Biopython

Biopython is an open-source collection of non-commercial Python modules for computational biology and bioinformatics. It makes robust and well-tested code easily accessible to researchers. Python is an object-oriented programming language and is a suitable choice for automation of common tasks. The availability of reusable libraries saves development time and lets researchers focus on addressing scientific questions. Biopython is constantly updated and maintained by a large team of volunteers across the globe. Biopython contains parsers for diverse bioinformatic sequence, alignment, and structure formats. Sequence formats include FASTA, FASTQ, GenBank, and EMBL. Alignment formats include Clustal, BLAST, PHYLIP, and NEXUS. Structural formats include the PDB, which contains the 3D atomic coordinates of the macromolecules. It has provisions to access information from biological databases like NCBI, Expasy, PBD, and BioSQL. This can be used in scripts or incorporated into their software. Biopython contains a standard sequence class, sequence alignment, and motif analysis tools. It also has clustering algorithms, a module for structural biology, and a module for phylogenetics analysis. == History == The development of Biopython began in 1999, and it was first released in July 2000. First "semi-complete" and "semi-stable" release was done in March 2001 and December 2002 respectively. It was developed during a similar time frame and with analogous goals to other projects that added bioinformatics capabilities to their respective programming languages, including BioPerl, BioRuby and BioJava. Early developers on the project included Jeff Chang, Andrew Dalke and Brad Chapman, though over 100 people have made contributions to date. In 2007, a similar Python project, namely PyCogent, was established. The initial scope of Biopython involved accessing, indexing and processing biological sequence files. The retrieved data from common biological databases will then be parsed into a python data structure. While this is still a major focus, over the following years added modules have extended its functionality to cover additional areas of biology. The key challenge in the design of parsers for bioinformatics file formats is the frequency at which the data formats change. This is due to inadequate curation of the structure of the data, and changes in the database contents. This problem is overcome by the application of a standard event-oriented parser design (see Key features and examples). As of version 1.77, Biopython no longer supports Python 2. The current stable release of Biopython version 1.85 was released on 15 January 2025. It only supports Python 3 and the recent releases of Biopython require NumPy (and not Numeric). == Design == Wherever possible, Biopython follows the conventions used by the Python programming language to make it easier for users familiar with Python. For example, Seq and SeqRecord objects can be manipulated via slicing, in a manner similar to Python's strings and lists. It is also designed to be functionally similar to other Bio projects, such as BioPerl. It is organized into modular sub-packages, e.g., Bio.Seq, Bio.Align, Bio.PDB, Bio.Entrez each of them useful in a different bioinformatics domain. It used principles, like encapsulation and polymorphism, notably in classes Seq, SeqRecord, and Bio.PDB.Structure. It can also interoperate with other Python tools (Pandas, Matplotlib and SciPy). Biopython can read and write most common file formats for each of its functional areas, and its license is permissive and compatible with most other software licenses, which allows Biopython to be used in a variety of software projects. == Requirements == Biopython is currently supported and tested with the following Python implementations: Python 3 or PyPy3 NumPy == Key features and examples == === Input and output === Biopython can read and write to a number of common formats. When reading files, descriptive information in the file is used to populate the members of Biopython classes, such as SeqRecord. This allows records of one file format to be converted into others. Very large sequence files can exceed a computer's memory resources, so Biopython provides various options for accessing records in large files. They can be loaded entirely into memory in Python data structures, such as lists or dictionaries, providing fast access at the cost of memory usage. Alternatively, the files can be read from disk as needed, with slower performance but lower memory requirements. === Sequences === A core concept in Biopython is the biological sequence, and this is represented by the Seq class. A Biopython Seq object is similar to a Python string in many respects: it supports the Python slice notation, can be concatenated with other sequences and is immutable. This object includes both general string-like and biological sequence-specific methods. It is best to store information about the biological type (DNA, RNA, protein) separately from the sequence, rather than using an explicit alphabet argument. === Sequence annotation === The SeqRecord class describes sequences, along with information such as name, description and features in the form of SeqFeature objects. Each SeqFeature object specifies the type of the feature and its location. Feature types can be ‘gene’, ‘CDS’ (coding sequence), ‘repeat_region’, ‘mobile_element’ or others, and the position of features in the sequence can be exact or approximate. === Accessing online databases === Through the