Ontology for Biomedical Investigations

Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) is an open-access, integrated ontology for the description of biological and clinical investigations. OBI provides a model for the design of an investigation, the protocols and instrumentation used, the materials used, the data generated and the type of analysis performed on it. The project is being developed as part of the OBO Foundry and as such adheres to all the principles therein such as orthogonal coverage (i.e. clear delineation from other foundry member ontologies) and the use of a common formal language. In OBI the common formal language used is the Web Ontology Language (OWL). As of March 2008, a pre-release version of the ontology was made available at the project's SVN repository. == Scope == The Ontology for Biomedical Investigations (OBI) addresses the need for controlled vocabularies to support integration and joint ("cross-omics") analysis of experimental data, a need originally identified in the transcriptomics domain by the FGED Society, which developed the MGED Ontology as an annotation resource for microarray data.Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al. (November 2007). "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology. 25 (11): 1251–5. doi:10.1038/nbt1346. PMC 2814061. PMID 17989687. OBI uses the basic formal ontology upper-level ontology as a means of describing general entities that do not belong to a specific problem domain. As such, all OBI classes are a subclass of some BFO class. The ontology has the scope of modeling all biomedical investigations and as such contains ontology terms for aspects such as: biological material – for example blood plasma instrument (and parts of an instrument therein) – for example DNA microarray, centrifuge information content – such as an image or a digital information entity such as an electronic medical record design and execution of an investigation (and individual experiments therein) – for example study design, electrophoresis material separation data transformation (incorporating aspects such as data normalization and data analysis) – for example principal components analysis dimensionality reduction, mean calculation Less 'concrete' aspects such as the role a given entity may play in a particular scenario (for example the role of a chemical compound in an experiment) and the function of an entity (for example the digestive function of the stomach to nutriate the body) are also covered in the ontology. == OBI consortium == The MGED Ontology was originally identified in the transcriptomics domain by the FGED Society and was developed to address the needs of data integration. Following a mutual decision to collaborate, this effort later became a wider collaboration between groups such as FGED, PSI and MSI in response to the needs of areas such as transcriptomics, proteomics and metabolomics and the FuGO (Functional Genomics Investigation Ontology) was created. This later became the OBI covering the wider scope of all biomedical investigations. As an international, cross-domain initiative, the OBI consortium draws upon a pool of experts from a variety of fields, not limited to biology. The current list of OBI consortium members is available at the OBI consortium website. The consortium is made up of a coordinating committee which is a combination of two subgroups, the Community Representative (those representing a particular biomedical community) and the Core Developers (ontology developers who may or may not be members of any single community). Separate to the coordinating committee is the Developers Working Group which consists of developers within the communities collaborating in the development of OBI at the discretion of current OBI Consortium members. == Papers on OBI ==

Seed (programming)

Seed is a JavaScript interpreter and a library of the GNOME project to create standalone applications in JavaScript. It uses the JavaScript engine JavaScriptCore of the WebKit project. It is possible to easily create modules in C. Seed is integrated in GNOME since the 2.28 version and is used by two games in the GNOME Games package. It is also used by the Web web browser for the design of its extensions. The module is also officially supported by the GTK+ project. == Hello world in Seed == This example uses the standard output to output the string "Hello, World". == A program using GTK+ == This code shows an empty window named "Example". == Modules == To use a module, just instantiate a class having for name imports. followed by the name of the module respecting the case sensitivity. The modules using GObject Introspection, who starts by imports.gi. : Gtk Gst GObject Gio Clutter GLib Gdk WebKit GdkPixbuf, GdkPixbuf Libxml Cairo DBus MPFR Os (system library) Canvas (using Cairo) multiprocessing readline Archived 2009-11-09 at the Wayback Machine ffi sqlite sandbox Archived 2009-11-09 at the Wayback Machine == List of the Seed versions == The names of the versions of Seed are albums of famous rock bands.

