Information About a Cellular Assay (MIACA) for reporting a cellular assay, and CA-OM, the modular cellular assay object model, to facilitate exchange of data and accompanying information, and to compare and integrate data that originate from different, albeit complementary approaches, and to elucidate higher order principles. Documents describing MIACA are available and provide further information as well as the checklist of terms that should be reported. === MIAPE, proteomic experiments === The Minimum Information About a Proteomic Experiment documents describe information which should be given along with a proteomic experiment. The parent document describes the processes and principles underpinning the development of a series of domain specific documents which now cover all aspects of a MS-based proteomics workflow. === MIMIx, molecular interactions === This document has been developed and maintained by the Molecular Interaction worktrack of the HUPO-PSI (www.psidev.info) and describes the Minimum Information about a Molecular Interaction experiment. === MIAPAR, protein affinity reagents === The Minimum Information About a Protein Affinity Reagent has been developed and maintained by the Molecular Interaction worktrack of the HUPO-PSI (www.psidev.info)in conjunction with the HUPO Antibody Initiative and a European consortium of binder producers and seeks to encourage users to improve their description of binding reagents, such as antibodies, used in the process of protein identification. === MIABE, bioactive entities === The Minimum Information About a Bioactive Entity was produced by representatives from both large pharma and academia who are looking to improve the description of usually small molecules which bind to, and potentially modulate the activity of, specific targets in a living organism. This document encompasses drug-like molecules as well as herbicides, pesticides and food additives. It is primarily maintained through the EMBL-EBI Industry program (www.ebi.ac.uk/industry). === MIGS/MIMS, genome/metagenome sequences === This specification is being developed by the Genomic Standards Consortium === MIFlowCyt, flow cytometry === === Minimum Information about a Flow Cytometry Experiment === The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) is a standard related to flow cytometry which establishes criteria to record information on experimental overview, samples, instrumentation and data analysis. It promotes consistent annotation of clinical, biological and technical issues surrounding a flow cytometry experiment. === MINDR, dual gene expression reporters === Requires (1) reporting absolute values of reporter readouts, (2) list of positive and negative controls, and (3) sequences of all reporter constructs. === MISFISHIE, In Situ Hybridization and Immunohistochemistry Experiments === === MIAPA, Phylogenetic Analysis === Criteria for Minimum Information About a Phylogenetic Analysis were described in 2006. === MIRAGE, Glycomics === The MIRAGE project is supported and coordinated by the Beilstein-Institut to establish guidelines for data handling and processing in glycomics research [1] === MIAO, ORF === === MIAMET, METabolomics experiment === === MIAFGE, Functional Genomics Experiment === === MIRIAM, Minimum Information Required in the Annotation of Models === The Minimal Information Required In the Annotation of Models (MIRIAM), is a set of rules for the curation and annotation of quantitative models of biological systems. === MIASE, Minimum Information About a Simulation Experiment =