Bio.Entrez module, users of Biopython can download biological data from NCBI databases. Each of the functions provided by the Entrez search engine is available through functions in this module, including searching for and downloading records. === Phylogeny === The Bio.Phylo module provides tools for working with and visualising phylogenetic trees. A variety of file formats are supported for reading and writing, including Newick, NEXUS and phyloXML. Common tree manipulations and traversals are supported via the Tree and Clade objects. Examples include converting and collating tree files, extracting subsets from a tree, changing a tree's root, and analysing branch features such as length or score. Rooted trees can be drawn in ASCII or using matplotlib (see Figure 1), and the Graphviz library can be used to create unrooted layouts (see Figure 2). === Genome diagrams === The GenomeDiagram module provides methods of visualising sequences within Biopython. Sequences can be drawn in a linear or circular form (see Figure 3), and many output formats are supported, including PDF and PNG. Diagrams are created by making tracks and then adding sequence features to those tracks. By looping over a sequence's features and using their attributes to decide if and how they are added to the diagram's tracks, one can exercise much control over the appearance of the final diagram. Cross-links can be drawn between different tracks, allowing one to compare multiple sequences in a single diagram. === Macromolecular structure === The Bio.PDB module can load molecular structures from PDB and mmCIF files, and was added to Biopython in 2003. The Structure object is central to this module, and it organises macromolecular structure in a hierarchical fashion: Structure objects contain Model objects which contain Chain objects which contain Residue objects which contain Atom objects. Disordered residues and atoms get their own classes, DisorderedResidue and DisorderedAtom, that describe their uncertain positions. Using Bio.PDB, one can navigate through individual components of a macromolecular structure file, such as examining each atom in a protein. Common analyses can be carried out, such as measuring distances or angles, comparing residues and calculating residue depth. === Population genetics === The Bio.PopGen module adds support to Biopython for Genepop, a software package for statistical analysis of population genetics. This allows for analyses of Hardy–Weinberg equilibrium, linkage disequilibrium and other features of a population's allele frequencies. This module can also carry out population genetic simulations using coalescent theory with the fastsimcoal2 program. === Wrappers for command line tools === Biopython previously included command-line wrappers for tools such as BLAST, Clustal, EMBOSS, and SAMtools. This option allowed users to run external tool commands from within the code using specialized Biopython classes. However, Bio.Application modules and their wrappers have deprecated and will be removed in future Biopython releases. The main reason for this is the high maintenance burden of updating them with the evolving external tools. The recommended approach is to directly construct and execute command-line tool commands using Python’s built-in subprocess module. This method provides flexibility and removes the dependency on the Biopython wrappers. subprocess is a native Python module useful for running ext

Prosthesis

In medicine, a prosthesis (pl.: prostheses; from Ancient Greek: πρόσθεσις, romanized: prósthesis, lit. 'addition, application, attachment'), or a prosthetic implant, is an artificial device that replaces a missing body part, which may be lost through physical trauma, disease, or a condition present at birth (congenital disorder). Prostheses may restore the normal functions of the missing body part, or may perform a cosmetic function. A person who has undergone an amputation is sometimes referred to as an amputee, Rehabilitation for someone with an amputation is primarily coordinated by a physiatrist as part of an inter-disciplinary team consisting of physiatrists, prosthetists, nurses, physical therapists, and occupational therapists. Prostheses can be created by hand or with computer-aided design (CAD), a software interface that helps creators design and analyze the creation with computer-generated 2-D and 3-D graphics as well as analysis and optimization tools. == Types == A person's prosthetic device should be designed and assembled to meet their individual appearance and functional needs. Depending on personal circumstances, co-morbidities, budget or health insurance coverage, and access to medical care, decisions may need to balance aesthetics and function. In addition, for some individuals, a myoelectric device, a body-powered device, or an activity-specific device may be appropriate options. The person's future goals and vocational aspirations and potential capabilities may help them choose between one or more devices. Craniofacial prostheses include intra-oral and extra-oral prostheses. Extra-oral prostheses are further divided into hemifacial, auricular (ear), nasal, orbital and ocular. Intra-oral prostheses include dental prostheses, such as dentures, obturators, and dental implants. Prostheses of the neck include larynx substitutes, trachea and upper esophageal replacements, Some prostheses of the torso include breast prostheses which may be either single or bilateral, full breast devices or nipple prostheses. Penile prostheses are used