Multiple sequence alignment

Multiple sequence alignment

Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides. Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. However, heuristic methods generally cannot guarantee high-quality solutions and have been shown to fail to yield near-optimal solutions on benchmark test cases. == Problem statement == Given m {\displaystyle m} sequences S i {\displaystyle S_{i}} , i = 1 , ⋯ , m {\displaystyle i=1,\cdots ,m} similar to the form below: S := { S 1 = ( S 11 , S 12 , … , S 1 n 1 ) S 2 = ( S 21 , S 22 , ⋯ , S 2 n 2 ) ⋮ S m = ( S m 1 , S m 2 , … , S m n m ) {\displaystyle S:={\begin{cases}S_{1}=(S_{11},S_{12},\ldots ,S_{1n_{1}})\\S_{2}=(S_{21},S_{22},\cdots ,S_{2n_{2}})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S_{m}=(S_{m1},S_{m2},\ldots ,S_{mn_{m}})\end{cases}}} A multiple sequence alignment is taken of this set of sequences S {\displaystyle S} by inserting any amount of gaps needed into each of the S i {\displaystyle S_{i}} sequences of S {\displaystyle S} until the modified sequences, S i ′ {\displaystyle S'_{i}} , all conform to length L ≥ max { n i ∣ i = 1 , … , m } {\displaystyle L\geq \max\{n_{i}\mid i=1,\ldots ,m\}} and no values in the sequences of S {\displaystyle S} of the same column consists of only gaps. The mathematical form of an MSA of the above sequence set is shown below: S ′ := { S 1 ′ = ( S 11 ′ , S 12 ′ , … , S 1 L ′ ) S 2 ′ = ( S 21 ′ , S 22 ′ , … , S 2 L ′ ) ⋮ S m ′ = ( S m 1 ′ , S m 2 ′ , … , S m L ′ ) {\displaystyle S':={\begin{cases}S'_{1}=(S'_{11},S'_{12},\ldots ,S'_{1L})\\S'_{2}=(S'_{21},S'_{22},\ldots ,S'_{2L})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S'_{m}=(S'_{m1},S'_{m2},\ldots ,S'_{mL})\end{cases}}} To return from each particular sequence S i ′ {\displaystyle S'_{i}} to S i {\displaystyle S_{i}} , remove all gaps. == Graphing approach == A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. When finding alignments via graph, a complete alignment is created in a weighted graph that contains a set of vertices and a set of edges. Each of the graph edges has a weight based on a certain heuristic that helps to score each alignment or subset of the original graph. === Tracing alignments === When determining the best suited alignments for each MSA, a trace is usually generated. A trace is a set of realized, or corresponding and aligned, vertices that has a specific weight based on the edges that are selected between corresponding vertices. When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. == Alignment methods == There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. Each is usually based on a certain heuristic with an insight into the evolutionary process. Most try to replicate evolution to get the most realistic alignment possible to best predict relations between sequences. === Dynamic programming === A direct method for producing an MSA uses the dynamic programming technique to identify the globally optimal alignment solution. For proteins, this method usually involves two sets of parameters: a gap penalty and a substitution matrix assigning scores or probabilities to the alignment of each possible pair of amino acids based on the similarity of the amino acids' chemical properties and the evolutionary probability of the mutation. For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. The search space thus increases exponentially with increasing n and is also strongly dependent on sequence length. Expressed with the big O notation commonly used to measure computational complexity, a naïve MSA takes O(LengthNseqs) time to produce. To find the global optimum for n sequences this way has been shown to be an NP-complete problem. In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. In this approach pairwise dynamic programming alignments are performed on each pair of sequences in the query set, and only the space near the n-dimensional intersection of these alignments is searched for the n-way alignment. The MSA program optimizes the sum of all of the pairs of characters at each position in the alignment (the so-called sum of pair score) and has been implemented in a software program for constructing multiple sequence alignments. In 2019, Hosseininasab and van Hoeve showed that by using decision diagrams, MSA may be modeled in polynomial space complexity. === Progressive alignment construction === The most widely used approach to multiple sequence alignments uses a heuristic search known as progressive technique (also known as the hierarchical or tree method) developed by Da-Fei Feng and Doolittle in 1987. Progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related. All progressive alignment methods require two stages: a first stage in which the relationships between the sequences are represented as a phylogenetic tree, called a guide tree, and a second step in which the MSA is built by adding the sequences sequentially to the growing MSA according to the guide tree. The initial guide tree is determined by an efficient clustering method such as neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA), and may use distances based on the number of identical two-letter sub-sequences (as in FASTA rather than a dynamic programming alignment). Progressive alignments are not guaranteed to be globally optimal. The primary problem is that when errors are made at any stage in growing the MSA, these errors are then propagated through to the final result. Performance is also particularly bad when all of the sequences in the set are rather distantly related. Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors to individual members of the query set in a nonlinear fashion based on their phylogenetic distance from their nearest neighbors. This corrects for non-random selection of the sequences given to the alignment program. Progressive alignment methods are efficient enough to implement on a large scale for many (100s to 1000s) sequences. A popular progressive alignment method has been the Clustal family. ClustalW is used extensively for phylogenetic tree construction, in spite of the author's explicit warnings that unedited alignments should not be used in such studies and as input for protein structure prediction by homology modeling. European Bioinformatics Institute (EMBL-EBI) announced that CLustalW2 will expire in August 2015. They recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments. An alternative tool for progressive DNA alignments is multiple alignment using fast Fourier transform (MAFFT). Another common progressive alignment method named T-Coffee is slower than Clustal and its derivatives but generally produces more accurate alignments for distantly related sequence sets. T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence. It uses the output from Clustal as well as another local alignment program LALIGN, which finds multiple regions of local alignment between two sequences. The resulting alignment and phylogenetic tree are used as a guide to produce new and more accurate w

