Orange (software)

Orange is an open-source data visualization, machine learning and data mining toolkit. It features a visual programming front-end for exploratory qualitative data analysis and interactive data visualization. == Description == Orange is a component-based visual programming software package for data visualization, machine learning, data mining, and data analysis. Orange components are called widgets. They range from simple data visualization, subset selection, and preprocessing to empirical evaluation of learning algorithms and predictive modeling. Visual programming is implemented through an interface in which workflows are created by linking predefined or user-designed widgets, while advanced users can use Orange as a Python library for data manipulation and widget alteration. == Software == Orange is an open-source software package released under GPL and hosted on GitHub. Versions up to 3.0 include core components in C++ with wrappers in Python. From version 3.0 onwards, Orange uses common Python open-source libraries for scientific computing, such as numpy, scipy and scikit-learn, while its graphical user interface operates within the cross-platform Qt framework. The default installation includes a number of machine learning, preprocessing and data visualization algorithms in 6 widget sets (data, transform, visualize, model, evaluate and unsupervised). Additional functionalities are available as add-ons (text-mining, image analytics, bioinformatics, etc.). Orange is supported on macOS, Windows and Linux and can also be installed from the Python Package Index repository (pip install Orange3). == Features == Orange consists of a canvas interface onto which the user places widgets and creates a data analysis workflow. Widgets offer basic functionalities such as reading the data, showing a data table, selecting features, training predictors, comparing learning algorithms, visualizing data elements, etc. The user can interactively explore visualizations or feed the selected subset into other widgets. Canvas: graphical front-end for data analysis Widgets: Data: widgets for data input, data filtering, sampling, imputation, feature manipulation and feature selection Visualize: widgets for common visualization (box plot, histograms, scatter plot) and multivariate visualization (mosaic display, sieve diagram). Classify: a set of supervised machine learning algorithms for classification Regression: a set of supervised machine learning algorithms for regression Evaluate: cross-validation, sampling-based procedures, reliability estimation and scoring of prediction methods Unsupervised: unsupervised learning algorithms for clustering (k-means, hierarchical clustering) and data projection techniques (multidimensional scaling, principal component analysis, correspondence analysis). == Add-ons == Orange users can extend their core set of components with components in the add-ons. Supported add-ons include: Associate: components for mining frequent itemsets and association rule learning. Bioinformatics: components for gene expression analysis, enrichment, and access to expression databases (e.g., Gene Expression Omnibus) and pathway libraries. Data fusion: components for fusing different data sets, collective matrix factorization, and exploration of latent factors. Educational: components for teaching machine learning concepts, such as k-means clustering, polynomial regression, stochastic gradient descent, ... Explain: provides an extension with components for the model explanation, including Shapley value analysis Geo: components for working with geospatial data. Image analytics: components for working with images and ImageNet embeddings Network: components for graph and network analysis. Text mining: components for natural language processing and text mining. Time series: widget components for time series analysis and modeling. Single-cell: support for single-cell gene expression analysis, including components for loading single-cell data, filtering and batch effect removal, marker genes discovery, scoring of cells and genes, and cell type prediction. Spectroscopy: components for analyzing and visualization of (hyper)spectral datasets. Survival analysis: add-on for data analysis dealing with survival data. It includes widgets for standard survival analysis techniques, such as the Kaplan-Meier plot, the Cox regression model, and several derivative widgets. World Happiness: support for downloading socioeconomic data from a database, including OECD and World Development Indicators. Provides access to thousands of country indicators from various economic databases. Fairness: add-on for evaluation and creation of fair machine learning models without discrimination. Widgets range from computing fairness metrics like statistical parity to post-, pre-, in-processing methods to build fair models. == Objectives == The program provides a platform for experiment selection, recommendation systems, and predictive modelling and is used in biomedicine, bioinformatics, genomic research, and teaching. In science, it is used as a platform for testing new machine learning algorithms and for implementing new techniques in genetics and bioinformatics. In education, it was used for teaching machine learning and data mining methods to students of biology, biomedicine, and informatics. == Extensions == Various projects build on Orange either by extending the core components with add-ons or using only the Orange Canvas to exploit the implemented visual programming features and GUI. OASYS — ORange SYnchrotron Suite scOrange — single cell biostatistics Quasar — data analysis in natural sciences == History == In 1996, the University of Ljubljana and Jožef Stefan Institute started development of ML, a machine learning framework in C++, and Python bindings were developed for this framework in 1997, which, together with emerging Python modules, formed a joint framework called Orange. Over the following years, most contemporary major algorithms for data mining and machine learning were implemented in C++ (Orange's core) or Python modules. In 2002, first prototypes to create a flexible graphical user interface were designed using Pmw Python megawidgets. In 2003, the graphical user interface was redesigned and re-developed for Qt framework using PyQt Python bindings. The visual programming framework was defined, and the development of widgets (graphical components of the data analysis pipeline) began. In 2005, extensions for data analysis in bioinformatics was created. In 2008, Mac OS X DMG and Fink-based installation packages were developed. In 2009, over 100 widgets were created and maintained. In 2009, Orange 2.0 beta was released, offering installation packages on the website based on the daily compiling cycle. In 2012, a new object hierarchy was imposed, replacing the old module-based structure. In 2013, a significant redesign of the graphical user interface included a new toolbox and depiction of workflows. In 2015, Orange 3.0 was released. Orange stores the data in NumPy arrays; machine learning algorithms mostly use scikit-learn. In 2015, a text analysis add-on for Orange3 was released. In 2016, Orange released version 3.3. Development scheduled a monthly cycle for stable releases. In 2016, Orange began development and release of an Image Analytics add-on, with server-side deep neural networks for image embedding In 2017, a Spectroscopy add-on for the analysis of spectral data was introduced. In 2017, Geo, an add-on for dealing with geo-location data and visualisation of geo maps was introduced In 2018, Orange began development and release of an add-on for single-cell data analysis. In 2019, Orange separated its graphical interface for development as a separate project, orange-canvas-core In 2020, Orange introduced the Explain add-on with widgets for explaining classification models and regression models, highlighting the strength and contributions specific features make towards predicting a specific class. In 2022, World Happiness, an add-on for the Orange3 data mining suite, was introduced, providing widgets for accessing socioeconomic data from various databases such as World Happiness Report, World Development Indicators, OECD. In 2022, Orange extended the Explain add-on with an Individual Conditional Expectation plot and the Permutation Feature Importance technique. In 2023, Orange introduced the Fairness add-on, including widgets to calculate bias metrics, as well as widgets for pre-, post-, and in-processing methods, allowing the creation of models less susceptible to systematic error due to the vagaries of the data set.

