Jpred

Jpred v.4 is the latest version of the JPred Protein Secondary Structure Prediction Server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction, that has existed since 1998 in different versions. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 134 000 jobs per month and has carried out over 2 million predictions in total for users in 179 countries. == JPred 2 == The static HTML pages of JPred 2 are still available for reference. == JPred 3 == The JPred v3 followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References). This release added new functionality and fixed many bugs. The highlights are: New, friendlier user interface Retrained and optimised version of Jnet (v2) - mean secondary structure prediction accuracy of >81% Batch submission of jobs Better error checking of input sequences/alignments Predictions now (optionally) returned via e-mail Users may provide their own query names for each submission JPred now makes a prediction even when there are no PSI-BLAST hits to the query PS/PDF output now incorporates all the predictions == JPred 4 == The current version of JPred (v4) has the following improvements and updates incorporated: Retrained on the latest UniRef90 and SCOPe/ASTRAL version of Jnet (v2.3.1) - mean secondary structure prediction accuracy of >82%. Upgraded the Web Server to the latest technologies (Bootstrap framework, JavaScript) and updating the web pages – improving the design and usability through implementing responsive technologies. Added RESTful API and mass-submission and results retrieval scripts - resulting in peak throughput above 20,000 predictions per day. Added prediction jobs monitoring tools. Upgraded the results reporting – both, on the web-site, and through the optional email summary reports: improved batch submission, added results summary preview through Jalview results visualization summary in SVG and adding full multiple sequence alignments into the reports. Improved help-pages, incorporating tool-tips, and adding one-page step-by-step tutorials. Sequence residues are categorised or assigned to one of the secondary structure elements, such as alpha-helix, beta-sheet and coiled-coil. Jnet uses two neural networks for its prediction. The first network is fed with a window of 17 residues over each amino acid in the alignment plus a conservation number. It uses a hidden layer of nine nodes and has three output nodes, one for each secondary structure element. The second network is fed with a window of 19 residues (the result of first network) plus the conservation number. It has a hidden layer with nine nodes and has three output nodes.

Google Tasks

Google Tasks is a task management application developed by Google and included with Google Workspace. Included initially as a feature in Gmail and Google Calendar, Google Tasks launched as a core product with a standalone app in 2018. It is available for Android and iOS, as well as in the right-hand side panel on Google Workspace apps on the web and in Google Calendar. == History and development == Google Tasks began as an integration within other apps in G Suite (now Google Workspace), allowing to-do items to be created in Calendar and Gmail. Upon graduating to a core service on June 28, 2018, Google Tasks launched as a dedicated mobile app in which tasks can be sorted into lists, managed, and completed. Google Tasks launched the ability to create tasks from Google Chat messages in 2022.