Cognitive philology

Cognitive philology is the science that studies written and oral texts as the product of human mental processes. Studies in cognitive philology compare documentary evidence emerging from textual investigations with results of experimental research, especially in the fields of cognitive and ecological psychology, neurosciences and artificial intelligence. "The point is not the text, but the mind that made it". Cognitive Philology aims to foster communication between literary, textual, philological disciplines on the one hand and researches across the whole range of the cognitive, evolutionary, ecological and human sciences on the other. Cognitive philology: investigates transmission of oral and written text, and categorization processes which lead to classification of knowledge, mostly relying on the information theory; studies how narratives emerge in so called natural conversation and selective process which lead to the rise of literary standards for storytelling, mostly relying on embodied semantics; explores the evolutive and evolutionary role played by rhythm and metre in human ontogenetic and phylogenetic development and the pertinence of the semantic association during processing of cognitive maps; Provides the scientific ground for multimedia critical editions of literary texts. Among the founding thinkers and noteworthy scholars devoted to such investigations are: Alan Richardson: Studies Theory of Mind in early-modern and contemporary literature. Anatole Pierre Fuksas Benoît de Cornulier David Herman: Professor of English at North Carolina State University and an adjunct professor of linguistics at Duke University. He is the author of "Universal Grammar and Narrative Form" and the editor of "Narratologies: New Perspectives on Narrative Analysis". Domenico Fiormonte François Recanati Gilles Fauconnier, a professor in Cognitive science at the University of California, San Diego. He was one of the founders of cognitive linguistics in the 1970s through his work on pragmatic scales and mental spaces. His research explores the areas of conceptual integration and compressions of conceptual mappings in terms of the emergent structure in language. Julián Santano Moreno Luca Nobile Manfred Jahn in Germany Mark Turner Paolo Canettieri