List of Fortran software and tools

This is a list of Fortran software and tools, including IDEs, compilers, libraries, debugging tools, numerical and scientific computing tools, and related projects. == Fortran compilers == Absoft Pro Fortran — Absoft Pro Fortran is discontinued and ran on Linux and macOS AOCC — from AMD Classic Flang — part of the LLVM Project LLVM Flang — part of the LLVM Project Fortran 77 — Fortran 77 was developed by Digital Equipment Corporation, it is discontinued. G95 – portable open-source Fortran 95 compiler GCC (GNU Fortran) PGI compilers – NVIDIA developed compilers after acquiring The Portland Group IBM XL Fortran — IBM XL Fortran is current and runs on Linux (Power/AIX) and integrates with Eclipse Intel Fortran Compiler – part of Intel OneAPI HPC toolkit LFortran — LFortran is current, cross-platform, and has IDE support. MinGW – cross compiler and forked into Mingw-w64 nAG Fortran Compiler - from nAG Open64 — Open64 is an open-source compiler that has been terminated and ran on Linux Open Watcom — Open Watcom is current, runs on MS-DOS and OS/2, and has IDE support. Oracle Fortran — Oracle Fortran is discontinued, ran on Linux and Solaris. ROSE — source-to-source compiler framework developed at Lawrence Livermore National Laboratory Silverfrost FTN95 — FTN95 from Silverfrost is current, runs on Windows, and has IDE support. == Integrated development environments (IDEs) and editors == Code::Blocks — supports Fortran with plugins Eclipse IDE — with Fortran support via Photran Emacs — extensible text editor with built-in Fortran modes and support for modern tooling via language servers Geany — lightweight cross-platform IDE based on GTK IntelliJ IDEA — cross-platform IDE by JetBrains with Fortran pluggin KDevelop — KDE-based IDE NetBeans — Apache software foundation IDE with Fortran configuration OpenWatcom — IDE and compiler suite for C, C++, and Fortran Simply Fortran — standalone Fortran IDE for Windows, Linux, and macOS Vim — modal text editor with native Fortran syntax support and extensive plugin-based development features Visual Studio — with Intel Fortran integration Visual Studio Code — supports Fortran via extensions == Mathematical libraries == == Scientific libraries == ABINIT — software suite to calculate optical, mechanical, vibrational, and other observable properties of materials Cantera — chemical kinetics, thermodynamics, and transport tool suite CERN Program Library — collection of Fortran libraries for physics applications from CERN CP2K — quantum chemistry and solid-state physics software package for atomistic simulations Dalton — molecular electronic structure program FFTPACK — subroutines for the fast Fourier transform Kinetic PreProcessor – open-source software tool used in atmospheric chemistry MESA — Modules for Experiments in Stellar Astrophysics Nek5000 — MPI parallel higher-order spectral element CFD solver NWChem — open-source high-performance computational chemistry software Octopus — real-space Time-Dependent Density Functional Theory code MODTRAN – model atmospheric propagation of electromagnetic radiation MOLCAS — quantum chemistry software package for multiconfigurational electronic structure calculations NOVAS – software library for astrometry-related numerical computations Physics Analysis Workstation – data analysis and graphical presentation in high-energy physics Quantum ESPRESSO — integrated suite for electronic-structure calculations and materials modeling SIESTA — first-principles materials simulation code using density functional theory Tinker — software tools for molecular design == Debugging and performance tools == GDB — GNU Debugger with Fortran support Valgrind — memory debugging and profiling tool VTune Profiler — performance analysis tool Allinea Forge — debugger and profiler for HPC applications == Build and package management == Autotools — build system supporting Fortran projects CMake — cross-platform build system supporting Fortran Make — build automation tool Spack — package manager for HPC software including Fortran libraries == Machine learning and AI libraries == Athena Fiats (Functional Inference And Training for Surrogates) FNN (Fortran Neural Network) FortNN Fortran-TF-lib (Fortran interface to TensorFlow) FTorch (Fortran interface to PyTorch) MlFortran RoseNNa == Parallel and high-performance computing tools == MPI Fortran bindings — standard interface for distributed-memory parallelism OpenMP — shared-memory parallel programming support through compiler directives Coarray Fortran — parallel programming model introduced in Fortran 2008 ScaLAPACK — parallel linear algebra package built on top of LAPACK == Testing frameworks == FUnit — open-source unit testing framework developed at NASA’s Langley Research Center, for Fortran 90, 95, and 2003. pFUnit — unit testing framework for Fortran, modeled after JUnit == Documentation and code analysis tools == FORD — automatic documentation generator for modern Fortran projects SQuORE — software quality and management platform with code analysis support Understand — static analysis and code comprehension tool for large Fortran projects