AIXI

AIXI is a theoretical mathematical formalism for artificial general intelligence. It combines Solomonoff induction with sequential decision theory. AIXI was first proposed by Marcus Hutter in 2000 and several results regarding AIXI are proved in Hutter's 2005 book Universal Artificial Intelligence. AIXI is a reinforcement learning (RL) agent. It maximizes the expected total rewards received from the environment. Intuitively, it simultaneously considers every computable hypothesis (or environment). In each time step, it looks at every possible program and evaluates how many rewards that program generates depending on the next action taken. The promised rewards are then weighted by the subjective belief that this program constitutes the true environment. This belief is computed from the length of the program: longer programs are considered less likely, in line with Occam's razor. AIXI then selects the action that has the highest expected total reward in the weighted sum of all these programs. == Etymology == According to Hutter, the word "AIXI" can have several interpretations. AIXI can stand for AI based on Solomonoff's distribution, denoted by ξ {\displaystyle \xi } (which is the Greek letter xi), or e.g. it can stand for AI "crossed" (X) with induction (I). There are other interpretations. == Definition == AIXI is a reinforcement learning agent that interacts with some stochastic and unknown but computable environment μ {\displaystyle \mu } . The interaction proceeds in time steps, from t = 1 {\displaystyle t=1} to t = m {\displaystyle t=m} , where m ∈ N {\displaystyle m\in \mathbb {N} } is the lifespan of the AIXI agent. At time step t, the agent chooses an action a t ∈ A {\displaystyle a_{t}\in {\mathcal {A}}} (e.g. a limb movement) and executes it in the environment, and the environment responds with a "percept" e t ∈ E = O × R {\displaystyle e_{t}\in {\mathcal {E}}={\mathcal {O}}\times \mathbb {R} } , which consists of an "observation" o t ∈ O {\displaystyle o_{t}\in {\mathcal {O}}} (e.g., a camera image) and a reward r t ∈ R {\displaystyle r_{t}\in \mathbb {R} } , distributed according to the conditional probability μ ( o t r t | a 1 o 1 r 1 . . . a t − 1 o t − 1 r t − 1 a t ) {\displaystyle \mu (o_{t}r_{t}|a_{1}o_{1}r_{1}...a_{t-1}o_{t-1}r_{t-1}a_{t})} , where a 1 o 1 r 1 . . . a t − 1 o t − 1 r t − 1 a t {\displaystyle a_{1}o_{1}r_{1}...a_{t-1}o_{t-1}r_{t-1}a_{t}} is the "history" of actions, observations and rewards. The environment μ {\displaystyle \mu } is thus mathematically represented as a probability distribution over "percepts" (observations and rewards) which depend on the full history, so there is no Markov assumption (as opposed to other RL algorithms). Note again that this probability distribution is unknown to the AIXI agent. Furthermore, note again that μ {\displaystyle \mu } is computable, that is, the observations and rewards received by the agent from the environment μ {\displaystyle \mu } can be computed by some program (which runs on a Turing machine), given the past actions of the AIXI agent. The only goal of the AIXI agent is to maximize ∑ t = 1 m r t {\displaystyle \sum _{t=1}^{m}r_{t}} , that is, the sum of rewards from time step 1 to m. The AIXI agent is associated with a stochastic policy π : ( A × E ) ∗ → A {\displaystyle \pi :({\mathcal {A}}\times {\mathcal {E}})^{}\rightarrow {\mathcal {A}}} , which is the function it uses to choose actions at every time step, where A {\displaystyle {\mathcal {A}}} is the space of all possible actions that AIXI can take and E {\displaystyle {\mathcal {E}}} is the space of all possible "percepts" that can be produced by the environment. The environment (or probability distribution) μ {\displaystyle \mu } can also be thought of as a stochastic policy (which is a function): μ : ( A × E ) ∗ × A → E {\displaystyle \mu :({\mathcal {A}}\times {\mathcal {E}})^{}\times {\mathcal {A}}\rightarrow {\mathcal {E}}} , where the ∗ {\displaystyle } is the Kleene star operation. In general, at time step t {\displaystyle t} (which ranges from 1 to m), AIXI, having previously executed actions a 1 … a t − 1 {\displaystyle a_{1}\dots a_{t-1}} (which is often abbreviated in the literature as a < t {\displaystyle a_{