to treat erectile dysfunction, perform phalloplasty procedures in men, and to build a new penis in female-to-male gender reassignment surgeries. === Limb prostheses === Limb prostheses include both upper- and lower-extremity prostheses. Upper-extremity prostheses are used at varying levels of amputation: forequarter, shoulder disarticulation, transhumeral prosthesis, elbow disarticulation, transradial prosthesis, wrist disarticulation, full hand, partial hand, finger, partial finger. A transradial prosthesis is an artificial limb that replaces an arm missing below the elbow. Upper limb prostheses can be categorized in three main categories: Passive devices, Body Powered devices, and Externally Powered (myoelectric) devices. Passive devices can either be passive hands, mainly used for cosmetic purposes, or passive tools, mainly used for specific activities (e.g. leisure or vocational). An extensive overview and classification of passive devices can be found in a literature review by Maat et.al. A passive device can be static, meaning the device has no movable parts, or it can be adjustable, meaning its configuration can be adjusted (e.g. adjustable hand opening). Despite the absence of active grasping, passive devices are very useful in bimanual tasks that require fixation or support of an object, or for gesticulation in social interaction. According to scientific data a third of the upper limb amputees worldwide use a passive prosthetic hand. Body Powered or cable-operated limbs work by attaching a harness and cable around the opposite shoulder of the damaged arm. A recent body-powered approach has explored the utilization of the user's breathing to power and control the prosthetic hand to help eliminate actuation cable and harness. The third category of available prosthetic devices comprises myoelectric arms. This particular class of devices distinguishes itself from the previous ones due to the inclusion of a battery system. This battery serves the dual purpose of providing energy for both actuation and sensing components. While actuation predominantly relies on motor or pneumatic systems, a variety of solutions have been explored for capturing muscle activity, including techniques such as Electromyography, Sonomyography, Myokinetic, and others. These methods function by detecting the minute electrical currents generated by contracted muscles during upper arm movement, typically employing electrodes or other suitable tools. Subsequently, these acquired signals are converted into gripping patterns or postures that the artificial hand will then execute. In the prosthetics industry, a trans-radial prosthetic arm is often referred to as a "BE" or below elbow prosthesis. Lower-extremity prostheses provide replacements at varying levels of amputation. These include hip disarticulation, transfemoral prosthesis, knee disarticulation, transtibial prosthesis, Syme's amputation, foot, partial foot, and toe. The two main subcategories of lower extremity prosthetic devices are trans-tibial (any amputation transecting the tibia bone or a congenital anomaly resulting in a tibial deficiency) and trans-femoral (any amputation transecting the femur bone or a congenital anomaly resulting in a femoral deficiency). A transfemoral prosthesis is an artificial limb that replaces a leg missing above the knee. Transfemoral amputees can have a very difficult time regaining normal movement. In general, a transfemoral amputee must use approximately 80% more energy to walk than a person with two whole legs. This is due to the complexities in movement associated with the knee. In newer and more improved designs, hydraulics, carbon fiber, mechanical linkages, motors, computer microprocessors, and innovative combinations of these technologies are employed to give more control to the user. In the prosthetics industry, a trans-femoral prosthetic leg is often referred to as an "AK" or above the knee prosthesis. A transtibial prosthesis is an artificial limb that replaces a leg missing below the knee. A transtibial amputee is usually able to regain normal movement more readily than someone with a transfemoral amputation, due in large part to retaining the knee, which allows for easier movement. Lower extremity prosthetics describe artificially replaced limbs located at the hip level or lower. In the prosthetics industry, a transtibial prosthetic leg is often referred to as a "BK" or below the knee prosthesis. Prostheses are manufactured and fit by clinical prosthetists. Prosthetists are healthcare professionals responsible for making, fitting, and adjusting prostheses and for lower limb prostheses will assess both gait and prosthetic alignment. Once a prosthesis has been fit and adjusted by a prosthetist, a rehabilitation physiotherapist (called physical therapist in America) will help teach a new prosthetic user to walk with a leg prosthesis. To do so, the physical therapist may provide verbal instructions and may also help guide the person using touch or tactile cues. This may be done in a clinic or home. There is some research suggesting that such training in the home may be more successful if the treatment includes the use of a treadmill. Using a treadmill, along with the physical therapy treatment, helps the person to experience many of the challenges of walking with a prosthesis. In the United Kingdom, 75% of lower limb amputations are performed due to inadequate circulation (dysvascularity). This condition is often associated with many other medical conditions (co-morbidities) including