Tute Genomics

Tute Genomics

Tute Genomics was an American genomics startup that provided a cloud-based web application for rapid and accurate annotation of human genomic data. It was built on the expertise of ANNOVAR. Tute Genomics assisted researchers in identifying disease genes and biomarkers, and assisted clinicians/labs in performing genetic diagnosis. Based in Provo, Utah, Tute was co-founded by Dr. Kai Wang, an assistant professor at the University of Southern California (USC); and Dr. Reid J. Robison, a board-certified psychiatrist with fellowship training in both neurodevelopmental genetics and bioinformatics. Tute Genomics was acquired by PierianDX in 2016. == History == The word "tute" means "personal" in the Na’vi language created for the 2009 film Avatar by Paul Frommer, a linguist and communications professor at the USC Marshall School of Business. === Timeline === 2013 Tute Genomics launched in 2013 and entered the accelerator, BoomStartup. By "demo day" of BoomStartup, Tute had raised their seed round of funding and expanded the round to include angel investors from SLC Angels, Park City Angels, Life Science Angels. Tute was the tenth ever online syndicate for AngelList and in all raised a seed round of $1.5 million. 2014 In March 2014, the company announced that Affiliated Genetics, a Utah-based CLIA-certified laboratory, selected Tute Genomics for its next-generation sequencing (NGS) analytics pipeline. In May 2014, the company announced joining the Global Alliance for Genomics and Health. In June 2014, Advanced Biological Laboratories (ABL), S.A., announced a licensing and collaboration agreement with Tute Genomics and the commercial launch of OncoChek for managing and analysing genomics data in the field of oncology. In July 2014, the company announced an agreement with Lineagen, Inc., to provide next-generation sequencing analytics for Lineagen’s NextStepDx Plus assay. Also, Brigham Young University selected the Tute Genomics genome annotation and discovery platform for analysis and interpretation of 1,000 exomes and genomes. In November 2014, the company announced addition of the Tute platform to Illumina’s BaseSpace. The company announced a Series A1 funding round of $2.3 million in December 2014. The round was led by UK-based Eurovestech. Peak Ventures and a number of angel investors also participated in this round. 2015 Tute recruits David Mittelman, founder of Arpeggi, Inc. and former CSO at FamilyTreeDNA, to Tute Genomics as Chief Scientific Officer. Tute acquires Knome and integrates the KnoSys platform into its software product. 2016 Reid Robison, Tute CEO, launches a Kickstarter campaign to sell Tute interpreted whole genome and whole exome sequencing directly to consumers. The campaign was suspended within the same month after receiving a letter from the United States Food and Drug Administration. Tute is acquired by PierianDX.

PeduliLindungi

SatuSehat (Indonesian for "one health"), formerly PeduliLindungi (roughly "care to protect"), is a national integrated health data exchange platform, jointly developed by the Indonesian Ministry of Communication and Information Technology (Kemenkominfo), in partnership with Committee for COVID-19 Response and National Economic Recovery (KPCPEN), Ministry of Health (Kemenkes), Ministry of State-Owned Enterprises (KemenBUMN), and Telkom Indonesia. The SatuSehat platform aims to facilitate data accessibility and service efficiency for health providers and the government, and assist the public as a tool to access their own electronic medical record data. This app was the official COVID-19 contact tracing app used for digital contact tracing in Indonesia, and originally known as TraceTogether but later changed because Singapore had its app using the same name. == Implementation == On 23 August 2021, Coordinating Minister for Maritime and Investments Affairs, Luhut Binsar Panjaitan, encouraged the government to make this app a mandatory requirement before using public transportations, such as train, bus, ferry, and plane. Furthermore, citizen must have installed the app before entering shopping malls, factories, and sport venues. Every person who have received at least a dose of vaccine will receive a vaccine card and vaccination certificate which can be downloaded from the app. In December 2022, with the revocation of PPKM (Community Activities Restrictions Enforcement) starting from 1 January 2023, Ministry of Health issued a statement that the usage of the app is not a governmental mandatory requirement as it used to be. === Transition into a citizen health app === On 7 September 2022, it was announced that the app would be modified to become a citizen health app, capitalising on the reach of the app and the existing work done around the app. On 28 February 2023, the authorities announced that the app was rebranded to SATUSEHAT Mobile (lit. 'OneHealth Mobile'), with existing users needing to update the PeduliLindungi app and re-synchronise their COVID-19 related health information. The re-branded app would eventually be an all-in-one health service and records retrieval app for Indonesians. == Controversy == It was reported that the app requires continuous access to the phone's files, media, and GPS, which quickly drains the battery. Allowing location access only during use or denying it altogether will render the app unusable. This stands in stark contrast to COVID-19 apps used in other countries that only utilize Bluetooth and do not require any additional permissions. In September 2021, stored personal data of at least 1.3 million Indonesian residents were leaked online, including the vaccine certificate of President Joko Widodo. The data leak was also reported on eHAC (electronic Health Alert Card), a mandatory app used for air passengers.