ELMo

ELMo (embeddings from language model) is a word embedding method for representing a sequence of words as a corresponding sequence of vectors. It was created by researchers at the Allen Institute for Artificial Intelligence, and University of Washington and first released in February 2018. It is a bidirectional LSTM which takes character-level as inputs and produces word-level embeddings, trained on a corpus of about 30 million sentences and 1 billion words. The architecture of ELMo accomplishes a contextual understanding of tokens. Deep contextualized word representation is useful for many natural language processing tasks, such as coreference resolution and polysemy resolution. ELMo was historically important as a pioneer of self-supervised generative pretraining followed by fine-tuning, where a large model is trained to reproduce a large corpus, then the large model is augmented with additional task-specific weights and fine-tuned on supervised task data. It was an instrumental step in the evolution towards transformer-based language modelling. == Architecture == ELMo is a multilayered bidirectional LSTM on top of a token embedding layer. The output of all LSTMs concatenated together consists of the token embedding. The input text sequence is first mapped by an embedding layer into a sequence of vectors. Then two parts are run in parallel over it. The forward part is a 2-layered LSTM with 4096 units and 512 dimension projections, and a residual connection from the first to second layer. The backward part has the same architecture, but processes the sequence back-to-front. The outputs from all 5 components (embedding layer, two forward LSTM layers, and two backward LSTM layers) are concatenated and multiplied by a linear matrix ("projection matrix") to produce a 512-dimensional representation per input token. ELMo was pretrained on a text corpus of 1 billion words. The forward part is trained by repeatedly predicting the next token, and the backward part is trained by repeatedly predicting the previous token. After the ELMo model is pretrained, its parameters are frozen, except for the projection matrix, which can be fine-tuned to minimize loss on specific language tasks. This is an early example of the pretraining-fine-tune paradigm. The original paper demonstrated this by improving state of the art on six benchmark NLP tasks. === Contextual word representation === The architecture of ELMo accomplishes a contextual understanding of tokens. For example, the first forward LSTM of ELMo would process each input token in the context of all previous tokens, and the first backward LSTM would process each token in the context of all subsequent tokens. The second forward LSTM would then incorporate those to further contextualize each token. Deep contextualized word representation is useful for many natural language processing tasks, such as coreference resolution and polysemy resolution. For example, consider the sentenceShe went to the bank to withdraw money.In order to represent the token "bank", the model must resolve its polysemy in context. The first forward LSTM would process "bank" in the context of "She went to the", which would allow it to represent the word to be a location that the subject is going towards. The first backward LSTM would process "bank" in the context of "to withdraw money", which would allow it to disambiguate the word as referring to a financial institution. The second forward LSTM can then process "bank" using the representation vector provided by the first backward LSTM, thus allowing it to represent it to be a financial institution that the subject is going towards. == Historical context == ELMo is one link in a historical evolution of language modelling. Consider a simple problem of document classification, where we want to assign a label (e.g., "spam", "not spam", "politics", "sports") to a given piece of text. The simplest approach is the "bag of words" approach, where each word in the document is treated independently, and its frequency is used as a feature for classification. This was computationally cheap but ignored the order of words and their context within the sentence. GloVe and Word2Vec built upon this by learning fixed vector representations (embeddings) for words based on their co-occurrence patterns in large text corpora. Like BERT (but unlike "bag of words" such as Word2Vec and GloVe), ELMo word embeddings are context-sensitive, producing different representations for words that share the same spelling. It was trained on a corpus of about 30 million sentences and 1 billion words. Previously, bidirectional LSTM was used for contextualized word representation. ELMo applied the idea to a large scale, achieving state of the art performance. After the 2017 publication of Transformer architecture, the architecture of ELMo was changed from a multilayered bidirectional LSTM to a Transformer encoder, giving rise to BERT. BERT has a similar pretrain-fine-tune workflow, but uses a Transformer with implications for more parallelizable training.