Zero-shot learning

Zero-shot learning (ZSL) is a problem setup in deep learning where, at test time, a learner observes samples from classes which were not observed during training, and needs to predict the class that they belong to. The name is a play on words based on the earlier concept of one-shot learning, in which classification can be learned from only one, or a few, examples. Zero-shot methods generally work by associating observed and non-observed classes through some form of auxiliary information, which encodes observable distinguishing properties of objects. For example, given a set of images of animals to be classified, along with auxiliary textual descriptions of what animals look like, an artificial intelligence model which has been trained to recognize horses, but has never been given a zebra, can still recognize a zebra when it also knows that zebras look like striped horses. This problem is widely studied in computer vision, natural language processing, and machine perception. == Background and history == The first paper on zero-shot learning in natural language processing appeared in a 2008 paper by Chang, Ratinov, Roth, and Srikumar, at the AAAI'08, but the name given to the learning paradigm there was dataless classification. The first paper on zero-shot learning in computer vision appeared at the same conference, under the name zero-data learning. The term zero-shot learning itself first appeared in the literature in a 2009 paper from Palatucci, Hinton, Pomerleau, and Mitchell at NIPS'09. This terminology was repeated later in another computer vision paper and the term zero-shot learning caught on, as a take-off on one-shot learning that was introduced in computer vision years earlier. In computer vision, zero-shot learning models learned parameters for seen classes along with their class representations and rely on representational similarity among class labels so that, during inference, instances can be classified into new classes. In natural language processing, the key technical direction developed builds on the ability to "understand the labels"—represent the labels in the same semantic space as that of the documents to be classified. This supports the classification of a single example without observing any annotated data, the purest form of zero-shot classification. The original paper made use of the Explicit Semantic Analysis (ESA) representation but later papers made use of other representations, including dense representations. This approach was also extended to multilingual domains, fine entity typing and other problems. Moreover, beyond relying solely on representations, the computational approach has been extended to depend on transfer from other tasks, such as textual entailment and question answering. The original paper also points out that, beyond the ability to classify a single example, when a collection of examples is given, with the assumption that they come from the same distribution, it is possible to bootstrap the performance in a semi-supervised like manner (or transductive learning). Unlike standard generalization in machine learning, where classifiers are expected to correctly classify new samples to classes they have already observed during training, in ZSL, no samples from the classes have been given during training the classifier. It can therefore be viewed as an extreme case of domain adaptation. == Prerequisite information for zero-shot classes == Naturally, some form of auxiliary information has to be given about these zero-shot classes, and this type of information can be of several types. Learning with attributes: classes are accompanied by pre-defined structured description. For example, for bird descriptions, this could include "red head", "long beak". These attributes are often organized in a structured compositional way, and taking that structure into account improves learning. While this approach was used mostly in computer vision, there are some examples for it also in natural language processing. Learning from textual description. As pointed out above, this has been the key direction pursued in natural language processing. Here class labels are taken to have a meaning and are often augmented with definitions or free-text natural-language description. This could include for example a wikipedia description of the class. Class-class similarity. Here, classes are embedded in a continuous space. A zero-shot classifier can predict that a sample corresponds to some position in that space, and the nearest embedded class is used as a predicted class, even if no such samples were observed during training. == Generalized zero-shot learning == The above ZSL setup assumes that at test time, only zero-shot samples are given, namely, samples from new unseen classes. In generalized zero-shot learning, samples from both new and known classes, may appear at test time. This poses new challenges for classifiers at test time, because it is very challenging to estimate if a given sample is new or known. Some approaches to handle this include: a gating module, which is first trained to decide if a given sample comes from a new class or from an old one, and then, at inference time, outputs either a hard decision, or a soft probabilistic decision a generative module, which is trained to generate feature representation of the unseen classes—a standard classifier can then be trained on samples from all classes, seen and unseen. == Domains of application == Zero shot learning has been applied to the following fields: image classification semantic segmentation image generation object detection natural language processing computational biology abstract reasoning