diabetes and heart disease that may make it a challenge to recover and use a prosthetic limb to regain mobility and independence. For people who have inadequate circulation and have lost a lower limb, there is insufficient evidence due to a lack of research, to inform them regarding their choice of prosthetic rehabilitation approaches. Lower extremity prostheses are often categorized by the level of amputation or after the name of a surgeon: Transfemoral (Above-knee) Transtibial (Below-knee) Ankle disarticulation (more commonly known as Syme's amputation) Knee disarticulation (also see knee replacement) Hip disarticulation, (also see hip replacement) Hemi-pelvictomy Partial foot amputations (Pirogoff, Talo-Navicular and Calcaneo-cuboid (Chopart), Tarso-metatarsal (Lisfranc), Trans-metatarsal, Metatarsal-phalangeal, Ray amputations, toe amputations). Van Nes rotationplasty ==== Prosthetic raw materials ==== Prosthetic are made lightweight for better convenience for the amputee. Some of these materials include: Plastics: Polyethylene Polypropylene Acrylics Polyurethane Wood (early prosthetics) Rubber (early prosthetics) Lightweight metals: Aluminum Composites: Carbon fiber reinforced polymers Wheeled prostheses have also been used extensively in the rehabilitation of injured domestic animals, including dogs, cats, pigs, rabbits, and

Magnetic ink character recognition

Magnetic ink character recognition code, known in short as MICR code, is a character recognition technology used mainly by the banking industry to streamline the processing and clearance of cheques and other documents. MICR encoding, called the MICR line, is at the bottom of cheques and other vouchers and typically includes the document-type indicator, bank code, bank account number, cheque number, cheque amount (usually added after a cheque is presented for payment), and a control indicator. The format for the bank code and bank account number is country-specific. The technology allows MICR readers to scan and read the information directly into a data-collection device. Unlike barcode and similar technologies, MICR characters can be read easily by humans. MICR encoded documents can be processed much faster and more accurately than conventional OCR encoded documents. == Pre-Unicode standard representation == The ISO standard ISO 2033:1983, and the corresponding Japanese Industrial Standard JIS X 9010:1984 (originally JIS C 6229–1984), define character encodings for OCR-A, OCR-B and E-13B. == International spread == There are two major MICR fonts in use: E-13B and CMC-7. There is no particular international agreement on which countries use which font. In practice, this does not create particular problems as cheques and other vouchers do not usually flow out of a particular jurisdiction. The E-13B font has been adopted as an international standard in ISO 1004-1:2013, and is the standard in Australia, Canada, the United Kingdom, the United States, as well as Central America and much of Asia, besides other countries. The CMC-7 font has been adopted as an international standard in ISO 1004-2:2013, and is widely used in Europe, including France and Italy, Mexico, and South America, including Argentina, Brazil, Chile, besides other countries. Israel is the only country that can use both fonts simultaneously, though the practice makes the system significantly less efficient. This situation is the product of the Israelis adopting CMC-7, while the Palestinians opted for E-13B. == Fonts == === E-13B === E-13B is a 14-character set, comprising the 10 decimal digits, and the following symbols: ⑆ (transit: used to delimit a bank code); ⑈ (on-us: used to delimit a customer account number); ⑇ (amount: used to delimit a transaction amount); ⑉ (dash: used to delimit parts of numbers—e.g., routing numbers or account numbers). In the check printing and banking industries the E-13B MICR line is also commonly referred to as the TOAD line. This reference comes from the 4 characters: Transit, On-us, Amount, and Dash. Compared to CMC-7, some pairs of E-13B characters (notably 2 and 5) can produce relatively similar results when magnetically scanned; however, as a fallback if magnetic reading fails, E-13B also performs well under optical character recognition. The E-13B repertoire can be represented in Unicode (see below). The official Unicode names contain misnomers. For example, the ⑈ on-us symbol is official titled "OCR Dash". Prior to Unicode, it could be encoded according to ISO 2033:1983, which encodes digits in their usual ASCII locations, transit as 0x3A, on-us as 0x3C, amount as 0x3B, and dash as 0x3D. For EBCDIC, IBM code page 1001 encodes digits in their usual EBCDIC locations, transit as 0xDB, on-us as 0xEB, amount as 0xCB, and dash as 0xFB. IBM code page 1032 extends code page 1001 by adding alternative encodings for transit at 0x5C, 0x7A and 0xC1, on-us at 0x4C, 0x61 and 0xC3, amount at 0x5B, 0x5E and 0xC2 and dash at 0x60, 0x7E and 0xC4, in addition to a zero-width space at 0x5A. These alternative representations were added for interoperability with Siemens and Océ printers. === CMC-7 === CMC-7 includes 10 numeric digits, 26 capital letters, and 5 control characters: S I (internal), S II (terminator), S III (amount), S IV (an unused character), and S V (routing). CMC-7 has a barcode format, with every character having two distinct large gaps in different places, as well as distinct patterns in between, to minimize any chance for character confusion while reading magnetically; however, these