AI Coding Vscode Extension

AI Coding Vscode Extension — independent reviews, comparisons, pricing and step-by-step guides on Aizhi.

Global serializability

In concurrency control of databases, transaction processing (transaction management), and other transactional distributed applications, global serializability (or modular serializability) is a property of a global schedule of transactions. A global schedule is the unified schedule of all the individual database (and other transactional object) schedules in a multidatabase environment (e.g., federated database). Complying with global serializability means that the global schedule is serializable, has the serializability property, while each component database (module) has a serializable schedule as well. In other words, a collection of serializable components provides overall system serializability, which is usually incorrect. A need in correctness across databases in multidatabase systems makes global serializability a major goal for global concurrency control (or modular concurrency control). With the proliferation of the Internet, Cloud computing, Grid computing, and small, portable, powerful computing devices (e.g., smartphones), as well as increase in systems management sophistication, the need for atomic distributed transactions and thus effective global serializability techniques, to ensure correctness in and among distributed transactional applications, seems to increase. In a federated database system or any other more loosely defined multidatabase system, which are typically distributed in a communication network, transactions span multiple (and possibly distributed) databases. Enforcing global serializability in such system, where different databases may use different types of concurrency control, is problematic. Even if every local schedule of a single database is serializable, the global schedule of a whole system is not necessarily serializable. The massive communication exchanges of conflict information needed between databases to reach conflict serializability globally would lead to unacceptable performance, primarily due to computer and communication latency. Achieving global serializability effectively over different types of concurrency control has been open for several years. == The global serializability problem == === Problem statement === The difficulties described above translate into the following problem: Find an efficient (high-performance and fault tolerant) method to enforce Global serializability (global conflict serializability) in a heterogeneous distributed environment of multiple autonomous database systems. The database systems may employ different concurrency control methods. No limitation should be imposed on the operations of either local transactions (confined to a single database system) or global transactions (span two or more database systems). === Quotations === Lack of an appropriate solution for the global serializability problem has driven researchers to look for alternatives to serializability as a correctness criterion in a multidatabase environment (e.g., see Relaxing global serializability below), and the problem has been characterized as difficult and open. The following two quotations demonstrate the mindset about it by the end of the year 1991, with similar quotations in numerous other articles: "Without knowledge about local as well as global transactions, it is highly unlikely that efficient global concurrency control can be provided... Additional complications occur when different component DBMSs [Database Management Systems] and the FDBMSs [Federated Database Management Systems] support different concurrency mechanisms... It is unlikely that a theoretically elegant solution that provides conflict serializability without sacrificing performance (i.e., concurrency and/or response time) and availability exists." === Proposed solutions === Several solutions, some partial, have been proposed for the global serializability problem. Among them: Global conflict graph (serializability graph, precedence graph) checking Distributed Two-phase locking (Distributed 2PL) Distributed Timestamp ordering Tickets (local logical timestamps which define local total orders, and are propagated to determine global partial order of transactions) == Relaxing global serializability == Some techniques have been developed for relaxed global serializability (i.e., they do not guarantee global serializability; see also Relaxing serializability). Among them (with several publications each): Quasi serializability Two-level serializability Another common reason nowadays for Global serializability relaxation is the requirement of availability of internet products and services. This requirement is typically answered by large scale data replication. The straightforward solution for synchronizing replicas' updates of a same database object is including all these updates in a single atomic distributed transaction. However, with many replicas such a transaction is very large, and may span several computers and networks that some of them are likely to be unavailable. Thus such a transaction is likely to end with abort and miss its purpose. Consequently, Optimistic replication (Lazy replication) is often utilized (e.g., in many products and services by Google, Amazon, Yahoo, and alike), while global serializability is relaxed and compromised for eventual consistency. In this case relaxation is done only for applications that are not expected to be harmed by it. Classes of schedules defined by relaxed global serializability properties either contain the global serializability class, or are incomparable with it. What differentiates techniques for relaxed global conflict serializability (RGCSR) properties from those of relaxed conflict serializability (RCSR) properties that are not RGCSR is typically the different way global cycles (span two or more databases) in the global conflict graph are handled. No distinction between global and local cycles exists for RCSR properties that are not RGCSR. RCSR contains RGCSR. Typically RGCSR techniques eliminate local cycles, i.e., provide local serializability (which can be achieved effectively by regular, known concurrency control methods); however, obviously they do not eliminate all global cycles (which would achieve global serializability).
Read more →
VITAL (machine learning software)