Google Mobile Services

Google Mobile Services (GMS) is a collection of proprietary applications and application programming interfaces (APIs) services from Google that are typically pre-installed on the majority of Android devices, such as smartphones, tablets, and smart TVs. GMS is not a part of the Android Open Source Project (AOSP), which means an Android manufacturer needs to obtain a license from Google in order to legally pre-install GMS on an Android device. This license is provided by Google without any licensing fees except in the EU. == Core applications == The following are core applications that are part of Google Mobile Services: Google Search Google Chrome YouTube Google Play Google Drive Gmail Google Meet Google Maps Google Photos Google TV YouTube Music === Historically === Google+ Google Hangouts Google Wallet Google Play Magazines Google Play Music Google Play Movies & TV Google Duo == Reception, competitors, and regulators == === FairSearch === Numerous European firms filed a complaint to the European Commission stating that Google had manipulated their power and dominance within the market to push their Services to be used by phone manufacturers. The firms were joined under the name FairSearch, and the main firms included were Microsoft, Expedia, TripAdvisor, Nokia and Oracle. FairSearch's major problem with Google's practices was that they believed Google were forcing phone manufacturers to use their Mobile Services. They claimed Google managed this by asking these manufacturers to sign a contract stating that they must preinstall specific Google Mobile Services, such as Maps, Search and YouTube, in order to get the latest version of Android. Google swiftly responded stating that they "continue to work co-operatively with the European Commission". === Aptoide === The third-party Android app store Aptoide also filed an EU competition complaint against Google once again stating that they are misusing their power within the market. Aptoide alleged that Google was blocking third-party app stores from being on Google Play, as well as blocking Google Chrome from downloading any third-party apps and app stores. As of June 2014, Google had not responded to these allegations. === Abuse of Android dominance === In May 2019, Umar Javeed, Sukarma Thapar, Aaqib Javeed vs. Google LLC & Ors. the Competition Commission of India ordered an antitrust probe against Google for abusing its dominant position with Android to block market rivals. In Prima Facie opinion the commission held that mandatory pre-installation of the entire Google Mobile Services (GMS) suite, under Mobile Application Distribution Agreements (MADA), amounts to the imposition of unfair conditions on the device manufacturers. === EU antitrust ruling === On July 18, 2018, the European Commission fined Google €4.34 billion for breaching EU antitrust rules which resulted in a change of licensing policy for the GMS in the EU. A new paid licensing agreement for smartphones and tablets shipped into the EEA was created. The change is that the GMS is now decoupled from the base Android and will be offered under a separate paid licensing agreement. === Privacy policy === At the same time, Google faced problems with various European data protection agencies, most notably In the United Kingdom and France. The problem they faced was that they had a set of 60 rules merged into one, which allowed Google to "track users more closely". Google once again came out and stated that their new policies still abide by European Union laws. === Android distributions without Google Mobile Services === After surveillance and privacy concerns, several custom android distributions have been implemented, such as GrapheneOS, LineageOS, CalyxOS, iodéOS or /e/OS, and they come either without any GMS installed by default or with microG, that adds a compatibility layer.

Image destriping

Image destriping is the process of removing stripes or streaks from images and videos without disrupting the original image/video. These artifacts plague a range of fields in scientific imaging including atomic force microscopy, light sheet fluorescence microscopy, and planetary satellite imaging. The most common image processing techniques to reduce stripe artifacts is with Fourier filtering. Unfortunately, filtering methods risk altering or suppressing useful image data. Methods developed for multiple-sensor imaging systems in planetary satellites use statistical-based methods to match signal distribution across multiple sensors. More recently, a new class of approaches leverage compressed sensing, to regularize an optimization problem, and recover stripe free images. In many cases, these destriped images have little to no artifacts, even at low signal to noise ratios.

Sensory, Inc.