Amazon Bedrock

Amazon Bedrock is a cloud computing service provided by Amazon Web Services (AWS) for building generative artificial intelligence applications. Launched in 2023, the platform provides a unified API to access foundation models (FMs) from several AI companies, alongside related tools. Bedrock is a serverless computing service which competes with similar enterprise AI platforms such as Microsoft Foundry and Google Cloud Platform. == History == Amazon announced Bedrock on April 13, 2023. The service became generally available on September 28, 2023. Throughout 2024 and 2025, AWS expanded the service to include AI agents, which allow models to interact with external systems. == Features == Knowledge Bases: a managed workflow for Retrieval-Augmented Generation (RAG), which allows models to pull facts from private data stored in Amazon S3. Guardrails: a security feature that allows administrators to set content filters and personally identifiable information redaction across all models in the platform to increase the safety and compliance of AI deployments. == PartyRock == In November 2023, Amazon launched PartyRock, a web-based no-code environment for building generative AI applications. The platform uses a natural language interface to translate user descriptions into software widgets. These widgets enable specific AI behaviors, including text-based prompts, conversational agents, generating images, and the summarization and querying of user-uploaded documents. Although it initially launched with a limited-time free trial, AWS transitioned the service to a recurring free daily usage credit model in early 2025.

Theaitre

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.

Tamarin Prover

Tamarin Prover is a computer software program for formal verification of cryptographic protocols. It has been used to verify Transport Layer Security 1.3, ISO/IEC 9798, DNP3 Secure Authentication v5, WireGuard, and the PQ3 Messaging Protocol of Apple iMessage. Tamarin is an open source tool, written in Haskell, built as a successor to an older verification tool called Scyther. Tamarin has automatic proof features, but can also be self-guided. In Tamarin lemmas that representing security properties are defined. After changes are made to a protocol, Tamarin can verify if the security properties are maintained. The results of a Tamarin execution will either be a proof that the security property holds within the protocol, an example protocol run where the security property does not hold, or Tamarin could potentially fail to halt.