bars are too close and narrow to be reliably recognised at a typical scan resolution if falling back to optical scanning. CMC-7 can also produce superficially successful, but incorrect, scans of upside-down MICR lines. Unicode does not include support for the CMC-7 control symbols. IBM code page 1033 encodes: Digits and capitals in their usual EBCDIC locations S I (internal) as 0x5E, 0x61 or 0xCB; S II (terminator) as 0x4C, 0x5B or 0xEB; S III (amount) as 0x60, 0x7E or 0xFB; S IV as 0x50, 0x7A or 0xDB; S V (routing) as 0x5C, 0x6E or 0xBB. == MICR reader == MICR characters are printed on documents in one of the two MICR fonts, using magnetizable (commonly known as magnetic) ink or toner, usually containing iron oxide. In scanning, the document is passed through a MICR reader, which performs two functions: magnetization of the ink, and detection of the characters. The characters are read by a MICR reader head, a device similar to the playback head of a tape recorder. As each character passes over the head, it produces a unique waveform that can be easily identified by the system. MICR readers are the primary tool for cheque sorting and are used across the cheque distribution network at multiple stages. For example, a merchant will use a MICR reader to sort cheques by bank and send the sorted cheques to a clearing house for redistribution to those banks. Upon receipt, the banks perform another MICR sort to determine which customer's account is charged and to which branch the cheque should be sent on its way back to the customer. However, many banks no longer offer this last step of returning the cheque to the customer. Instead, cheques are scanned and stored digitally. Sorting of cheques is done as per the geographical coverage of banks in a nation. == Unicode == OCR and MICR characters have been included in the Unicode Standard since at least version 1.1 (June 1993). Since the Unicode Character Database only tracks characters starting with version 1.1, they may also have been present in Unicode 1.0 or 1.0.1. The Unicode block that includes OCR and MICR characters is called Optical Character Recognition and covers U+2440–U+245F. Of the characters in this block, four are from the MICR E-13B font: U+2446 ⑆ OCR BRANCH BANK IDENTIFICATION U+2447 ⑇ OCR AMOUNT OF CHECK U+2448 ⑈ OCR DASH (corrected alias MICR ON US SYMBOL) U+2449 ⑉ OCR CUSTOMER ACCOUNT NUMBER (corrected alias MICR DASH SYMBOL) The names of the latter two characters were inadvertently switched when they were named in ISO/IEC 10646:1993, and they have been assigned accurate names as formal aliases. Per the Unicode Stability Policy, the existing names remain, allowing their use as stable identifiers. Additionally, all four characters have informative (non-formal) aliases in the Unicode charts: "transit", "amount", "on-us", and "dash" respectively. Prior to Unicode, these symbols had been encoded by the ISO-IR-98 encoding defined by ISO 2033:1983, in which they were simply named SYMBOL ONE through SYMBOL FOUR. They were encoded immediately following the digits, which were encoded at their ASCII locations. Although ISO 2033 also specifies encoding for OCR-A and OCR-B, its encoding for E-13B is known simply as ISO_2033-1983 by the IANA. == History == Before the mid-1940s, cheques were processed manually using the Sort-A-Matic or Top Tab Key method. The processing and cheque clearing was very time-consuming and was a significant cost in cheque clearance and bank operations. As the number of cheques increased, ways were sought for automating the process. Standards were developed to ensure uniformity in financial institutions. By the mid-1950s, the Stanford Research Institute and General Electric Computer Laboratory had developed the first automated system to process cheques using MICR. The same team also developed the E-13B MICR font. "E" refers to the font being the fifth considered, and "B" to the fact that it was the second version. The "13" refers to the 0.013-inch character grid. The trial of MICR E-13B font was shown to the American Bankers Association (ABA) in July 1956, which adopted it in 1958 as the MICR standard for negotiable documents in the United States. ABA adopted MICR as its standard because machines could read MICR accurately, and MICR could be printed using existing technology. In addition, MICR remained machine readable, even through overstamping, marking, mutilation and more. The first cheques using MICR were printed by the end of 1959. Although compliance with MICR standards was voluntary in the United States, it had been almost universally adopted in the United States by 1963. In 1963, ANSI adopted the ABA's E-13B font as the American standard for MICR printing, and E-13B was also standardized as ISO 1004:1995. Other countries set their own standards, though the MICR readers and m

Isolation forest