Sensory, Inc. is an American company which develops software AI technologies for speech, sound and vision. It is based in Santa Clara, California. Sensory’s technologies have shipped in over three billion products from hundreds of leading consumer electronics manufacturers including AT&T, Hasbro, Huawei, Google, Amazon, Samsung, LG, Mattel, Motorola, Plantronics, GoPro, Sony, Tencent, Garmin, LG, Microsoft, Lenovo, and more. Sensory has over 60 issued patents covering speech recognition in consumer electronics, biometric authentication, sensor/speech combinations, wake word technology, and more. == History == Sensory, Inc. was founded in 1994, originally as Sensory Circuits, by Forrest Mozer, Mike Mozer and Todd Mozer. The three had also co-founded ESS Technology years earlier. In 1999 Sensory acquired Fluent Speech Technologies, which was formed and started by a group of professors out of the Oregon Graduate Institute (formerly OGI, now OHSU). Fluent Speech Technologies developed high performance embedded speech engines, the technology from this acquisition is now the core technology used throughout Sensory's chip and software line. === Company timeline === 1994 – Founded 1995 – Introduces the RSC 164 - first commercially successful speech recognition IC 1998 – Introduces first speaker verification IC 2000 – Acquires Oregon based Fluent-Speech Technologies 2002 – Acquires Texas Instruments line of speech output ICs (the SC series) 2007 – Introduces first Voice User Interface for Bluetooth silicon (CSR BC-5) - BlueGenie 2008 - Sensory and BlueAnt partner on the V1 - Revolutionary new Bluetooth headset with a voice user interface. First wearable to use a voice user interface for control and best-reviewed speech recognition product in history 2009 – Introduced world's smallest text to speech system (TTS) and Truly HandsfreeTM Triggers/ wake words. 2010 – Introduced the NLP-5x – First Natural Language Voice Processor and TrulyHandsfree wake words in SDKs for Android, iOS, Linux, and Windows. NLP5x used the first generation of TrulyHandsfree wake words with low power and enhanced accuracy. 2011 – Sensory partners with Google and Microsoft to enable TrulyHandsfree as a front end to Goog411 and Bing411 2012 – Partnered with Tensilica to offer ultra-low power TrulyHandsfree wake words; introduced Speaker Verification and Speaker Identification for mobile phones and other consumer electronics. 2012 - TrulyHandsfree released into Samsung's Galaxy S2 for "Hey Galaxy" wake word 2013 – TrulyHandsfree wake words migrated to many new platforms and began shipping as MotoVoice in the Google-owned MotoX. Sensory's TrulyHandsfree in mobile takes off with the Galaxy S3 and S4 and Galaxy Note and is licensed into wearables like Google Glass. 2014 – Announced new initiative in Vision; added LG and Motorola as customers; received the 2014 Global Mobile Award for Best Mobile Technology Breakthrough at the GSMA Mobile World Congress in Barcelona, Spain (judges commented, "A big advance for the wearables market, this offers many benefits for consumers, increasing uptake and usage of many mobile apps, driving revenue for operators and content providers.") 2015-2018 - Licensed Google, Amazon, MSFT, Baidu, Huawei, ZTE, and many others with TrulyHandsfree wake words. Sensory develops first wake words for OK Google, Hey Siri, and Hey Cortana. 2019 - Sensory launched two new solutions: SoundID, sound identification, and TrulyNatural, embedded large vocabulary speech recognition. Sensory also acquired Vocalize.ai, an independent testing lab. 2020 - Sensory introduced VoiceHub, which allows the automated generation of wake words. 2021 - Sensory expands VoiceHub with speech recognition and NLU capabilities. The company initiated a new cloud platform, SensoryCloud.ai. 2022-Sensory rolls out SensoryCloud.ai with speech to text, text to speech, face & voice biometrics 2024- Sensory Automotive & TrulyNatural Speech-to-text On-Device launched == Technology and products == Sensory originally developed both hardware (Integrated Circuit - IC or "chip") and software platforms but migrated to software only around 2005 and added cloud and hybrid computing capabilities in 2021. Sensory's RSC-164 IC (Integrated Circuit or "chip") was used on NASA's Mars Polar Lander in the Mars Microphone on the Lander. Speech Synthesis SC-6x chips – acquired some speech synthesis technology from Texas Instruments. Sensory’s embedded AI solutions include the following: TrulyHandsfree (THF) - wake word detection and phrase spotting. TrulyNatural (TNL) - large vocabulary continuous speech recognition with NLU. TrulySecure (TS) - face and voice biometrics. TrulySecureSpeakerVerification (TSSV) - speaker and sound identification. VoiceHub - Online portal for creating custom wake words and speech recognition models with NLU. Sensory Automotive- Sensory Automotive is a full voice and vision suite of AI technologies that operate efficiently in the car without connecting to a network. The cloud initiative, SensoryCloud.ai, is targeting Speech To Text (STT), Text To Speech (TTS), Wake Word verification, face and voice recognition, and sound identification.

Boyfriend Maker

Boyfriend Maker was a dating sim, romance chatbot smartphone app for iOS (iPhone) and Android devices, developed by Japanese studio 36 You Games (styled as 36You) and distributed under the freemium business model. Boyfriend Maker incorporated advanced artificial intelligence chat technology a decade before products such as ChatGPT. According to the developer's website, Boyfriend Maker is an "app that lets you interact and chat with quirky virtual boyfriends". While each virtual boyfriend has certain unique characteristics, the various instances of the boyfriend are powered by a chat engine, that (at least within a language and market) can utilise vocabulary and knowledge acquired in a chat with one user in subsequent chats with other users. == Gameplay == Users gain experience points and in-game coins. Users can customize their virtual boyfriend's appearance by selecting items such as hair, clothing, face, and a necklace. == Apple delisting and reintroduction == In late November 2012, the original iOS Boyfriend Maker app was delisted from the Apple App Store due to "ribald" chat, according to the New York Times. Boyfriend Maker was removed by Apple due to "reports of references to violent sexual acts and pedophilia". Boyfriend Maker had an age rating of 4+, even though the chat bot "responds with often strange and explicit text unsuitable for young children". User-posted chat excerpts indicate that the virtual boyfriend would sometimes transition abruptly to sexual chat in response to a seemingly innocent question. In one user-posted example, in response to the question, "what kind of wedding cake will we have" the boyfriend responds, "a good sex ima be on top of u u gonna ride oon me bitin the pillow gurrl ima fuck da shit out of u". The developer's use of the SimSimi-created third-party chat engine may be responsible for the sexual text. As the virtual boyfriend converses with human users, the SimSimi chat engine acquires vocabulary from users of the game and applies this "learned" vocabulary in chats with other users. The chat engine might also employ lines harvested from human-human chat logs, song lyrics, movies or TV shows. In April 2013, a detuned and presumably tamer version of the app, titled Boyfriend Plus, was permitted on Apple's App Store.