VITAL (Validating Investment Tool for Advancing Life Sciences) was a Board Management Software machine learning proprietary software developed by Aging Analytics, a company registered in Bristol (England) and dissolved in 2017. Andrew Garazha (the firm's Senior Analyst) declared that the project aimed "through iterative releases and updates to create a piece of software capable of making autonomous investment decisions." According to Nick Dyer-Witheford, VITAL 1.0 was a "basic algorithm". On 13 May 2014, Deep Knowledge Ventures, a Hong Kong venture capital firm, claimed to have appointed VITAL to its board of directors in order to prove that artificial intelligence could be an instrument for investment decision-making. The announcement received great press coverage despite the fact commentators consider this a publicity stunt. Fortune reported in 2019 that VITAL is no longer used. == Criticism == Academics and journalists viewed VITAL's board appointment with skepticism. University of Sheffield computer science professor Noel Sharkey called it "a publicity hype". Michael Osborne, a University of Oxford associate professor in machine learning, found it is "a gimmick to call that an actual board member". Simon Sharwood of The Register, wrote there is "a strong whiff of stunt and/or promotion about this". In a 2019 speech, the Chief Scientist of Australia, Alan Finkel, commented, "At the time, most of us probably dismissed Vital as a PR exercise. I admit, I used her story three years ago to get a laugh in one of my speeches." Florian Möslein, a law professor at the University of Marburg, wrote in 2018 that "Vital has widely been acknowledged as the 'world's first artificial intelligence company director'". Vice journalist Jason Koebler suggested that the software did not have any article intelligence capabilities and concluded "VITAL can’t talk, and it can’t hear, and it can’t be a real, functional executive of a company." Sharwood of The Register noted that because VITAL was not a natural person, it could not be a board member under Hong Kong's corporate governance laws. However, in a 2017 interview to The Nikkei, Dmitry Kaminskiy, managing partner of Deep Knowledge Ventures, stated that VITAL had observer status on the board and no voting rights. University of Sheffield computer science professor Noel Sharkey said of VITAL, "On first sight, it looks like a futuristic idea but on reflection it is really a little bit of publicity hype." Vice journalist Jason Koebler said "this is a gimmick" and said "There is literally nothing to suggest that VITAL has any sort of capabilities beyond any other proprietary analysis software". Michael Osborne, a University of Oxford associate professor in machine learning, found VITAL's appointment to be noncredible, saying it is "a bit of a gimmick to call that an actual board member". Osborne said that a core duty of board members to converse with each other, which the algorithm is incapable of doing, so its more likely functionality is to serve as a springboard for conversation among other board members. In a 2019 speech, the Chief Scientist of Australia, Alan Finkel, commented, "At the time, most of us probably dismissed Vital as a PR exercise. I admit, I used her story three years ago to get a laugh in one of my speeches." == Machine intelligence as board member == VITAL was created by a group of programmers employed by Aging Analytics According to Andrew Garazh, Aging Analytics Senior Analyst, VITAL was not a machine learning algorithm as the necessary datasets on investment rounds, intellectual property and clinical trial outcomes are generally not disclosed. Rather, VITAL used fuzzy logic based on 50 parameters to assess risk factors. Aging Analytics licensed the software to Deep Knowledge Ventures. It was used to help the human board members of Deep Knowledge Venture make investment decisions in biotechnology companies. For instance, it supported investments in Insilico Medicine, which creates ways for computers to help find drugs in research into aging. VITAL also supported investing in Pathway Pharmaceuticals, which uses the OncoFinder algorithm to choose and appraise cancer treatments. According to Dmitry Kaminskiy, managing partner of Deep Knowledge Ventures, the motivation for using VITAL was the large number of failed investments in the biotechnology sector and the desire to avoid investing in companies likely to fail. == Ethical and legal implications == Scholars addressed questions around the safety, privacy, accountability transparency and bias in algorithms. Writing in the philosophical journal Multitudes, the academic Ariel Kyrou raised questions about the consequences of a mistake made by an algorithm recommending a dangerous investment. He raised the hypothetical where VITAL was able to persuade the board to invest in a startup that had the facade of doing research into treatment for age-associated ills, but in actuality was run by terrorists who were raising funds. Kyrou raised a series of questions about who society would fault for VITAL's mistake. As the owner of VITAL, should Deep Knowledge Ventures be held accountable, or rather should the companies that supplied data to VITAL or the people who created VITAL be held liable? Simon Sharwood of The Register wrote that because the appointment of a software program to the board directors is not legally feasible in Hong Kong, there is "a strong whiff of stunt and/or promotion about this". Quoting a Thomson Reuters website describing Hong Kong legislation related to corporate governance, Sharwood pointed out that in Hong Kong "the board comprises all of the directors of the company" and "a director must normally be a natural person, except that a private company may have a body corporate as its director if the company is not a member of a listed group." He concluded that since VITAL cannot be considered a "natural person", it is merely a "cosmetic" appointment to the board and that "this software is no more a Board member than Caligula's horse was a senator". Sharwood further argued that corporations frequently purchase directors and officers liability insurance but that it would be practically impossible to get such insurance for VITAL. Sharwood also wrote that were VITAL to be hacked, any misinformation it outputs could be considered "false and misleading communications". In the book Research Handbook on the Law of Artificial Intelligence, Florian Mölein wrote that VITAL could not become a director as defined in Hong Kong's corporate laws, so the other directors just were approaching it as "a member of [the] board with observer status". Lin Shaowei raised concerns in a Journal of East China University of Political Science and Law article about how the software's appearance inspired a complex question about the relationship between corporate law and artificial intelligence. VITAL could be considered either a board director who has voting rights or an observer who does not. Lin said either choice raised questions about whether VITAL is subject to corporate law and who would be held accountable if VITAL recommends a choice that turns out to be damaging to the company. David Theo Goldberg in the Critical Times, a peer reviewed journal in Critical Global Theory, argues that VITAL processed a dataset to predict the most remunerative investment opportunities. Drawing his analysis on an article from Business Insider, Goldberg describes VITAL's decision-making predictiveness based "on surface pattern recognition and the identification of regularities and/or irregularities". In other words, Goldberg asserts that "the normativity of the surface" explains algorithmic knowledge of a "product" like VITAL. In Homo Deus, Yuval Noah Harari mentions VITAL as an example of the future risks that humankind faces. Harari argues that the human mind is being replaced by a world in which algorithms and data make the decisions. Specifically, it is argued that "as algorithms push humans out of the job market," executive boards driven by artificial intelligence are more likely to give priority to algorithms over the humans.
Read more →
Learning classifier system

Learning classifier systems, or LCS, are a paradigm of rule-based machine learning methods that combine a discovery component (e.g. typically a genetic algorithm in evolutionary computation) with a learning component (performing either supervised learning, reinforcement learning, or unsupervised learning). Learning classifier systems seek to identify a set of context-dependent rules that collectively store and apply knowledge in a piecewise manner in order to make predictions (e.g. behavior modeling, classification, data mining, regression, function approximation, or game strategy). This approach allows complex solution spaces to be broken up into smaller, simpler parts for the reinforcement learning that is inside artificial intelligence research. The founding concepts behind learning classifier systems came from attempts to model complex adaptive systems, using rule-based agents to form an artificial cognitive system (i.e. artificial intelligence). == Methodology == The architecture and components of a given learning classifier system can be quite variable. It is useful to think of an LCS as a machine consisting of several interacting components. Components may be added or removed, or existing components modified/exchanged to suit the demands of a given problem domain (like algorithmic building blocks) or to make the algorithm flexible enough to function in many different problem domains. As a result, the LCS paradigm can be flexibly applied to many problem domains that call for machine learning. The major divisions among LCS implementations are as follows: (1) Michigan-style architecture vs. Pittsburgh-style architecture, (2) reinforcement learning vs. supervised learning, (3) incremental learning vs. batch learning, (4) online learning vs. offline learning, (5) strength-based fitness vs. accuracy-based fitness, and (6) complete action mapping vs best action mapping. These divisions are not necessarily mutually exclusive. For example, XCS, the best known and best studied LCS algorithm, is Michigan-style, was designed for reinforcement learning but can also perform supervised learning, applies incremental learning that can be either online or offline, applies accuracy-based fitness, and seeks to generate a complete action mapping. === Elements of a generic LCS algorithm === Keeping in mind that LCS is a paradigm for genetic-based machine learning rather than a specific method, the following outlines key elements of a generic, modern (i.e. post-XCS) LCS algorithm. For simplicity let us focus on Michigan-style architecture with supervised learning. See the illustrations on the right laying out the sequential steps involved in this type of generic LCS. ==== Environment ==== The environment is the source of data upon which an LCS learns. It can be an offline, finite training dataset (characteristic of a data mining, classification, or regression problem), or an online sequential stream of live training instances. Each training instance is assumed to include some number of features (also referred to as attributes, or independent variables), and a single endpoint of interest (also referred to as the class, action, phenotype, prediction, or dependent variable). Part of LCS learning can involve feature selection, therefore not all of the features in the training data need to be informative. The set of feature values of an instance is commonly referred to as the state. For simplicity let's assume an example problem domain with Boolean/binary features and a Boolean/binary class. For Michigan-style systems, one instance from the environment is trained on each learning cycle (i.e. incremental learning). Pittsburgh-style systems perform batch learning, where rule sets are evaluated in each iteration over much or all of the training data. ==== Rule/classifier/population ==== A rule is a context dependent relationship between state values and some prediction. Rules typically take the form of an {IF:THEN} expression, (e.g. {IF 'condition' THEN 'action'}, or as a more specific example, {IF 'red' AND 'octagon' THEN 'stop-sign'}). A critical concept in LCS and rule-based machine learning alike, is that an individual rule is not in itself a model, since the rule is only applicable when its condition is satisfied. Think of a rule as a "local-model" of the solution space. Rules can be represented in many different ways to handle different data types (e.g. binary, discrete-valued, ordinal, continuous-valued). Given binary data LCS traditionally applies a ternary rule representation (i.e. rules can include either a 0, 1, or '#' for each feature in the data). The 'don't care' symbol (i.e. '#') serves as a wild card within a rule's condition allowing rules, and the system as a whole to generalize relationships between features and the target endpoint to be predicted. Consider the following rule (#1###0 ~ 1) (i.e. condition ~ action). This rule can be interpreted as: IF the second feature = 1 AND the sixth feature = 0 THEN the class prediction = 1. We would say that the second and sixth features were specified in this rule, while the others were generalized. This rule, and the corresponding prediction are only applicable to an instance when the condition of the rule is satisfied by the instance. This is more commonly referred to as matching. In Michigan-style LCS, each rule has its own fitness, as well as a number of other rule-parameters associated with it that can describe the number of copies of that rule that exist (i.e. the numerosity), the age of the rule, its accuracy, or the accuracy of its reward predictions, and other descriptive or experiential statistics. A rule along with its parameters is often referred to as a classifier. In Michigan-style systems, classifiers are contained within a population [P] that has a user defined maximum number of classifiers. Unlike most stochastic search algorithms (e.g. evolutionary algorithms), LCS populations start out empty (i.e. there is no need to randomly initialize a rule population). Classifiers will instead be initially introduced to the population with a covering mechanism. In any LCS, the trained model is a set of rules/classifiers, rather than any single rule/classifier. In Michigan-style LCS, the entire trained (and optionally, compacted) classifier population forms the prediction model. ==== Matching ==== One of the most critical and often time-consuming elements of an LCS is the matching process. The first step in an LCS learning cycle takes a single training instance from the environment and passes it to [P] where matching takes place. In step two, every rule in [P] is now compared to the training instance to see which rules match (i.e. are contextually relevant to the current instance). In step three, any matching rules are moved to a match set [M]. A rule matches a training instance if all feature values specified in the rule condition are equivalent to the corresponding feature value in the training instance. For example, assuming the training instance is (001001 ~ 0), these rules would match: (###0## ~ 0), (00###1 ~ 0), (#01001 ~ 1), but these rules would not (1##### ~ 0), (000##1 ~ 0), (#0#1#0 ~ 1). Notice that in matching, the endpoint/action specified by the rule is not taken into consideration. As a result, the match set may contain classifiers that propose conflicting actions. In the fourth step, since we are performing supervised learning, [M] is divided into a correct set [C] and an incorrect set [I]. A matching rule goes into the correct set if it proposes the correct action (based on the known action of the training instance), otherwise it goes into [I]. In reinforcement learning LCS, an action set [A] would be formed here instead, since the correct action is not known. ==== Covering ==== At this point in the learning cycle, if no classifiers made it into either [M] or [C] (as would be the case when the population starts off empty), the covering mechanism is applied (fifth step). Covering is a form of online smart population initialization. Covering randomly generates a rule that matches the current training instance (and in the case of supervised learning, that rule is also generated with the correct action. Assuming the training instance is (001001 ~ 0), covering might generate any of the following rules: (#0#0## ~ 0), (001001 ~ 0), (#010## ~ 0). Covering not only ensures that each learning cycle there is at least one correct, matching rule in [C], but that any rule initialized into the population will match at least one training instance. This prevents LCS from exploring the search space of rules that do not match any training instances. ==== Parameter updates/credit assignment/learning ==== In the sixth step, the rule parameters of any rule in [M] are updated to reflect the new experience gained from the current training instance. Depending on the LCS algorithm, a number of updates can take place at this step. For supervised learning, we can simply update the accuracy/error of a
Read more →
Count sketch