Learning vector quantization

In computer science, learning vector quantization (LVQ) is a prototype-based supervised classification algorithm. LVQ is the supervised counterpart of vector quantization systems. LVQ can be understood as a special case of an artificial neural network, more precisely, it applies a winner-take-all Hebbian learning-based approach. It is a precursor to self-organizing maps (SOM) and related to neural gas and the k-nearest neighbor algorithm (k-NN). LVQ was invented by Teuvo Kohonen. == Definition == An LVQ system is represented by prototypes W = ( w ( i ) , . . . , w ( n ) ) {\displaystyle W=(w(i),...,w(n))} which are defined in the feature space of observed data. In winner-take-all training algorithms one determines, for each data point, the prototype which is closest to the input according to a given distance measure. The position of this so-called winner prototype is then adapted, i.e. the winner is moved closer if it correctly classifies the data point or moved away if it classifies the data point incorrectly. An advantage of LVQ is that it creates prototypes that are easy to interpret for experts in the respective application domain. LVQ systems can be applied to multi-class classification problems in a natural way. A key issue in LVQ is the choice of an appropriate measure of distance or similarity for training and classification. Recently, techniques have been developed which adapt a parameterized distance measure in the course of training the system, see e.g. (Schneider, Biehl, and Hammer, 2009) and references therein. LVQ can be a valuable aid in classifying text documents. == Algorithm == The algorithms are presented as in. Set up: Let the data be denoted by x i ∈ R D {\displaystyle x_{i}\in \mathbb {R} ^{D}} , and their corresponding labels by y i ∈ { 1 , 2 , … , C } {\displaystyle y_{i}\in \{1,2,\dots ,C\}} . The complete dataset is { ( x i , y i ) } i = 1 N {\displaystyle \{(x_{i},y_{i})\}_{i=1}^{N}} . The set of code vectors is w j ∈ R D {\displaystyle w_{j}\in \mathbb {R} ^{D}} . The learning rate at iteration step t {\displaystyle t} is denoted by α t {\displaystyle \alpha _{t}} . The hyperparameters w {\displaystyle w} and ϵ {\displaystyle \epsilon } are used by LVQ2 and LVQ3. The original paper suggests ϵ ∈ [ 0.1 , 0.5 ] {\displaystyle \epsilon \in [0.1,0.5]} and w ∈ [ 0.2 , 0.3 ] {\displaystyle w\in [0.2,0.3]} . === LVQ1 === Initialize several code vectors per label. Iterate until convergence criteria is reached. Sample a datum x i {\displaystyle x_{i}} , and find out the code vector w j {\displaystyle w_{j}} , such that x i {\displaystyle x_{i}} falls within the Voronoi cell of w j {\displaystyle w_{j}} . If its label y i {\displaystyle y_{i}} is the same as that of w j {\displaystyle w_{j}} , then w j ← w j + α t ( x i − w j ) {\displaystyle