Moral graph

In graph theory, a moral graph is used to find the equivalent undirected form of a directed acyclic graph. It is a key step of the junction tree algorithm, used in belief propagation on graphical models. The moralized counterpart of a directed acyclic graph is formed by adding edges between all pairs of non-adjacent nodes that have a common child, and then making all edges in the graph undirected. Equivalently, a moral graph of a directed acyclic graph G is an undirected graph in which each node of the original G is now connected to its Markov blanket. The name stems from the fact that, in a moral graph, two nodes that have a common child are required to be married by sharing an edge. Moralization may also be applied to mixed graphs, called in this context "chain graphs". In a chain graph, a connected component of the undirected subgraph is called a chain. Moralization adds an undirected edge between any two vertices that both have outgoing edges to the same chain, and then forgets the orientation of the directed edges of the graph. == Weakly recursively simplicial == A graph is weakly recursively simplicial if it has a simplicial vertex and the subgraph after removing a simplicial vertex and some edges (possibly none) between its neighbours is weakly recursively simplicial. A graph is moral if and only if it is weakly recursively simplicial. A chordal graph (a.k.a., recursive simplicial) is a special case of weakly recursively simplicial when no edge is removed during the elimination process. Therefore, a chordal graph is also moral. But a moral graph is not necessarily chordal. == Recognising moral graphs == Unlike chordal graphs that can be recognised in polynomial time, Verma & Pearl (1993) proved that deciding whether or not a graph is moral is NP-complete.