Count sketch is a type of dimensionality reduction that is particularly efficient in statistics, machine learning and algorithms. It was invented by Moses Charikar, Kevin Chen and Martin Farach-Colton in an effort to speed up the AMS Sketch by Alon, Matias and Szegedy for approximating the frequency moments of streams (these calculations require counting of the number of occurrences for the distinct elements of the stream). The sketch is nearly identical to the Feature hashing algorithm by John Moody, but differs in its use of hash functions with low dependence, which makes it more practical. In order to still have a high probability of success, the median trick is used to aggregate multiple count sketches, rather than the mean. These properties allow use for explicit kernel methods, bilinear pooling in neural networks and is a cornerstone in many numerical linear algebra algorithms. == Intuitive explanation == The inventors of this data structure offer the following iterative explanation of its operation: at the simplest level, the output of a single hash function s mapping stream elements q into {+1, -1} is feeding a single up/down counter C. After a single pass over the data, the frequency n ( q ) {\displaystyle n(q)} of a stream element q can be approximated, although extremely poorly, by the expected value E [ C ⋅ s ( q ) ] {\displaystyle {\mathbf {E}}[C\cdot s(q)]} ; a straightforward way to improve the variance of the previous estimate is to use an array of different hash functions s i {\displaystyle s_{i}} , each connected to its own counter C i {\displaystyle C_{i}} . For each i, the E [ C i ⋅ s i ( q ) ] = n ( q ) {\displaystyle {\mathbf {E}}[C_{i}\cdot s_{i}(q)]=n(q)} still holds, so averaging across the i range will tighten the approximation; the previous construct still has a major deficiency: if a lower-frequency-but-still-important output element a exhibits a hash collision with a high-frequency element even for one of the s i {\displaystyle s_{i}} hashes, n ( a ) {\displaystyle n(a)} estimate can be significantly affected. Avoiding this requires reducing the frequency of collision counter updates between any two distinct elements. This is achieved by replacing each C i {\displaystyle C_{i}} in the previous construct with an array of m counters (making the counter set into a two-dimensional matrix C i , j {\displaystyle C_{i,j}} ), with index j of a particular counter to be incremented/decremented selected via another set of hash functions h i {\displaystyle h_{i}} that map element q into the range {1..m}. Since E [ C i , h i ( q ) ⋅ s i ( q ) ] = n ( q ) {\displaystyle {\mathbf {E}}[C_{i,h_{i}(q)}\cdot s_{i}(q)]=n(q)} , averaging across all values of i will work. == Mathematical definition == 1. For constants w {\displaystyle w} and t {\displaystyle t} (to be defined later) independently choose d = 2 t + 1 {\displaystyle d=2t+1} random hash functions h 1 , … , h d {\displaystyle h_{1},\dots ,h_{d}} and s 1 , … , s d {\displaystyle s_{1},\dots ,s_{d}} such that h i : [ n ] → [ w ] {\displaystyle h_{i}:[n]\to [w]} and s i : [ n ] → { ± 1 } {\displaystyle s_{i}:[n]\to \{\pm 1\}} . It is necessary that the hash families from which h i {\displaystyle h_{i}} and s i {\displaystyle s_{i}} are chosen be pairwise independent. 2. For each item q i {\displaystyle q_{i}} in the stream, add s j ( q i ) {\displaystyle s_{j}(q_{i})} to the h j ( q i ) {\displaystyle h_{j}(q_{i})} th bucket of the j {\displaystyle j} th hash. At the end of this process, one has w d {\displaystyle wd} sums ( C i j ) {\displaystyle (C_{ij})} where C i , j = ∑ h i ( k ) = j s i ( k ) . {\displaystyle C_{i,j}=\sum _{h_{i}(k)=j}s_{i}(k).} To estimate the count of q {\displaystyle q} s one computes the following value: r q = median i = 1 d s i ( q ) ⋅ C i , h i ( q ) . {\displaystyle r_{q}={\text{median}}_{i=1}^{d}\,s_{i}(q)\cdot C_{i,h_{i}(q)}.} The values s i ( q ) ⋅ C i , h i ( q ) {\displaystyle s_{i}(q)\cdot C_{i,h_{i}(q)}} are unbiased estimates of how many times q {\displaystyle q} has appeared in the stream. The estimate r q {\displaystyle r_{q}} has variance O ( m i n { m 1 2 / w 2 , m 2 2 / w } ) {\displaystyle O(\mathrm {min} \{m_{1}^{2}/w^{2},m_{2}^{2}/w\})} , where m 1 {\displaystyle m_{1}} is the length of the stream and m 2 2 {\displaystyle m_{2}^{2}} is ∑ q ( ∑ i [ q i = q ] ) 2 {\displaystyle \sum _{q}(\sum _{i}[q_{i}=q])^{2}} . Furthermore, r q {\displaystyle r_{q}} is guaranteed to never be more than 2 m 2 / w {\displaystyle 2m_{2}/{\sqrt {w}}} off from the true value, with probability 1 − e − O ( t ) {\displaystyle 1-e^{-O(t)}} . === Vector formulation === Alternatively Count-Sketch can be seen as a linear mapping with a non-linear reconstruction function. Let M ( i ∈ [ d ] ) ∈ { − 1 , 0 , 1 } w × n {\displaystyle M^{(i\in [d])}\in \{-1,0,1\}^{w\times n}} , be a collection of d = 2 t + 1 {\displaystyle d=2t+1} matrices, defined by M h i ( j ) , j ( i ) = s i ( j ) {\displaystyle M_{h_{i}(j),j}^{(i)}=s_{i}(j)} for j ∈ [ w ] {\displaystyle j\in [w]} and 0 everywhere else. Then a vector v ∈ R n {\displaystyle v\in \mathbb {R} ^{n}} is sketched by C ( i ) = M ( i ) v ∈ R w {\displaystyle C^{(i)}=M^{(i)}v\in \mathbb {R} ^{w}} . To reconstruct v {\displaystyle v} we take v j ∗ = median i C j ( i ) s i ( j ) {\displaystyle v_{j}^{}={\text{median}}_{i}C_{j}^{(i)}s_{i}(j)} . This gives the same guarantees as stated above, if we take m 1 = ‖ v ‖ 1 {\displaystyle m_{1}=\|v\|_{1}} and m 2 = ‖ v ‖ 2 {\displaystyle m_{2}=\|v\|_{2}} . == Relation to Tensor sketch == The count sketch projection of the outer product of two vectors is equivalent to the convolution of two component count sketches. The count sketch computes a vector convolution C ( 1 ) x ∗ C ( 2 ) x T {\displaystyle C^{(1)}x\ast C^{(2)}x^{T}} , where C ( 1 ) {\displaystyle C^{(1)}} and C ( 2 ) {\displaystyle C^{(2)}} are independent count sketch matrices. Pham and Pagh show that this equals C ( x ⊗ x T ) {\displaystyle C(x\otimes x^{T})} – a count sketch C {\displaystyle C} of the outer product of vectors, where ⊗ {\displaystyle \otimes } denotes Kronecker product. The fast Fourier transform can be used to do fast convolution of count sketches. By using the face-splitting product such structures can be computed much faster than normal matrices.
Read more →
Comparison of video editing software