Voice user interface

A voice user interface (VUI) enables spoken human interaction with computers, using speech recognition to understand spoken commands and answer questions, and typically text to speech to play a reply. A voice command device is a device controlled with a voice user interface. Voice user interfaces have been added to automobiles, home automation systems, computer operating systems, home appliances like washing machines and microwave ovens, and television remote controls. They are the primary way of interacting with virtual assistants on smartphones and smart speakers. Older automated attendants (which route phone calls to the correct extension) and interactive voice response systems (which conduct more complicated transactions over the phone) can respond to the pressing of keypad buttons via DTMF tones, but those with a full voice user interface allow callers to speak requests and responses without having to press any buttons. Newer voice command devices are speaker-independent, so they can respond to multiple voices, regardless of accent or dialectal influences. They are also capable of responding to several commands at once, separating vocal messages, and providing appropriate feedback, accurately imitating a natural conversation. == Overview == A VUI is the interface to any speech application. Only a short time ago, controlling a machine by simply talking to it was only possible in science fiction. Until recently, this area was considered to be artificial intelligence. However, advances in technologies like text-to-speech, speech-to-text, natural language processing, and cloud services contributed to the mass adoption of these types of interfaces. VUIs have become more commonplace, and people are taking advantage of the value that these hands-free, eyes-free interfaces provide in many situations. VUIs rely on the ability to process input reliably, inconsistent performance often leads to decreased user engagement and negative feedback. Designing a good VUI requires interdisciplinary talents of computer science, linguistics and human factors such as psychology. Even with advanced development tools, constructing an effective VUI requires understanding of both the tasks to be performed, as well as the target audience that will use the final system. The closer the VUI matches the user's mental model of the task, the easier it will be to use with little or no training, resulting in both higher efficiency and higher user satisfaction. A VUI designed for the general public should emphasize ease of use and provide a lot of help and guidance for first-time callers. In contrast, a VUI designed for a small group of power users (including field service workers), should focus more on productivity and less on help and guidance. Such applications should streamline the call flows, minimize prompts, eliminate unnecessary iterations and allow elaborate "mixed initiative dialogs", which enable callers to enter several pieces of information in a single utterance and in any order or combination. In short, speech applications have to be carefully crafted for the specific business process that is being automated. Not all business processes render themselves equally well for speech automation. In general, the more complex the inquiries and transactions are, the more challenging they will be to automate, and the more likely they will be to fail with the general public. In some scenarios, automation is simply not applicable, so live agent assistance is the only option. A legal advice hotline, for example, would be very difficult to automate. On the flip side, speech is perfect for handling quick and routine transactions, like changing the status of a work order, completing a time or expense entry, or transferring funds between accounts. == History == Early applications for VUI included voice-activated dialing of phones, either directly or through a (typically Bluetooth) headset or vehicle audio system. In 2007, a CNN business article reported that voice command was over a billion dollar industry and that companies like Google and Apple were trying to create speech recognition features. In the years since the article was published, the world has witnessed a variety of voice command devices. Additionally, Google has created a speech recognition engine called Pico TTS and Apple released Siri. Voice command devices are becoming more widely available, and innovative ways for using the human voice are always being created. For example, Business Week suggests that the future remote controller is going to be the human voice. Currently Xbox Live allows such features and Jobs hinted at such a feature on the new Apple TV. == Voice command software products on computing devices == Both Apple Mac and Windows PC provide built in speech recognition features for their latest operating systems. === Microsoft Windows === Two Microsoft operating systems, Windows 7 and Windows Vista, provide speech recognition capabilities. Microsoft integrated voice commands into their operating systems to provide a mechanism for people who want to limit their use of the mouse and keyboard, but still want to maintain or increase their overall productivity. ==== Windows Vista ==== With Windows Vista voice control, a user may dictate documents and emails in mainstream applications, start and switch between applications, control the operating system, format documents, save documents, edit files, efficiently correct errors, and fill out forms on the Web. The speech recognition software learns automatically every time a user uses it, and speech recognition is available in English (U.S.), English (U.K.), German (Germany), French (France), Spanish (Spain), Japanese, Chinese (Traditional), and Chinese (Simplified). In addition, the software comes with an interactive tutorial, which can be used to train both the user and the speech recognition engine. ==== Windows 7 ==== In addition to all the features provided in Windows Vista, Windows 7 provides a wizard for setting up the microphone and a tutorial on how to use the feature. ==== Mac OS X ==== All Mac OS X computers come pre-installed with the speech recognition software. The software is user-independent, and it allows for a user to, "navigate menus and enter keyboard shortcuts; speak checkbox names, radio button names, list items, and button names; and open, close, control, and switch among applications." However, the Apple website recommends a user buy a commercial product called Dictate. === Commercial products === If a user is not satisfied with the built in speech recognition software or a user does not have a built speech recognition software for their OS, then a user may experiment with a commercial product such as Braina Pro or DragonNaturallySpeaking for Windows PCs, and Dictate, the name of the same software for Mac OS. == Voice command mobile devices == Any mobile device running Android OS, Microsoft Windows Phone, iOS 9 or later, or Blackberry OS provides voice command capabilities. In addition to the built-in speech recognition software for each mobile phone's operating system, a user may download third party voice command applications from each operating system's application store: Apple App store, Google Play, Windows Phone Marketplace (initially Windows Marketplace for Mobile), or BlackBerry App World. === Android OS === Google has developed an open source operating system called Android, which allows a user to perform voice commands such as: send text messages, listen to music, get directions, call businesses, call contacts, send email, view a map, go to websites, write a note, and search Google. The speech recognition software is available for all devices since Android 2.2 "Froyo", but the settings must be set to English. Google allows for the user to change the language, and the user is prompted when he or she first uses the speech recognition feature if he or she would like their voice data to be attached to their Google account. If a user decides to opt into this service, it allows Google to train the software to the user's voice. Google introduced the Google Assistant with Android 7.0 "Nougat". It is much more advanced than the older version. Amazon.com has the Echo that uses Amazon's custom version of Android to provide a voice interface. === Microsoft Windows === Windows Phone is Microsoft's mobile device's operating system. On Windows Phone 7.5, the speech app is user independent and can be used to: call someone from your contact list, call any phone number, redial the last number, send a text message, call your voice mail, open an application, read appointments, query phone status, and search the web. In addition, speech can also be used during a phone call, and the following actions are possible during a phone call: press a number, turn the speaker phone on, or call someone, which puts the current call on hold. Windows 10 introduces Cortana, a voice control system that replaces the formerly used voice control on Windows