Multimodal learning

Multimodal learning is a type of deep learning that integrates and processes multiple types of data, referred to as modalities, such as text, audio, images, or video. This integration allows for a more holistic understanding of complex data, improving model performance in tasks like visual question answering, cross-modal retrieval, text-to-image generation, aesthetic ranking, and image captioning. Multimodal learning was proposed in 2011 at the beginning of the deep learning period. Large multimodal models, such as Google Gemini and GPT-4o, have become increasingly popular since 2023, enabling increased versatility and a broader understanding of real-world phenomena. == Motivation == Data usually comes with different modalities which carry different information. For example, it is very common to caption an image to convey the information not presented in the image itself. Similarly, sometimes it is more straightforward to use an image to describe information which may not be obvious from text. As a result, if different words appear in similar images, then these words likely describe the same thing. Conversely, if a word is used to describe seemingly dissimilar images, then these images may represent the same object. Thus, in cases dealing with multi-modal data, it is important to use a model which is able to jointly represent the information such that the model can capture the combined information from different modalities. == Multimodal transformers == Models such as CLIP (Contrastive Language–Image Pretraining) learn joint representations of images and text by optimizing contrastive objectives, allowing the model to match images with their corresponding textual descriptions. == Multimodal deep Boltzmann machines == A Boltzmann machine is a type of stochastic neural network invented by Geoffrey Hinton and Terry Sejnowski in 1985. Boltzmann machines can be seen as the stochastic, generative counterpart of Hopfield nets. They are named after the Boltzmann distribution in statistical mechanics. The units in Boltzmann machines are divided into two groups: visible units and hidden units. Each unit is like a neuron with a binary output that represents whether it is activated or not. General Boltzmann machines allow connection between any units. However, learning is impractical using general Boltzmann Machines because the computational time is exponential to the size of the machine. A more efficient architecture is called restricted Boltzmann machine where connection is only allowed between hidden unit and visible unit, which is described in the next section. Multimodal deep Boltzmann machines can process and learn from different types of information, such as images and text, simultaneously. This can notably be done by having a separate deep Boltzmann machine for each modality, for example one for images and one for text, joined at an additional top hidden layer. == Applications == Multimodal machine learning has numerous applications across various domains: Cross-modal retrieval: cross-modal retrieval allows users to search for data across different modalities (e.g., retrieving images based on text descriptions), improving multimedia search engines and content recommendation systems. Classification and missing data retrieval: multimodal Deep Boltzmann Machines outperform traditional models like support vector machines and latent Dirichlet allocation in classification tasks and can predict missing data in multimodal datasets, such as images and text. Healthcare diagnostics: multimodal models integrate medical imaging, genomic data, and patient records to improve diagnostic accuracy and early disease detection, especially in cancer screening. Content generation: models like DALL·E generate images from textual descriptions, benefiting creative industries, while cross-modal retrieval enables dynamic multimedia searches. Robotics and human-computer interaction: multimodal learning improves interaction in robotics and AI by integrating sensory inputs like speech, vision, and touch, aiding autonomous systems and human-computer interaction. Emotion recognition: combining visual, audio, and text data, multimodal systems enhance sentiment analysis and emotion recognition, applied in customer service, social media, and marketing.

Mutation (evolutionary algorithm)