Isolation forest is an unsupervised learning algorithm for anomaly detection that works on the principle of isolating anomalies, instead of the most common techniques of profiling normal points. In statistics, an anomaly (a.k.a. outlier) is an observation or event that deviates so much from other events to arouse suspicion it was generated by a different mean. For example, the graph in Fig.1 represents ingress traffic to a web server, expressed as the number of requests in 3-hours intervals, for a period of one month. It is quite evident by simply looking at the picture that some points (marked with a red circle) are unusually high, to the point of inducing suspect that the web server might have been under attack at that time. On the other hand, the flat segment indicated by the red arrow also seems unusual and might possibly be a sign that the server was down during that time period. Anomalies in a big dataset may follow very complicated patterns, which are difficult to detect "by eye" in the great majority of cases. This is the reason why the field of anomaly detection is well suited for the application of machine learning techniques. The most common techniques employed for anomaly detection are based on the construction of a profile of what is "normal": anomalies are reported as those instances in the dataset that do not conform to the normal profile. Isolation Forest uses a different approach: instead of trying to build a model of normal instances, it explicitly isolates anomalous points in the dataset. The main advantage of this approach is the possibility of exploiting sampling techniques to an extent that is not allowed to the profile-based methods, creating a very fast algorithm with a low memory demand. == History == The Isolation Forest (iForest) algorithm was initially proposed by Fei Tony Liu, Kai Ming Ting and Zhi-Hua Zhou in 2008. The authors took advantage of two quantitative properties of anomalous data points in a sample, that is: they are the minority consisting of fewer instances and they have attribute-values that are very different from those of normal instances Since anomalies are typically few and very different from the other points in the sample, they must be easier to "isolate" compared to normal points. On the basis of this principle, Isolation Forest builds an ensemble of "Isolation Trees" (iTrees) for the data set and marks as anomalies the points that have short average path lengths on the iTrees. In a later paper, published in 2012 the same authors described a set of experiments to prove that iForest: has a low linear time complexity and a small memory requirement is able to deal with high dimensional data with irrelevant attributes can be trained with or without anomalies in the training set can provide detection results with different levels of granularity without re-training In 2013 Zhiguo Ding and Minrui Fei proposed a framework based on iForest to resolve the problem of detecting anomalies in streaming data. More application of iForest to streaming data are described in papers by Swee Chuan Tan et al., G. A. Susto et al. and Yu Weng et al. One of the main problems of the application of iForest to anomaly detection was not with the model itself, but rather in the way the "anomaly score" was computed. This problem was highlighted by Sahand Hariri, Matias Carrasco Kind and Robert J. Brunner in a 2018 paper, wherein they proposed an improved iForest model named Extended Isolation Forest (EIF). In the same paper the authors describe the improvements made to the original model and how they are able to enhance the consistency and reliability of the anomaly score produced for a given data point. == Algorithm == At the basis of the Isolation Forest algorithm there is the tendency of anomalous instances in a dataset to be easier to separate from the rest of the sample (isolate), compared to normal points. In order to isolate a data point the algorithm recursively generates partitions on the sample by randomly selecting an attribute and then randomly selecting a split value for the attribute, between the minimum and maximum values allowed for that attribute. An example of random partitioning in a 2D dataset of normally distributed points is given in Fig. 2 for a non-anomalous point and Fig. 3 for a point that's more likely to be an anomaly. It is apparent from the pictures how anomalies require fewer random partitions to be isolated, compared to normal points. From a mathematical point of view, recursive partitioning can be represented by a tree structure named Isolation Tree, while the number of partitions required to isolate a point can be interpreted as the length of the path, within the tree, to reach a terminating node starting from the root. For example, the path length of point xi in Fig. 2 is greater than the path length of xj in Fig. 3. More formally, let X = { x1, ..., xn } be a set of d-dimensional points and X' ⊂ X a subset of X. An Isolation Tree (iTree) is defined as a data structure with the following properties: for each node T in the Tree, T is either an external-node with no child, or an internal-node with one "test" and exactly two daughter nodes (Tl, Tr) a test at node T consists of an attribute q and a split value p such that the test q < p determines the traversal of a data point to either Tl or Tr. In order to build an iTree, the algorithm recursively divides X' by randomly selecting an attribute q and a split value p, until either (i) the node has only one instance or (ii) all data at the node have the same values. When the iTree is fully grown, each point in X is isolated at one of the external nodes. Intuitively, the anomalous points are those (easier to isolate, hence) with the smaller path length in the tree, where the path length h(xi) of point x i ∈ X {\displaystyle x_{i}\in X} is defined as the number of edges xi traverses from the root node to get to an external node. A probabilistic explanation of iTree is provided in the iForest original paper. == Properties of Isolation Forest == Sub-sampling: since iForest does not need to isolate all of normal instances, it can frequently ignore the big majority of the training sample. As a consequence, iForest works very well when the