This is a comparison of non-linear video editing software applications. See also a more complete list of video editing software. == General information == This table gives basic general information about the different editors: === Active === === Discontinued / Inactive === ==== Definition ==== professional: used for full length Hollywood movies; professional (small): mainly used for paid commercials, short films or podcasts/YouTube channels; prosumer: Mainly targeting private use, anything that can do more than just trimming a film; basic: trimming a film; == System requirements == This table lists the operating systems that different editors can run on without emulation, as well as other system requirements. Note that minimum system requirements are listed; some features (like High Definition support) may be unavailable with these specifications. "Unix" includes the similar Linux, BSD and Unix-like operating systems. == High definition/High resolution import == The table below indicates the ability of each program to import various High Definition video or High resolution video formats for editing. == Feature set == == Output options == Please note that recording to Blu-ray does not imply 1080@50p/60p . Most only support up to 1080i 25/30 frames per second recording. Also not all formats can be output.
Read more →
GeWorkbench

geWorkbench (genomics Workbench) is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing funded through the NIH Roadmap (NIH Common Fund). Many systems and structure biology tools developed by MAGNet investigators are available as geWorkbench plugins. == Features == Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc. Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence and protein structure data (e.g., MarkUs). Integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. Component integration through platform management of inputs and outputs. Among data that can be shared between components are expression datasets, interaction networks, sample and marker (gene) sets and sequences. Dataset history tracking - complete record of data sets used and input settings. Integration with 3rd party tools such as GenePattern, Cytoscape, and Genomespace. Demonstrations of each feature described can be found at GeWorkbench-web Tutorials. == Versions == geWorkbench is open-source software that can be downloaded and installed locally. A zip file of the released version Java source is also available. Prepackaged installer versions also exist for Windows, Macintosh, and Linux.
Read more →
International Conference on Computer Vision

The International Conference on Computer Vision (ICCV) is a research conference sponsored by the Institute of Electrical and Electronics Engineers (IEEE) held every other year. It is considered to be one of the top conferences in computer vision, alongside CVPR and ECCV, and it is held on years in which ECCV is not. The conference is usually spread over four to five days. Typically, experts in the focus areas give tutorial talks on the first day, then the technical sessions (and poster sessions in parallel) follow. Recent conferences have also had an increasing number of focused workshops and a commercial exhibition. == Awards == === Azriel Rosenfeld Lifetime Achievement Award === The Azriel Rosenfeld Award, or Azriel Rosenfeld Lifetime Achievement Award, recognizes researchers who have made significant contributions to the field of computer vision over their careers. It is named in memory of computer scientist and mathematician Azriel Rosenfeld. The following people have received this award: === Helmholtz Prize === The ICCV Helmholtz Prize, known as the Test of Time Award before 2013, is awarded every other year at the ICCV, recognizing ICCV papers from ten or more years earlier that had a significant impact on computer vision research. Winners are selected by the IEEE Computer Society's Technical Committee on Pattern Analysis and Machine Intelligence. The award is named after the 19th century physician and physicist Hermann von Helmholtz, and the ICCV's award is not related to the various Helmholtz Prizes in physics, or the Hermann von Helmholtz Prize in neuroscience. === Marr Prize === The ICCV best-paper award is the Marr Prize, named after British neuroscientist David Marr. === Mark Everingham Prize === The Mark Everingham Prize is an award given yearly by the Technical Committee on Pattern Analysis and Machine Intelligence of the IEEE Computer Society at the IEEE International Conference on Computer Vision or the European Conference on Computer Vision to commemorate the late Mark Everingham, "one of the rising stars of computer vision", and to encourage others to follow in his footsteps by acting to further progress in the computer vision community as a whole. The prize is given to a researcher, or a team of researchers, who have made a selfless contribution of significant benefit to other members of the computer vision community. The Mark Everingham Prize for Rigorous Evaluation was an award given in 2012 at the British Machine Vision Conference. === PAMI Distinguished Researcher Award === The PAMI Distinguished Researcher Award (until 2013 called Significant Researcher Award) is awarded to candidates whose research projects have significantly contributed to the progress of computer vision. Awards are made based on major research contributions, as well as the role of those contributions in influencing and inspiring other research. Candidates are nominated by the community. The following people have received this award: == Conference list == The conference is usually held in the Spring in various international locations.
Read more →
Differential evolution