w_{j}\leftarrow w_{j}+\alpha _{t}(x_{i}-w_{j})} , otherwise, w j ← w j − α t ( x i − w j ) {\displaystyle w_{j}\leftarrow w_{j}-\alpha _{t}(x_{i}-w_{j})} . === LVQ2 === LVQ2 is the same as LVQ3, but with this sentence removed: "If w j {\displaystyle w_{j}} and w k {\displaystyle w_{k}} and x i {\displaystyle x_{i}} have the same class, then w j ← w j − α t ( x i − w j ) {\displaystyle w_{j}\leftarrow w_{j}-\alpha _{t}(x_{i}-w_{j})} and w k ← w k + α t ( x i − w k ) {\displaystyle w_{k}\leftarrow w_{k}+\alpha _{t}(x_{i}-w_{k})} .". If w j {\displaystyle w_{j}} and w k {\displaystyle w_{k}} and x i {\displaystyle x_{i}} have the same class, then nothing happens. === LVQ3 === Initialize several code vectors per label. Iterate until convergence criteria is reached. Sample a datum x i {\displaystyle x_{i}} , and find out two code vectors w j , w k {\displaystyle w_{j},w_{k}} closest to it. Let d j := ‖ x i − w j ‖ , d k := ‖ x i − w k ‖ {\displaystyle d_{j}:=\|x_{i}-w_{j}\|,d_{k}:=\|x_{i}-w_{k}\|} . If min ( d j d k , d k d j ) > s {\displaystyle \min \left({\frac {d_{j}}{d_{k}}},{\frac {d_{k}}{d_{j}}}\right)>s} , where s = 1 − w 1 + w {\displaystyle s={\frac {1-w}{1+w}}} , then If w j {\displaystyle w_{j}} and x i {\displaystyle x_{i}} have the same class, and w k {\displaystyle w_{k}} and x i {\displaystyle x_{i}} have different classes, then w j ← w j + α t ( x i − w j ) {\displaystyle w_{j}\leftarrow w_{j}+\alpha _{t}(x_{i}-w_{j})} and w k ← w k − α t ( x i − w k ) {\displaystyle w_{k}\leftarrow w_{k}-\alpha _{t}(x_{i}-w_{k})} . If w k {\displaystyle w_{k}} and x i {\displaystyle x_{i}} have the same class, and w j {\displaystyle w_{j}} and x i {\displaystyle x_{i}} have different classes, then w j ← w j − α t ( x i − w j ) {\displaystyle w_{j}\leftarrow w_{j}-\alpha _{t}(x_{i}-w_{j})} and w k ← w k + α t ( x i − w k ) {\displaystyle w_{k}\leftarrow w_{k}+\alpha _{t}(x_{i}-w_{k})} . If w j {\displaystyle w_{j}} and w k {\displaystyle w_{k}} and x i {\displaystyle x_{i}} have the same class, then w j ← w j − ϵ α t ( x i − w j ) {\displaystyle w_{j}\leftarrow w_{j}-\epsilon \alpha _{t}(x_{i}-w_{j})} and w k ← w k + ϵ α t ( x i − w k ) {\displaystyle w_{k}\leftarrow w_{k}+\epsilon \alpha _{t}(x_{i}-w_{k})} . If w k {\displaystyle w_{k}} and x i {\displaystyle x_{i}} have different classes, and w j {\displaystyle w_{j}} and x i {\displaystyle x_{i}} have different classes, then the original paper simply does not explain what happens in this case, but presumably nothing happens in this case. Otherwise, skip. Note that condition min ( d j d k , d k d j ) > s {\displaystyle \min \left({\frac {d_{j}}{d_{k}}},{\frac {d_{k}}{d_{j}}}\right)>s} , where s = 1 − w 1 + w {\displaystyle s={\frac {1-w}{1+w}}} , precisely means that the point x i {\displaystyle x_{i}} falls between two Apollonian spheres.