AIXI

AIXI is a theoretical mathematical formalism for artificial general intelligence. It combines Solomonoff induction with sequential decision theory. AIXI was first proposed by Marcus Hutter in 2000 and several results regarding AIXI are proved in Hutter's 2005 book Universal Artificial Intelligence. AIXI is a reinforcement learning (RL) agent. It maximizes the expected total rewards received from the environment. Intuitively, it simultaneously considers every computable hypothesis (or environment). In each time step, it looks at every possible program and evaluates how many rewards that program generates depending on the next action taken. The promised rewards are then weighted by the subjective belief that this program constitutes the true environment. This belief is computed from the length of the program: longer programs are considered less likely, in line with Occam's razor. AIXI then selects the action that has the highest expected total reward in the weighted sum of all these programs. == Etymology == According to Hutter, the word "AIXI" can have several interpretations. AIXI can stand for AI based on Solomonoff's distribution, denoted by ξ {\displaystyle \xi } (which is the Greek letter xi), or e.g. it can stand for AI "crossed" (X) with induction (I). There are other interpretations. == Definition == AIXI is a reinforcement learning agent that interacts with some stochastic and unknown but computable environment μ {\displaystyle \mu } . The interaction proceeds in time steps, from t = 1 {\displaystyle t=1} to t = m {\displaystyle t=m} , where m ∈ N {\displaystyle m\in \mathbb {N} } is the lifespan of the AIXI agent. At time step t, the agent chooses an action a t ∈ A {\displaystyle a_{t}\in {\mathcal {A}}} (e.g. a limb movement) and executes it in the environment, and the environment responds with a "percept" e t ∈ E = O × R {\displaystyle e_{t}\in {\mathcal {E}}={\mathcal {O}}\times \mathbb {R} } , which consists of an "observation" o t ∈ O {\displaystyle o_{t}\in {\mathcal {O}}} (e.g., a camera image) and a reward r t ∈ R {\displaystyle r_{t}\in \mathbb {R} } , distributed according to the conditional probability μ ( o t r t | a 1 o 1 r 1 . . . a t − 1 o t − 1 r t − 1 a t ) {\displaystyle \mu (o_{t}r_{t}|a_{1}o_{1}r_{1}...a_{t-1}o_{t-1}r_{t-1}a_{t})} , where a 1 o 1 r 1 . . . a t − 1 o t − 1 r t − 1 a t {\displaystyle a_{1}o_{1}r_{1}...a_{t-1}o_{t-1}r_{t-1}a_{t}} is the "history" of actions, observations and rewards. The environment μ {\displaystyle \mu } is thus mathematically represented as a probability distribution over "percepts" (observations and rewards) which depend on the full history, so there is no Markov assumption (as opposed to other RL algorithms). Note again that this probability distribution is unknown to the AIXI agent. Furthermore, note again that μ {\displaystyle \mu } is computable, that is, the observations and rewards received by the agent from the environment μ {\displaystyle \mu } can be computed by some program (which runs on a Turing machine), given the past actions of the AIXI agent. The only goal of the AIXI agent is to maximize ∑ t = 1 m r t {\displaystyle \sum _{t=1}^{m}r_{t}} , that is, the sum of rewards from time step 1 to m. The AIXI agent is associated with a stochastic policy π : ( A × E ) ∗ → A {\displaystyle \pi :({\mathcal {A}}\times {\mathcal {E}})^{}\rightarrow {\mathcal {A}}} , which is the function it uses to choose actions at every time step, where A {\displaystyle {\mathcal {A}}} is the space of all possible actions that AIXI can take and E {\displaystyle {\mathcal {E}}} is the space of all possible "percepts" that can be produced by the environment. The environment (or probability distribution) μ {\displaystyle \mu } can also be thought of as a stochastic policy (which is a function): μ : ( A × E ) ∗ × A → E {\displaystyle \mu :({\mathcal {A}}\times {\mathcal {E}})^{}\times {\mathcal {A}}\rightarrow {\mathcal {E}}} , where the ∗ {\displaystyle } is the Kleene star operation. In general, at time step t {\displaystyle t} (which ranges from 1 to m), AIXI, having previously executed actions a 1 … a t − 1 {\displaystyle a_{1}\dots a_{t-1}} (which is often abbreviated in the literature as a < t {\displaystyle a_{

Alexis Spectral Data

Alexis Spectral Data is a software developed for colour matching processes that calculates from available spectral data the colour numbers used by computers to display colours on screen. It displays the colour for each spectral reflectance curve and records the calculated trichromatic values and colour numbers along with the spectral curves. This eliminates the need to scan the samples separately with a truecolour Scanner while creating the database. The spectral data can be introduced manually as a series of reflectance values at wavelengths measured in different standard illuminants with an arbitrary but fixed increment that must be kept for each spectral curve throughout the creation of the whole database. Therefore, older UV-VIS Spectrophotometers that can't be interfaced with computers can also be used for creating the database needed for colour matching. Alexis Spectral Data determines the whiteness degree in a less time-consuming method, which permits storage and easier handling of the obtained data. Alexis Spectral Data can export the trichromatic values, calculated from the spectral curves, to Alexis Analyser, software that handles only trichromatic data. The earliest information about the development of this software comes from a paper published by a student at the University Politehnica Bucharest in 1993. The software runs on Windows based computers but not on other operating systems.

Rule induction

Rule induction is an area of machine learning in which formal rules are extracted from a set of observations. The rules extracted may represent a full scientific model of the data, or merely represent local patterns in the data. Data mining in general and rule induction in detail are trying to create algorithms without human programming but with analyzing existing data structures. In the easiest case, a rule is expressed with “if-then statements” and was created with the ID3 algorithm for decision tree learning. Rule learning algorithm are taking training data as input and creating rules by partitioning the table with cluster analysis. A possible alternative over the ID3 algorithm is genetic programming which evolves a program until it fits to the data. Creating different algorithm and testing them with input data can be realized in the WEKA software. Additional tools are machine learning libraries for Python, like scikit-learn. == Paradigms == Some major rule induction paradigms are: Association rule learning algorithms (e.g., Agrawal) Decision rule algorithms (e.g., Quinlan 1987) Hypothesis testing algorithms (e.g., RULEX) Horn clause induction Version spaces Rough set rules Inductive Logic Programming Boolean decomposition (Feldman) == Algorithms == Some rule induction algorithms are: Charade Rulex Progol CN2