Differential evolution (DE) is an evolutionary algorithm to optimize a problem by iteratively trying to improve a candidate solution with regard to a given measure of quality. Such methods are commonly known as metaheuristics as they make few or no assumptions about the optimized problem and can search very large spaces of candidate solutions. However, metaheuristics such as DE do not guarantee an optimal solution is ever found. DE is used for multidimensional real-valued functions but does not use the gradient of the problem being optimized, which means DE does not require the optimization problem to be differentiable, as is required by classic optimization methods such as gradient descent and quasi-newton methods. DE can therefore also be used on optimization problems that are not even continuous, are noisy, change over time, etc. DE optimizes a problem by maintaining a population of candidate solutions and creating new candidate solutions by combining existing ones according to its simple formulae, and then keeping whichever candidate solution has the best score or fitness on the optimization problem at hand. In this way, the optimization problem is treated as a black box that merely provides a measure of quality given a candidate solution and the gradient is therefore not needed. == History == Storn and Price introduced Differential Evolution in 1995. Books have been published on theoretical and practical aspects of using DE in parallel computing, multiobjective optimization, constrained optimization, and the books also contain surveys of application areas. Surveys on the multi-faceted research aspects of DE can be found in journal articles. == Algorithm == A basic variant of the DE algorithm works by having a population of candidate solutions (called agents). These agents are moved around in the search-space by using simple mathematical formulae to combine the positions of existing agents from the population. If the new position of an agent is an improvement then it is accepted and forms part of the population, otherwise the new position is simply discarded. The process is repeated and by doing so it is hoped, but not guaranteed, that a satisfactory solution will eventually be discovered. Formally, let f : R n → R {\displaystyle f:\mathbb {R} ^{n}\to \mathbb {R} } be the fitness function which must be minimized (note that maximization can be performed by considering the function h := − f {\displaystyle h:=-f} instead). The function takes a candidate solution as argument in the form of a vector of real numbers. It produces a real number as output which indicates the fitness of the given candidate solution. The gradient of f {\displaystyle f} is not known. The goal is to find a solution m {\displaystyle \mathbf {m} } for which f ( m ) ≤ f ( p ) {\displaystyle f(\mathbf {m} )\leq f(\mathbf {p} )} for all p {\displaystyle \mathbf {p} } in the search-space, which means that m {\displaystyle \mathbf {m} } is the global minimum. Let x ∈ R n {\displaystyle \mathbf {x} \in \mathbb {R} ^{n}} designate a candidate solution (agent) in the population. The basic DE algorithm can then be described as follows: Choose the parameters NP ≥ 4 {\displaystyle {\text{NP}}\geq 4} , CR ∈ [ 0 , 1 ] {\displaystyle {\text{CR}}\in [0,1]} , and F ∈ [ 0 , 2 ] {\displaystyle F\in [0,2]} . NP : NP {\displaystyle {\text{NP}}} is the population size, i.e. the number of candidate agents or "parents". CR : The parameter CR ∈ [ 0 , 1 ] {\displaystyle {\text{CR}}\in [0,1]} is called the crossover probability. F : The parameter F ∈ [ 0 , 2 ] {\displaystyle F\in [0,2]} is called the differential weight. Typical settings are N P = 10 n {\displaystyle NP=10n} , C R = 0.9 {\displaystyle CR=0.9} and F = 0.8 {\displaystyle F=0.8} . Optimization performance may be greatly impacted by these choices; see below. Initialize all agents x {\displaystyle \mathbf {x} } with random positions in the search-space. Until a termination criterion is met (e.g. number of iterations performed, or adequate fitness reached), repeat the following: For each agent x {\displaystyle \mathbf {x} } in the population do: Pick three agents a , b {\displaystyle \mathbf {a} ,\mathbf {b} } , and c {\displaystyle \mathbf {c} } from the population at random, they must be distinct from each other as well as from agent x {\displaystyle \mathbf {x} } . ( a {\displaystyle \mathbf {a} } is called the "base" vector.) Pick a random index R ∈ { 1 , … , n } {\displaystyle R\in \{1,\ldots ,n\}} where n {\displaystyle n} is the dimensionality of the problem being optimized. Compute the agent's potentially new position y = [ y 1 , … , y n ] {\displaystyle \mathbf {y} =[y_{1},\ldots ,y_{n}]} as follows: For each i ∈ { 1 , … , n } {\displaystyle i\in \{1,\ldots ,n\}} , pick a uniformly distributed random number r i ∼ U ( 0 , 1 ) {\displaystyle r_{i}\sim U(0,1)} If r i < C R {\displaystyle r_{i} Read more →
D4Science

D4Science is a Data Infrastructure offering services by community-driven virtual research environments. In particular, it supports communities of practice willing to implement open science practices, thus it is an Open Science Infrastructure. The infrastructure follows the system of systems approach, where the constituent systems (Service providers) offer "resources" (namely services and by them data, computing, storage) assembled together to implement the overall set of D4Science services. In particular, D4Science aggregates "domain agnostic" service providers as well as community-specific ones to build a unifying space where the aggregated resources can be exploited via Virtual research Environments and their services. It is spread across several sites, the primary one is hosted by the Istituto di Scienza e Tecnologie dell'Informazione of National Research Council (Italy). At the earth of this infrastructure there is an Open Source Software named gCube system. == Services == D4Science offers: Virtual Research Environment as a Service providing any community of practice with a dedicated working environment supporting any knowledge production process in a collaborative way, in fact every VRE enables computer-supported cooperative work by design. D4Science-based VREs are web-based, community-oriented, collaborative, user-friendly, open-science-enabler working environments for scientists and practitioners willing to work together to perform a set of (research) task. From the end-user perspective, each VRE manifests in a unifying web application (and a set of application programming interfaces (APIs)): (a) comprising several applications organised in specific menu items and (b) running in a plain web browser. Every application is providing VRE users with facilities implemented by relying on one or more services provisioned by diverse providers. Among the basic services every VRE is equipped with there are a Social Networking area enabling collaborative and open discussions on any topic and disseminating information of interest for the community, for example, the availability of a research outcome; a Workspace for storing, organizing and sharing any version of a research artifact, including dataset and model implementation; a User Management dashboard for managing membership and roles; a Catalogue Service recording the assets worth being published thus to make it possible for others to be informed and make use of these assets. Science Gateway as a Service providing a community of practice with a dedicated science gateway hosting a selected set of virtual research environments. Data Analytics at scale for data analytics including: a proprietary data analytics platform (DataMiner) to execute analytics tasks either by relying on methods provided by the user or by others. It is endowed with importing and sharing facilities for analytics methods implemented in heterogeneous forms including R, Java, Python, and KNIME. The platform enacts tasks execution by a distributed and hybrid computing infrastructure. Moreover, one of the worth highlighting feature of this platform is its open science-friendliness. All the analytics methods integrated in it are exposed by a standard protocol (the OGC WPS protocol) clients can use to get informed on available methods as well as to start processes, monitor their execution and access results. Every analytics task performed by the platform automatically produces a provenance record catering for the reproducibility of the task; an RStudio-based development environment for R enabling to perform statistical computing tasks in the cloud. This RStudio environment is (i) preconfigured with libraries and packages to ease the execution of common data analytics tasks, and (ii) provides seamless access to the VRE Workspace enabling sharing of resources with other members of the same working environment. a Jupyter-based notebook environment for developing and executing interactive computing by JupyterLab instances. Each JupyterLab is (i) preconfigured with libraries and packages to ease the execution of common data analytics tasks, and (ii) provides access to the VRE Workspace enabling sharing of resources with other members of the same working environment. == Community == The D4Science Infrastructure serves more than 24,000 registered users (August 2024) through 177 active VREs offered via 20 Science gateways. This extensive infrastructure not only supports a diverse range of scientific communities but also fosters significant engagement and collaboration among researchers worldwide. Engagement within the D4Science community is robust, with users benefiting from user-friendly application environments tailored to their specific needs. The platform allows users to securely preserve, access, and share their data from anywhere, fostering a collaborative and inclusive research environment. Additionally, groups of users can create their own virtual environments and customise them with the applications they need, further enhancing the platform's flexibility and usability. Supported communities and cases range from Agri-food to Social Data Science, Earth Science and Marine Science. These diverse applications demonstrate the versatility and broad applicability of the D4Science Infrastructure, making it an invaluable resource for researchers across various scientific domains. == History == The D4Science development has been supported by several European-funded projects. DILIGENT (2004-2007) in the Sixth Framework Programme for Research and Technological Development was the forerunner where a testbed infrastructure built by integrating digital library and grid computing technologies and resources was conceived and developed to serve the needs of communities of practice involved in knowledge development. In the context of the Seventh Framework Programme for research, technological development and demonstration the development of the D4Science initiative. In this period the infrastructure was established and developed to serve communities of practices from domains ranging from Earth Science to Marine Science with worldwide scope In the context of the H2020 research and innovation programme the maturity level of the D4Science infrastructure was high enough to allow a large and very diverse set of communities of practice to benefit from it and its services and further contribute to its development. Moreover, the services offered by the infrastructure have been developed to support open science practices. The operation and improvement of the D4Science infrastructure facilities are still ongoing while its exploitation is progressively growing.
Read more →
Grammatical evolution