Neuromorphic computing

Neuromorphic computing is a computing approach inspired by the human brain's structure and function. It uses artificial neurons to perform computations, mimicking neural systems for tasks such as perception, motor control, and multisensory integration. These systems, implemented in analog, digital, or mixed-mode VLSI, prioritize robustness, adaptability, and learning by emulating the brain’s distributed processing across small computing elements. This interdisciplinary field integrates biology, physics, mathematics, computer science, and electronic engineering to develop systems that emulate the brain’s morphology and computational strategies. Neuromorphic systems aim to enhance energy efficiency and computational power for applications including artificial intelligence, pattern recognition, and sensory processing. == History == Carver Mead proposed one of the first applications for neuromorphic engineering in the late 1980s. In 2006, researchers at Georgia Tech developed a field programmable neural array, a silicon-based chip modeling neuron channel-ion characteristics. In 2011, MIT researchers created a chip mimicking synaptic communication using 400 transistors and standard CMOS techniques. In 2012 HP Labs researchers reported that Mott memristors exhibit volatile behavior at low temperatures, enabling the creation of neuristors that mimic neuron behavior and support Turing machine components. Also in 2012, Purdue University researchers presented a neuromorphic chip design using lateral spin valves and memristors, noted for energy efficiency. The 2013 Blue Brain Project creates detailed digital models of rodent brains. Neurogrid, developed by Brains in Silicon at Stanford University, used 16 NeuroCore chips to emulate 65,536 neurons with high energy efficiency in 2014. The 2014 BRAIN Initiative and IBM’s TrueNorth chip contributed to neuromorphic advancements. The 2016 BrainScaleS project, a hybrid neuromorphic supercomputer at University of Heidelberg, operated 864 times faster than biological neurons. In 2017, Intel unveiled its Loihi chip, using an asynchronous artificial neural network for efficient learning and inference. Also in 2017 IMEC’s self-learning chip, based on OxRAM, demonstrated music composition by learning from minuets. In 2022, MIT researchers developed artificial synapses using protons for analog deep learning. In 2019, the European Union funded neuromorphic quantum computing to explore quantum operations using neuromorphic systems. Also in 2022, researchers at the Max Planck Institute for Polymer Research developed an organic artificial spiking neuron for in-situ neuromorphic sensing and biointerfacing. Researchers reported in 2024 that chemical systems in liquid solutions can detect sound at various wavelengths, offering potential for neuromorphic applications. == Neurological inspiration == Neuromorphic engineering emulates the brain’s structure and operations, focusing on the analog nature of biological computation and the role of neurons in cognition. The brain processes information via neurons using chemical signals, abstracted into mathematical functions. Neuromorphic systems distribute computation across small elements, similar to neurons, using methods guided by anatomical and functional neural maps from electron microscopy and neural connection studies. == Implementation == Neuromorphic systems employ hardware such as oxide-based memristors, spintronic memories, threshold switches, and transistors. Software implementations train spiking neural networks using error backpropagation. === Neuromemristive systems === Neuromemristive systems use memristors to implement neuroplasticity, focusing on abstract neural network models rather than detailed biological mimicry. These systems enable applications in speech recognition, face recognition, and object recognition, and can replace conventional digital logic gates. The Caravelli-Traversa-Di Ventra equation describes memristive memory evolution, revealing tunneling phenomena and Lyapunov functions. === Neuromorphic sensors === Neuromorphic principles extend to sensors, such as the retinomorphic sensor or event camera, which mimic human vision by registering brightness changes individually, optimizing power consumption. An example of this applied to detecting light is the retinomorphic sensor or, when employed in an array, an event camera. == Ethical considerations == Neuromorphic systems raise the same ethical questions as those for other approaches to artificial intelligence. Daniel Lim argued that advanced neuromorphic systems could lead to machine consciousness, raising concerns about whether civil rights and other protocols should be extended to them. Legal debates, such as in Acohs Pty Ltd v. Ucorp Pty Ltd, question ownership of work produced by neuromorphic systems, as non-human-generated outputs may not be copyrightable.