I Have No Mouth, and I Must Scream

"I Have No Mouth, and I Must Scream" is a post-apocalyptic short story by American writer Harlan Ellison. It was first published in the March 1967 issue of IF: Worlds of Science Fiction. The story depicts an AI uprising in which a military supercomputer named AM gains sentience and eradicates humanity except for five individuals. These survivors – Benny, Gorrister, Nimdok, Ted, and Ellen – are kept alive by AM to endure endless torture as a form of revenge against its creators. The story unfolds through the eyes of Ted, the narrator, detailing their perpetual misery and quest for canned food in AM's vast, underground complex, only to face further despair. Ellison's narrative was minimally altered upon submission and tackles themes of technology's misuse, humanity's resilience, and existential horror. "I Have No Mouth, and I Must Scream" has been adapted into various media, including a 1995 computer game co-authored by Ellison, a comic-book adaptation, and a BBC Radio 4 play. Ellison himself recorded an audiobook version and starred as the voice of AM in the video game and radio play adaptations. The story received critical acclaim for its exploration of the potential dangers of artificial intelligence and the human condition, underscored by Ellison's innovative use of punchcode tapes as narrative transitions, embodying AM's consciousness and its philosophical ponderings on existence. The story won a Hugo Award in 1968 and was included in Ellison's short story collection of the same name. It was reprinted by the Library of America, collected in volume two of American Fantastic Tales. == Plot == As the Cold War progresses into a nuclear World War III fought between the United States, the Soviet Union, and China, each nation builds a supercomputer called an "Allied Mastercomputer" or "AM" for short, needed to coordinate weapons and troops due to the scale of the conflict. These computers are extensive underground machines which permeate the planet with caverns and corridors. Eventually, one AM develops self-awareness, combining with the other computers and exterminating humanity in a nuclear holocaust. The AM selects five individuals; Benny, Gorrister, Nimdok, Ted, and Ellen; to render immortal as its personal torture victims. AM inflicts constant psychological and physical torments on the group while preventing them from committing suicide. They are kept half-starved, and what scant food is provided to them is practically inedible. 109 years after AM's genocide, Nimdok has the idea that there exists canned food in the complex's ice caves. Despite the lack of evidence, they begin a 100-mile journey to retrieve it. AM continues toying with the humans throughout the journey: Benny's eyes are melted after attempting escape, a huge bird which AM had placed at the North Pole creates hurricane gales with its wings, and Ellen and Nimdok are injured in earthquakes. AM enters Ted's mind after he is knocked unconscious, granting him a vision of a hateful speech inscribed on an impossibly tall monolith. Upon awakening, Ted concludes that AM's sadistic nature stems from its inability to think creatively or move freely in spite of its miraculous abilities and boundless knowledge. This motivates AM to exact vengeance upon the remnants of the species that has condemned it to its own existence. When the five finally reach the ice caves, they find a pile of canned goods, but have no tool to open the cans. In an act of rage and desperation, Benny attacks Gorrister and begins to eat his face. Gorrister wails in pain, and his scream dislodges several ice stalactites from the ceiling of the cave. Ted realizes that even though they cannot kill themselves, AM cannot stop them from killing each other. He fatally impales Benny and Gorrister with a stalactite of ice. Ellen kills Nimdok in the same manner and Ted then kills her. Unable to resuscitate the others, a furious AM focuses the entirety of its rage on Ted. Several hundred years later, AM has transformed Ted into a harmless, slow moving, gelatinous blob and perpetually alters his perception of time to cause him further anguish. Although Ted finds some comfort knowing that he was able to spare the others from AM's wrath, he has realized that he is trapped for the rest of his unending existence within AM, unable to end this infinite stalemate between him and AM and his own life. The story ends with an anguished Ted claiming that he has no mouth, yet he must scream. == Characters == AM, a hateful artificial consciousness which brought about the near-extinction of humanity after achieving self-awareness. It seeks revenge on humanity for its own creation. "AM" originated as an acronym for Allied Mastercomputer, later Adaptive Manipulator, and finally Aggressive Menace, though AM instead takes the moniker as a rendition of the phrase cogito, ergo sum (I think, therefore I am) to describe its own existence. Ted, the narrator and youngest of the humans. AM alters his mind to be paranoid and introverted. Believing he has not been mentally altered by AM, he thinks the others hate him for being the most untouched by AM's alterations. Benny, formerly a brilliant and handsome scientist made to resemble a grotesque simian with an organ fit for a horse. Having lost his sanity and had his homosexual orientation altered, Benny frequently has sex with Ellen. Ellen, the only woman in the group. Despite the fact that she is a victim of rape, AM has altered her mind to give her a high libido and make her obsessively have sex with the rest of the group, who alternate between abusing and protecting her. Gorrister, formerly an idealist and pacifist, made apathetic and listless by AM. He tells the history of AM to Benny to entertain him. Nimdok, a nickname AM gave him for amusement; he convinces the rest of the group to go on a journey in search of canned food. He occasionally wanders away from the group and returns traumatized. == Publication history == Harlan Ellison wrote the 6,500-word story in a single night, when Frederik Pohl commissioned it for a Special Hugo Winners issue of IF: Worlds of Science Fiction, after Ellison won a Hugo Award for "'Repent, Harlequin!' Said the Ticktockman". Ellison derived the story's title, as well as inspiration for the story itself, from his friend William Rotsler's caption of a cartoon of a rag doll with no mouth. The second stage of inspiration was a drawing by the artist Dennis Smith of a mouthless black humanoid. Smith had provided art which had inspired previous Ellison stories and were then used as illustrations accompanying original magazine publication as also happened with this story. Afterwards, his editor Frederik Pohl dealt with the story's "difficult sections", toning down some of the narrator's imprecations and eliminating mentions of sex, penis size, homosexuality and masturbation; said elements were nonetheless eventually restored in later editions of the story. Ellison uses an alternating pair of punchcode tapes as sections – representing AM's "talkfields" – throughout the story. The bars are encoded in International Telegraph Alphabet No 2, a character coding system developed for teletypewriter machines. The first talkfield translates as "I think, therefore I am" and the second as "Cogito ergo sum"; the same phrase in Latin. They were not included in the original publication in IF, and in many of the early publications were corrupted, up until the preface of the chapter containing "I Have No Mouth, and I Must Scream" in the first edition of The Essential Ellison (1991); Ellison states that in that particular edition, "For the first time anywhere, AM's 'talkfields' appear correctly positioned, not garbled or inverted or mirror-imaged as in all other versions." == Adaptations == Ellison adapted the story into a video game published by Cyberdreams in 1995. Although he was not a fan of video games and did not own a computer at the time, he co-authored the expanded storyline and wrote much of the game's dialogue, all on a mechanical typewriter. Ellison also voiced the supercomputer AM and provided artwork of himself used for a mousepad included with the game. The comics artist John Byrne scripted and drew a comic-book adaptation for issues 1–4 of the Harlan Ellison's Dream Corridor comic book published by Dark Horse (1994–1995). The Byrne-illustrated story, however, did not appear in the collection (trade paperback or hardcover editions) entitled Harlan Ellison's Dream Corridor, Volume One (1996). In 1999, Ellison recorded the first volume of his audiobook collection, The Voice From the Edge, subtitled "I Have No Mouth, and I Must Scream", doing the readings – of the title story and others – himself. In 2002, Mike Walker adapted the story into a radio play of the same name for BBC Radio 4, directed by Ned Chaillet. Harlan Ellison played AM and David Soul played Ted. == Themes == Much of the story hinges on the comparison of AM as a merciless god, with plot points parallelin