Grammatical evolution (GE) is a genetic programming (GP) technique (or approach) from evolutionary computation pioneered by Conor Ryan, JJ Collins and Michael O'Neill in 1998 at the BDS Group in the University of Limerick. As in any other GP approach, the objective is to find an executable program, program fragment, or function, which will achieve a good fitness value for a given objective function. In most published work on GP, a LISP-style tree-structured expression is directly manipulated, whereas GE applies genetic operators to an integer string, subsequently mapped to a program (or similar) through the use of a grammar, which is typically expressed in Backus–Naur form. One of the benefits of GE is that this mapping simplifies the application of search to different programming languages and other structures. == Problem addressed == In type-free, conventional Koza-style GP, the function set must meet the requirement of closure: all functions must be capable of accepting as their arguments the output of all other functions in the function set. Usually, this is implemented by dealing with a single data-type such as double-precision floating point. While modern Genetic Programming frameworks support typing, such type-systems have limitations that Grammatical Evolution does not suffer from. == GE's solution == GE offers a solution to the single-type limitation by evolving solutions according to a user-specified grammar (usually a grammar in Backus-Naur form). Therefore, the search space can be restricted, and domain knowledge of the problem can be incorporated. The inspiration for this approach comes from a desire to separate the "genotype" from the "phenotype": in GP, the objects the search algorithm operates on and what the fitness evaluation function interprets are one and the same. In contrast, GE's "genotypes" are ordered lists of integers which code for selecting rules from the provided context-free grammar. The phenotype, however, is the same as in Koza-style GP: a tree-like structure that is evaluated recursively. This model is more in line with how genetics work in nature, where there is a separation between an organism's genotype and the final expression of phenotype in proteins, etc. Separating genotype and phenotype allows a modular approach. In particular, the search portion of the GE paradigm needn't be carried out by any one particular algorithm or method. Observe that the objects GE performs search on are the same as those used in genetic algorithms. This means, in principle, that any existing genetic algorithm package, such as the popular GAlib, can be used to carry out the search, and a developer implementing a GE system need only worry about carrying out the mapping from list of integers to program tree. It is also in principle possible to perform the search using some other method, such as particle swarm optimization (see the remark below); the modular nature of GE creates many opportunities for hybrids as the problem of interest to be solved dictates. Brabazon and O'Neill have successfully applied GE to predicting corporate bankruptcy, forecasting stock indices, bond credit ratings, and other financial applications. GE has also been used with a classic predator-prey model to explore the impact of parameters such as predator efficiency, niche number, and random mutations on ecological stability. It is possible to structure a GE grammar that for a given function/terminal set is equivalent to genetic programming. == Criticism == Despite its successes, GE has been the subject of some criticism. One issue is that as a result of its mapping operation, GE's genetic operators do not achieve high locality which is a highly regarded property of genetic operators in evolutionary algorithms. == Variants == Although GE was originally described in terms of using an Evolutionary Algorithm, specifically, a Genetic Algorithm, other variants exist. For example, GE researchers have experimented with using particle swarm optimization to carry out the searching instead of genetic algorithms with results comparable to that of normal GE; this is referred to as a "grammatical swarm"; using only the basic PSO model it has been found that PSO is probably equally capable of carrying out the search process in GE as simple genetic algorithms are. (Although PSO is normally a floating-point search paradigm, it can be discretized, e.g., by simply rounding each vector to the nearest integer, for use with GE.) Yet another possible variation that has been experimented with in the literature is attempting to encode semantic information in the grammar in order to further bias the search process. Other work showed that, with biased grammars that leverage domain knowledge, even random search can be used to drive GE. == Related work == GE was originally a combination of the linear representation as used by the Genetic Algorithm for Developing Software (GADS) and Backus Naur Form grammars, which were originally used in tree-based GP by Wong and Leung in 1995 and Whigham in 1996. Other related work noted in the original GE paper was that of Frederic Gruau, who used a conceptually similar "embryonic" approach, as well as that of Keller and Banzhaf, which similarly used linear genomes. == Implementations == There are several implementations of GE. These include the following.
Read more →
Multilayer perceptron