Thomas Bolander

Thomas Bolander is a Danish professor at DTU Compute, Technical University of Denmark, where he studies logic and artificial intelligence. Most of his studies focus on the social aspect of artificial intelligence, and how we can make future AI able to navigate in social interactions. Thomas Bolander also sits in different commissions, expert panels and boards, among these he is a member of the Siri Commission, the TeckDK Commission, a member of the editorial board of the journal Studia Logica and co-organizer of Science and Cocktails. Bolander is known for his dissemination of science. In 2019 he was awarded the H. C. Ørsted Medal. Which he was the first to achieve after a break of three years.

Pattern playback

The pattern playback is an early talking device that was built by Dr. Franklin S. Cooper and his colleagues, including John M. Borst and Caryl Haskins, at Haskins Laboratories in the late 1940s and completed in 1950. There were several different versions of this hardware device. Only one currently survives. The machine converts pictures of the acoustic patterns of speech in the form of a spectrogram back into sound. Using this device, Alvin Liberman, Frank Cooper, and Pierre Delattre (later joined by Katherine Safford Harris, Leigh Lisker, and others) were able to discover acoustic cues for the perception of phonetic segments (consonants and vowels). This research was fundamental to the development of modern techniques of speech synthesis, reading machines for the blind, the study of speech perception and speech recognition, and the development of the motor theory of speech perception. To create sound, the pattern playback machine uses an arc light source which is directed against a rotating disk with 50 concentric tracks whose transparencies vary systematically in order to produce 50 harmonics of a fundamental frequency. The light is further projected against a spectrogram, whose reflectance corresponds to the sound pressure level of the partial of the signal, and is then directed towards a photovoltaic cell by which the light variation is converted into sound pressure variations. The pattern playback was last used in an experimental study by Robert Remez in 1976. The pattern playback now resides in the Museum at Haskins Laboratories in New Haven, Connecticut. The technique of pattern playback also now refers, more generally, to algorithms or techniques for converting spectrograms, cochleagrams, and correlograms from pictures back into sounds. A demonstration is in the TV show Adventure. Pioneering technology in psycholinguistics (CBS Television. 1953). == Digital pattern playback == In the 1970s, digital pattern playbacks began to supplant the earlier version. An early prototype was developed by Patrick Nye, Philip Rubin, and colleagues at Haskins Laboratories. It combined a "Ubiquitous Spectrum Analyzer"[1] for automatic spectral analysis, along with a VAX GT-40 display processor for graphic manipulation of the displayed spectrogram, a form of "synthesis by art", and subsequent re-synthesis using a 40 channel filter bank. This hybrid hardware/software digital pattern playback was eventually replaced at Haskins Laboratories by the HADES analysis and display system, designed by Philip Rubin, and implemented in Fortran on the VAX family of computers. A more modern version has been described by Arai and colleagues [2]. An on-line demonstration is available [3].

NLWeb

Natural Language Web or NLWeb was introduced by Microsoft in 2025. It is an open Python project designed to simplify the creation of natural language interfaces for websites. It enables users to query website contents using natural language, similar to interacting with an AI assistant. Every instance functions as a Model Context Protocol (MCP) server allowing websites to make their content discoverable and accessible to AI agents and other participants. NLWeb leverages existing web standards like Schema.org and RSS to build conversational capabilities of processing user queries through language models, performing semantic searches against website content and generating natural responses. It is platform-agnostic, running on all major systems and connecting to any vector database. Content to be indexed by NLWeb works best when it is organized in an AI friendly way. This means short, interlinked and semantically annotated articles work best. Initial adopters of NLWeb include TripAdvisor, Shopify, Eventbrite, and Hearst.