sampling size is kept small, a property that is in contrast with the great majority of existing methods, where large sampling size is usually desirable. Swamping: when normal instances are too close to anomalies, the number of partitions required to separate anomalies increases, a phenomena known as swamping, which makes it more difficult for iForest to discriminate between anomalies and normal points. One of the main reasons for swamping is the presence of too many data for the purpose of anomaly detection, which implies one possible solution to the problem is sub-sampling. Since iForest respond very well to sub-sampling in terms of performance, the reduction of the number of points in the sample is also a good way to reduce the effect of swamping. Masking: when the number of anomalies is high it is possible that some of those aggregate in a dense and large cluster, making it more difficult to separate the single anomalies and, in turn, to detect such points as anomalous. Similarly to swamping, this phenomena (known as "masking") is also more likely when the number of points in the sample is big, and can be alleviated through sub-sampling. High Dimensional Data: one of the main limitation to standard, distance-based methods is their inefficiency in dealing with high dimensional datasets:. The main reason for that is, in a high dimensional space every point is equally sparse, so using a distance-based measure of separation is pretty ineffective. Unfortunately, high-dimensional data also affects the detection performance of iForest, but the performance can be vastly improved by adding a features selection test like Kurtosis to reduce the dimensionality of the sample space. Normal Instances Only: iForest performs well even if the training set does not contain any anomalous point, the reason being that iForest describes data distributions in such a way that high values of the path length h(xi) correspond to the presence of data points. As a consequence, the presence of anomalies is pretty irrelevant to iForest's detection performance. == Anomaly Detection with Isolation Forest == Anomaly detection with Isolation Forest is a process composed of two main stages: in the first stage, a training dataset is used to build iTrees as described in previous sections. in the second stage, each instance in test set is passed through the iTrees build in the previous stage, and a proper "anomaly score" is assigned to the instance using the algorithm described below Once all the instances in the test set have been assigned an anomaly score, it is possible to mark as "anomaly" any point whose score is greater than a predefined threshold, which depends on the domain the analysis is being applied to. === Anomaly Score === Th

AI Coding Assistants Reviews: What Actually Works in 2026

Comparing the best AI coding assistant? An AI coding assistant is software that uses machine learning to help you get more done — it lowers the barrier so anyone can produce professional output. Privacy matters too: check whether your data trains the model and whether a no-log or enterprise tier is available. Whether you are a beginner or a pro, the right AI coding assistant slots into your workflow and pays for itself fast. We tested the leading options and ranked them by quality, value, and ease of use.

Data augmentation

Data augmentation is a statistical technique which allows maximum likelihood estimation from incomplete data. Data augmentation has important applications in Bayesian analysis, and the technique is widely used in machine learning to reduce overfitting when training machine learning models, achieved by training models on several slightly-modified copies of existing data. == Synthetic oversampling techniques for traditional machine learning == Synthetic Minority Over-sampling Technique (SMOTE) is a method used to address imbalanced datasets in machine learning. In such datasets, the number of samples in different classes varies significantly, leading to biased model performance. For example, in a medical diagnosis dataset with 90 samples representing healthy individuals and only 10 samples representing individuals with a particular disease, traditional algorithms may struggle to accurately classify the minority class. SMOTE rebalances the dataset by generating synthetic samples for the minority class. For instance, if there are 100 samples in the majority class and 10 in the minority class, SMOTE can create synthetic samples by randomly selecting a minority class sample and its nearest neighbors, then generating new samples along the line segments joining these neighbors. This process helps increase the representation of the minority class, improving model performance. == Data augmentation for image classification == When convolutional neural networks grew larger in mid-1990s, there was a lack of data to use, especially considering that some part of the overall dataset should be spared for later testing. It was proposed to perturb existing data with affine transformations to create new examples with the same labels, which were complemented by so-called elastic distortions in 2003, and the technique was widely used as of 2010s. Data augmentation can enhance CNN performance and acts as a countermeasure against CNN profiling attacks. Data augmentation has become fundamental in image classification, enriching training dataset diversity to improve model generalization and performance. The evolution of this practice has introduced a broad spectrum of techniques, including geometric