In deep learning, a multilayer perceptron (MLP) is a kind of modern feedforward neural network consisting of fully connected neurons with nonlinear activation functions, organized in layers, notable for being able to distinguish data that is not linearly separable. Modern neural networks are trained using backpropagation and are colloquially referred to as "vanilla" networks. MLPs grew out of an effort to improve on single-layer perceptrons, which could only be applied to linearly separable data. A perceptron traditionally used a Heaviside step function as its nonlinear activation function. However, the backpropagation algorithm requires that modern MLPs use continuous activation functions such as sigmoid or ReLU. Multilayer perceptrons form the basis of deep learning, and are applicable across a vast set of diverse domains. == Timeline == In 1943, Warren McCulloch and Walter Pitts proposed the binary artificial neuron as a logical model of biological neural networks. In 1958, Frank Rosenblatt proposed the multilayered perceptron model, consisting of an input layer, a hidden layer with randomized weights that did not learn, and an output layer with learnable connections. In 1962, Rosenblatt published many variants and experiments on perceptrons in his book Principles of Neurodynamics, including up to 2 trainable layers by "back-propagating errors". However, it was not the backpropagation algorithm, and he did not have a general method for training multiple layers. In 1965, Alexey Grigorevich Ivakhnenko and Valentin Lapa published Group Method of Data Handling. It was one of the first deep learning methods, used to train an eight-layer neural net in 1971. In 1967, Shun'ichi Amari reported the first multilayered neural network trained by stochastic gradient descent, was able to classify non-linearily separable pattern classes. Amari's student Saito conducted the computer experiments, using a five-layered feedforward network with two learning layers. Backpropagation was independently developed multiple times in early 1970s. The earliest published instance was Seppo Linnainmaa's master thesis (1970). Paul Werbos developed it independently in 1971, but had difficulty publishing it until 1982. In 1986, David E. Rumelhart et al. popularized backpropagation. In 2003, interest in backpropagation networks returned due to the successes of deep learning being applied to language modelling by Yoshua Bengio with co-authors. In 2021, a very simple NN architecture combining two deep MLPs with skip connections and layer normalizations was designed and called MLP-Mixer; its realizations featuring 19 to 431 millions of parameters were shown to be comparable to vision transformers of similar size on ImageNet and similar image classification tasks. == Mathematical foundations == === Activation function === If a multilayer perceptron has a linear activation function in all neurons, that is, a linear function that maps the weighted inputs to the output of each neuron, then linear algebra shows that any number of layers can be reduced to a two-layer input-output model. In MLPs some neurons use a nonlinear activation function that was developed to model the frequency of action potentials, or firing, of biological neurons. The two historically common activation functions are both sigmoids, and are described by y ( v i ) = tanh ⁡ ( v i ) and y ( v i ) = ( 1 + e − v i ) − 1 {\displaystyle y(v_{i})=\tanh(v_{i})~~{\textrm {and}}~~y(v_{i})=(1+e^{-v_{i}})^{-1}} . The first is a hyperbolic tangent that ranges from −1 to 1, while the other is the logistic function, which is similar in shape but ranges from 0 to 1. Here y i {\displaystyle y_{i}} is the output of the i {\displaystyle i} th node (neuron) and v i {\displaystyle v_{i}} is the weighted sum of the input connections. Alternative activation functions have been proposed, including the rectifier and softplus functions. More specialized activation functions include radial basis functions (used in radial basis networks, another class of supervised neural network models). In recent developments of deep learning the rectified linear unit (ReLU) is more frequently used as one of the possible ways to overcome the numerical problems related to the sigmoids. === Layers === The MLP consists of three or more layers (an input and an output layer with one or more hidden layers) of nonlinearly-activating nodes. Since MLPs are fully connected, each node in one layer connects with a certain weight w i j {\displaystyle w_{ij}} to every node in the following layer. === Learning === Learning occurs in the perceptron by changing connection weights after each piece of data is processed, based on the amount of error in the output compared to the expected result. This is an example of supervised learning, and is carried out through backpropagation, a generalization of the least mean squares algorithm in the linear perceptron. We can represent the degree of error in an output node j {\displaystyle j} in the n {\displaystyle n} th data point (training example) by e j ( n ) = d j ( n ) − y j ( n ) {\displaystyle e_{j}(n)=d_{j}(n)-y_{j}(n)} , where d j ( n ) {\displaystyle d_{j}(n)} is the desired target value for n {\displaystyle n} th data point at node j {\displaystyle j} , and y j ( n ) {\displaystyle y_{j}(n)} is the value produced by the perceptron at node j {\displaystyle j} when the n {\displaystyle n} th data point is given as an input. The node weights can then be adjusted based on corrections that minimize the error in the entire output for the n {\displaystyle n} th data point, given by E ( n ) = 1 2 ∑ output node j e j 2 ( n ) {\displaystyle {\mathcal {E}}(n)={\frac {1}{2}}\sum _{{\text{output node }}j}e_{j}^{2}(n)} . Using gradient descent, the change in each weight w i j {\displaystyle w_{ij}} is Δ w j i ( n ) = − η ∂ E ( n ) ∂ v j ( n ) y i ( n ) {\displaystyle \Delta w_{ji}(n)=-\eta {\frac {\partial {\mathcal {E}}(n)}{\partial v_{j}(n)}}y_{i}(n)} where y i ( n ) {\displaystyle y_{i}(n)} is the output of the previous neuron i {\displaystyle i} , and η {\displaystyle \eta } is the learning rate, which is selected to ensure that the weights quickly converge to a response, without oscillations. In the previous expression, ∂ E ( n ) ∂ v j ( n ) {\displaystyle {\frac {\partial {\mathcal {E}}(n)}{\partial v_{j}(n)}}} denotes the partial derivate of the error E ( n ) {\displaystyle {\mathcal {E}}(n)} according to the weighted sum v j ( n ) {\displaystyle v_{j}(n)} of the input connections of neuron i {\displaystyle i} . The derivative to be calculated depends on the induced local field v j {\displaystyle v_{j}} , which itself varies. It is easy to prove that for an output node this derivative can be simplified to − ∂ E ( n ) ∂ v j ( n ) = e j ( n ) ϕ ′ ( v j ( n ) ) {\displaystyle -{\frac {\partial {\mathcal {E}}(n)}{\partial v_{j}(n)}}=e_{j}(n)\phi ^{\prime }(v_{j}(n))} where ϕ ′ {\displaystyle \phi ^{\prime }} is the derivative of the activation function described above, which itself does not vary. The analysis is more difficult for the change in weights to a hidden node, but it can be shown that the relevant derivative is − ∂ E ( n ) ∂ v j ( n ) = ϕ ′ ( v j ( n ) ) ∑ k − ∂ E ( n ) ∂ v k ( n ) w k j ( n ) {\displaystyle -{\frac {\partial {\mathcal {E}}(n)}{\partial v_{j}(n)}}=\phi ^{\prime }(v_{j}(n))\sum _{k}-{\frac {\partial {\mathcal {E}}(n)}{\partial v_{k}(n)}}w_{kj}(n)} . This depends on the change in weights of the k {\displaystyle k} th nodes, which represent the output layer. So to change the hidden layer weights, the output layer weights change according to the derivative of the activation function, and so this algorithm represents a backpropagation of the activation function.
Read more →
Operational taxonomic unit

An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "operational taxonomic unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. == Molecular OTU by clustering of marker gene sequences == In the approach represented by DNA barcoding, a particular locus is chosen to be used as the marker gene for classification. This locus should be universally present in the scope selected, variable enough to be different among close-related species, and be flanked by conservative sequences that allow for easy amplification and detection. There are databases containing sequences for such marker genes from many different species, allowing for comparison. (Sometimes only using one locus does not provide sufficient resolution, so multiple marker genes are used. This is the case for plants, where rbcL+matK is common.) Sequences obtained this way can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold set by the researcher. The exact threshold depends on the taxa in question and the mutational rates of the selected locus in the taxon. 97–99% are commonly used, but "it is now recognized to be somewhat arbitrary as sequence variation within and among species varies across taxa". 100% similarity (fully identical) is also common, also known as single variants. It remains debatable how well this commonly used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, research by Schmidt et al. (2014) demonstrated that 16S-derived microbial OTUs were generally ecologically consistent across habitats and several clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing. === OTU clustering approaches === There are three main approaches to clustering OTUs: De novo, for which the clustering is based on similarities between sequencing reads. Closed-reference, for which the clustering is performed against a reference database of sequences. Open-reference, where clustering is first performed against a reference database of sequences, then any remaining sequences that could not be mapped to the reference are clustered de novo. Using a reference provides taxonomic context for the OTUs found. Alternatively, taxonomic context can be found after the construction of clusters by comparing representative sequences from clusters against a reference database. There are also specialized classifiers for this purpose which are much faster than naive comparison using BLAST. === OTU clustering algorithms === Hierarchical clustering algorithms (HCA): uclust & cd-hit & ESPRIT Bayesian clustering: CROP == Molecular OTU by other methods == In addition to similarity-based grouping, marker gene sequences can be sorted into OTUs using molecular phylogeny, k-mer composition, or hybrid methods combining these methods with similarity. There are also Bayesian tree-less methods and machine learning approaches. Using phylogeny often involves manually assigning terminal clades or single nodes to an OTU, so this is usually only done for refinement. Genome skimming can be used to obtain high-copy DNA without the need to choose marker genes or to design PCR primers for the chosen genes. It can provide fairly good coverage of organelle DNA and repetitive elements such as ribosomal DNA, both of which can be used like marker genes in OTU analysis. Whole-genome sequencing is more expensive and involves the production and processing of more data. By considering the entire genome, many (sometimes over 100) marker genes can be used at the same time, producing highly resolved phylogenies that correctly identify problematic taxa. It is also possible to use entire genomes for OTU assignment. For example, genomes from different bacterial species almost always have an average nucleotide identity lower than 95%, a fact that can be used to define new OTUs (and likely new species).
Read more →
Croissant (metadata format)

Croissant is a metadata format design to support sharing of datasets for machine learning applications. It is a platform-agnostic schema used to standardize metadata in data repositories like Hugging Face, kaggle, Dataverse and OpenML. == Structure == Croissant builds upon schema.org, uses primarily JSON-LD, and divides metadata in four "layers": Dataset Metadata, Resource, Structure and Semantic: The Dataset Metadata layer constrains which schema.org properties should be used, including additional properties, linking together the resources (files) of the dataset with general metadata, like licensing and citation information. The Resource layer describes the individual files and sets of those using two new classes, FileObject and FileSet. A FileSet may be a collection of related images. The Structure layer specifies how the files are organized in the dataset. A RecordSet class describes how resources are present, configurations that may very a lot between modality. This specification facilitates interoperability of the datasets. Finally, the Semantic layer adds information for practical reuse of the dataset, such as splits for train, test and validation subsets. It also provides a default extension for metadata related to responsible AI. The use of a standard machine-readable structure increases, for example, the discoverability of datasets in search engines such as Google Dataset Search. == History == Croissant was shared in arXiv in March 2024 and published in the proceedings of NeurIPS 2024. It started as community driven as a MLCommons Croissant Working Group, including stakeholders organizations from academia and industry, including Google, the open data institute, Sage Bionetworks and King's College London. Variations of Croissant are developed to support datasets in different areas of research, such as Geo-Croissant for geospatial datasets. Other technical extensions, such as support for RDF, soon followed.
Read more →
Bondy's theorem

In mathematics, Bondy's theorem is a bound on the number of elements needed to distinguish the sets in a family of sets from each other. It belongs to the field of combinatorics, and is named after John Adrian Bondy, who published it in 1972. == Statement == The theorem is as follows: Let X be a set with n elements and let A1, A2, ..., An be distinct subsets of X. Then there exists a subset S of X with n − 1 elements such that the sets Ai ∩ S are all distinct. In other words, if we have a 0-1 matrix with n rows and n columns such that each row is distinct, we can remove one column such that the rows of the resulting n × (n − 1) matrix are distinct. == Example == Consider the 4 × 4 matrix [ 1 1 0 1 0 1 0 1 0 0 1 1 0 1 1 0 ] {\displaystyle {\begin{bmatrix}1&1&0&1\\0&1&0&1\\0&0&1&1\\0&1&1&0\end{bmatrix}}} where all rows are pairwise distinct. If we delete, for example, the first column, the resulting matrix [ 1 0 1 1 0 1 0 1 1 1 1 0 ] {\displaystyle {\begin{bmatrix}1&0&1\\1&0&1\\0&1&1\\1&1&0\end{bmatrix}}} no longer has this property: the first row is identical to the second row. Nevertheless, by Bondy's theorem we know that we can always find a column that can be deleted without introducing any identical rows. In this case, we can delete the third column: all rows of the 3 × 4 matrix [ 1 1 1 0 1 1 0 0 1 0 1 0 ] {\displaystyle {\begin{bmatrix}1&1&1\\0&1&1\\0&0&1\\0&1&0\end{bmatrix}}} are distinct. Another possibility would have been deleting the fourth column. == Learning theory application == From the perspective of computational learning theory, Bondy's theorem can be rephrased as follows: Let C be a concept class over a finite domain X. Then there exists a subset S of X with the size at most |C| − 1 such that S is a witness set for every concept in C. This implies that every finite concept class C has its teaching dimension bounded by |C| − 1.
Read more →
List of datasets for machine-learning research

These datasets are used in machine learning (ML) research and have been cited in peer-reviewed academic journals. Datasets are an integral part of the field of machine learning. Major advances in this field can result from advances in learning algorithms (such as deep learning), computer hardware, and, less intuitively, the availability of high-quality training datasets. High-quality labeled training datasets for supervised and semi-supervised machine-learning algorithms are usually difficult and expensive to produce because of the large amount of time needed to label the data. Although they do not need to be labeled, high-quality unlabeled datasets for unsupervised learning can also be difficult and costly to produce. Many organizations, including governments, publish and share their datasets, often using common metadata formats (such as Croissant). The datasets are classified, based on the licenses, into two groups: open data and non-open data. The datasets from various governmental-bodies are presented in List of open government data sites. The datasets are ported on open data portals. They are made available for searching, depositing and accessing through interfaces like Open API. The datasets are made available as various sorted types and subtypes. == List of sorting used for datasets == The data portal is classified based on its type of license. The open source license based data portals are known as open data portals which are used by many government organizations and academic institutions. == List of open data portals == == List of portals suitable for multiple types of applications == The data portal sometimes lists a wide variety of subtypes of datasets pertaining to many machine learning applications. == List of portals suitable for a specific subtype of applications == The data portals which are suitable for a specific subtype of machine learning application are listed in the subsequent sections. == Image data == == Text data == These datasets consist primarily of text for tasks such as natural language processing, sentiment analysis, translation, and cluster analysis. === Reviews === === News articles === === Messages === === Twitter and tweets === === Dialogues === === Legal === === Other text === == Sound data == These datasets consist of sounds and sound features used for tasks such as speech recognition and speech synthesis. === Speech === === Music === === Other sounds === == Signal data == Datasets containing electric signal information requiring some sort of signal processing for further analysis. === Electrical === === Motion-tracking === === Other signals === == Chemical data == Datasets from physical systems. === Chemical Reactions with transition states (TS) === === OpenReACT-CHON-EFH === OpenReACT-CHON-EFH (Open Reaction Dataset of Atomic ConfiguraTions comprising C, H, O and N with Energies, Forces and Hessians) is a 2025 open-access benchmark for machine-learning interatomic potentials. RTP set – 35,087 stationary-point geometries (reactant, transition state and product) drawn from 11,961 elementary reactions, each labeled with density-functional energies, atomic forces and full Hessian matrices at the ωB97X-D/6-31G(d) level. IRC set – 34,248 structures along 600 minimum-energy reaction paths, used to test extrapolation beyond trained stationary points. NMS set – 62,527 off-equilibrium geometries generated by normal-mode sampling to probe model robustness under thermal perturbations. The collection underpins the study Does Hessian Data Improve the Performance of Machine Learning Potentials? and was used to train and benchmark the machine-learning interatomic potentials reported therein. The dataset itself is distributed under a CC licence via Figshare. == Physical data == Datasets from physical systems. === High-energy physics === === Systems === === Astronomy === === Earth science === === Other physical === == Biological data == Datasets from biological systems. === Human === === Animal === === Fungi === === Plant === === Microbe === === Drug discovery === == Anomaly data == == Question answering data == This section includes datasets that deals with structured data. == Dialog or instruction prompted data == This section includes datasets that contains multi-turn text with at least two actors, a "user" and an "agent". The user makes requests for the agent, which performs the request. == Cybersecurity == == Climate and sustainability == == Code data == == Multivariate data == === Financial === === Weather === === Census === === Transit === === Internet === === Games === === Other multivariate === == Curated repositories of datasets == As datasets come in myriad formats and can sometimes be difficult to use, there has been considerable work put into curating and standardizing the format of datasets to make them easier to use for machine learning research. OpenML: Web platform with Python, R, Java, and other APIs for downloading hundreds of machine learning datasets, evaluating algorithms on datasets, and benchmarking algorithm performance against dozens of other algorithms. PMLB: A large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. Provides classification and regression datasets in a standardized format that are accessible through a Python API. Metatext NLP: https://metatext.io/datasets web repository maintained by community, containing nearly 1000 benchmark datasets, and counting. Provides many tasks from classification to QA, and various languages from English, Portuguese to Arabic. Appen: Off The Shelf and Open Source Datasets hosted and maintained by the company. These biological, image, physical, question answering, signal, sound, text, and video resources number over 250 and can be applied to over 25 different use cases.
Read more →