transformations, color space adjustments, and noise injection. === Geometric Transformations === Geometric transformations alter the spatial properties of images to simulate different perspectives, orientations, and scales. Common techniques include: Affine Transformation Rotation: Rotating images by a specified degree to help models recognize objects at various angles. Reflection: Reflecting images horizontally or vertically to introduce variability in orientation. Translation: Shifting images in different directions to teach models positional invariance. Scaling Shear Mapping Cropping: Removing sections of the image to focus on particular features or simulate closer views. Elastic Distortion Morphing within the same class: Generating new samples by applying morphing techniques between two images belonging to the same class, thereby increasing intra-class diversity. === Color Space Transformations === Color space transformations modify the color properties of images, addressing variations in lighting, color saturation, and contrast. Techniques include: Brightness Adjustment: Varying the image's brightness to simulate different lighting conditions. Contrast Adjustment: Changing the contrast to help models recognize objects under various clarity levels. Saturation Adjustment: Altering saturation to prepare models for images with diverse color intensities. Color Jittering: Randomly adjusting brightness, contrast, saturation, and hue to introduce color variability. === Noise Injection === Injecting noise into images simulates real-world imperfections, teaching models to ignore irrelevant variations. Techniques involve: Gaussian Noise: Adding Gaussian noise mimics sensor noise or graininess. Salt and Pepper Noise: Introducing black or white pixels at random simulates sensor dust or dead pixels. == Data augmentation for signal processing == Residual or block bootstrap can be used for time series augmentation. === Biological signals === Synthetic data augmentation is of paramount importance for machine learning classification, particularly for biological data, which tend to be high dimensional and scarce. The applications of robotic control and augmentation in disabled and able-bodied subjects still rely mainly on subject-specific analyses. Data scarcity is notable in signal processing problems such as for Parkinson's Disease Electromyography signals, which are difficult to source - Zanini, et al. noted that it is possible to use a generative adversarial network (in particular, a DCGAN) to perform style transfer in order to generate synthetic electromyographic signals that corresponded to those exhibited by sufferers of Parkinson's Disease. The approaches are also important in electroencephalography (brainwaves). Wang, et al. explored the idea of using deep convolutional neural networks for EEG-Based Emotion Recognition, results show that emotion recognition was improved when data augmentation was used. A common approach is to generate synthetic signals by re-arranging components of real data. Lotte proposed a method of "Artificial Trial Generation Based on Analogy" where three data examples x 1 , x 2 , x 3 {\displaystyle x_{1},x_{2},x_{3}} provide examples and an artificial x s y n t h e t i c {\displaystyle x_{synthetic}} is formed which is to x 3 {\displaystyle x_{3}} what x 2 {\displaystyle x_{2}} is to x 1 {\displaystyle x_{1}} . A transformation is applied to x 1 {\displaystyle x_{1}} to make it more similar to x 2 {\displaystyle x_{2}} , the same transformation is then applied to x 3 {\displaystyle x_{3}} which generates x s y n t h e t i c {\displaystyle x_{synthetic}} . This approach was shown to improve performance of a Linear Discriminant Analysis classifier on three different datasets. Current research shows great impact can be derived from relatively simple techniques. For example, Freer observed that introducing noise into gathered data to form additional data points improved the learning ability of several models which otherwise performed relatively poorly. Tsinganos et al. studied the approaches of magnitude warping, wavelet decomposition, and synthetic surface EMG models (generative approaches) for hand gesture recognition, finding classification performance increases of up to +16% when augmented data was introduced during training. More recently, data augmentation studies have begun to focus on the field of deep learning, more specifically on the ability of generative models to create artificial data which is then introduced during the classification model training process. In 2018, Luo et al. observed that useful EEG signal data could be generated by Conditional Wasserstein Generative Adversarial Networks (GANs) which was then introduced to the training set in a classical train-test learning framework. The authors found classification performance was improved when such techniques were introduced. === Mechanical signals === The prediction of mechanical signals based on data augmentation brings a new generation of technological innovations, such as new energy dispatch, 5G communication field, and robotics control engineering. In 2022, Yang et al. integrate constraints, optimization and control into a deep network framework based on data augmentation and data pruning with spatio-temporal data correlation, and improve the interpretability, safety and controllability of deep learning in real industrial projects through explicit mathematical programming equations and analytical solutions.

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