Mutation is a genetic operator used to maintain genetic diversity of the chromosomes of a population of an evolutionary algorithm (EA), including genetic algorithms in particular. It is analogous to biological mutation. The classic example of a mutation operator of a binary coded genetic algorithm (GA) involves a probability that an arbitrary bit in a genetic sequence will be flipped from its original state. A common method of implementing the mutation operator involves generating a random variable for each bit in a sequence. This random variable tells whether or not a particular bit will be flipped. This mutation procedure, based on the biological point mutation, is called single point mutation. Other types of mutation operators are commonly used for representations other than binary, such as floating-point encodings or representations for combinatorial problems. The purpose of mutation in EAs is to introduce diversity into the sampled population. Mutation operators are used in an attempt to avoid local minima by preventing the population of chromosomes from becoming too similar to each other, thus slowing or even stopping convergence to the global optimum. This reasoning also leads most EAs to avoid only taking the fittest of the population in generating the next generation, but rather selecting a random (or semi-random) set with a weighting toward those that are fitter. The following requirements apply to all mutation operators used in an EA: every point in the search space must be reachable by one or more mutations. there must be no preference for parts or directions in the search space (no drift). small mutations should be more probable than large ones. For different genome types, different mutation types are suitable. Some mutations are Gaussian, Uniform, Zigzag, Scramble, Insertion, Inversion, Swap, and so on. An overview and more operators than those presented below can be found in the introductory book by Eiben and Smith or in. == Bit string mutation == The mutation of bit strings ensue through bit flips at random positions. Example: The probability of a mutation of a bit is 1 l {\displaystyle {\frac {1}{l}}} , where l {\displaystyle l} is the length of the binary vector. Thus, a mutation rate of 1 {\displaystyle 1} per mutation and individual selected for mutation is reached. == Mutation of real numbers == Many EAs, such as the evolution strategy or the real-coded genetic algorithms, work with real numbers instead of bit strings. This is due to the good experiences that have been made with this type of coding. The value of a real-valued gene can either be changed or redetermined. A mutation that implements the latter should only ever be used in conjunction with the value-changing mutations and then only with comparatively low probability, as it can lead to large changes. In practical applications, the respective value range of the decision variables to be changed of the optimisation problem to be solved is usually limited. Accordingly, the values of the associated genes are each restricted to an interval [ x min , x max ] {\displaystyle [x_{\min },x_{\max }]} . Mutations may or may not take these restrictions into account. In the latter case, suitable post-treatment is then required as described below. === Mutation without consideration of restrictions === A real number x {\displaystyle x} can be mutated using normal distribution N ( 0 , σ ) {\displaystyle {\mathcal {N}}(0,\sigma )} by adding the generated random value to the old value of the gene, resulting in the mutated value x ′ {\displaystyle x'} : x ′ = x + N ( 0 , σ ) {\displaystyle x'=x+{\mathcal {N}}(0,\sigma )} In the case of genes with a restricted range of values, it is a good idea to choose the step size of the mutation σ {\displaystyle \sigma } so that it reasonably fits the range [ x min , x max ] {\displaystyle [x_{\min },x_{\max }]} of the gene to be changed, e.g.: σ = x max − x min 6 {\displaystyle \sigma ={\frac {x_{\text{max}}-x_{\text{min}}}{6}}} The step size can also be adjusted to the smaller permissible change range depending on the current value. In any case, however, it is likely that the new value x ′ {\displaystyle x'} of the gene will be outside the permissible range of values. Such a case must be considered a lethal mutation, since the obvious repair by using the respective violated limit as the new value of the gene would lead to a drift. This is because the limit value would then be selected with the entire probability of the values beyond the limit of the value range. The evolution strategy works with real numbers and mutation based on normal distribution. The step sizes are part of the chromosome and are subject to evolution together with the actual decision variables. === Mutation with consideration of restrictions === One possible form of changing the value of a gene while taking its value range [ x min , x max ] {\displaystyle [x_{\min },x_{\max }]} into account is the mutation relative parameter change of the evolutionary algorithm GLEAM (General Learning Evolutionary Algorithm and Method), in which, as with the mutation presented earlier, small changes are more likely than large ones. First, an equally distributed decision is made as to whether the current value x {\displaystyle x} should be increased or decreased and then the corresponding total change interval is determined. Without loss of generality, an increase is assumed for the explanation and the total change interval is then [ x , x max ] {\displaystyle [x,x_{\max }]} . It is divided into k {\displaystyle k} sub-areas of equal size with the width δ {\displaystyle \delta } , from which k {\displaystyle k} sub-change intervals of different size are formed: i {\displaystyle i} -th sub-change interval: [ x , x + δ ⋅ i ] {\displaystyle [x,x+\delta \cdot i]} with δ = ( x max − x ) k {\displaystyle \delta ={\frac {(x_{\text{max}}-x)}{k}}} and i = 1 , … , k {\displaystyle i=1,\dots ,k} Subsequently, one of the k {\displaystyle k} sub-change intervals is selected in equal distribution and a random number, also equally distributed, is drawn from it as the new value x ′ {\displaystyle x'} of the gene. The resulting summed probabilities of the sub-change intervals result in the probability distribution of the k {\displaystyle k} sub-areas shown in the adjacent figure for the exemplary case of k = 10 {\displaystyle k=10} . This is not a normal distribution as before, but this distribution also clearly favours small changes over larger ones. This mutation for larger values of k {\displaystyle k} , such as 10, is less well suited for tasks where the optimum lies on one of the value range boundaries. This can be remedied by significantly reducing k {\displaystyle k} when a gene value approaches its limits very closely. === Common properties === For both mutation operators for real-valued numbers, the probability of an increase and decrease is independent of the current value and is 50% in each case. In addition, small changes are considerably more likely than large ones. For mixed-integer optimization problems, rounding is usually used. == Mutation of permutations == Mutations of permutations are specially designed for genomes that are themselves permutations of a set. These are often used to solve combinatorial tasks. In the two mutations presented, parts of the genome are rotated or inverted. === Rotation to the right === The presentation of the procedure is illustrated by an example on the right: === Inversion === The presentation of the procedure is illustrated by an example on the right: === Variants with preference for smaller changes === The requirement raised at the beginning for mutations, according to which small changes should be more probable than large ones, is only inadequately fulfilled by the two permutation mutations presented, since the lengths of the partial lists and the number of shift positions are determined in an equally distributed manner. However, the longer the partial list and the shift, the greater the change in gene order. This can be remedied by the following modifications. The end index j {\displaystyle j} of the partial lists is determined as the distance d {\displaystyle d} to the start index i {\displaystyle i} : j = ( i + d ) mod | P 0 | {\displaystyle j=(i+d){\bmod {\left|P_{0}\right|}}} where d {\displaystyle d} is determined randomly according to one of the two procedures for the mutation of real numbers from the interval [ 0 , | P 0 | − 1 ] {\displaystyle \left[0,\left|P_{0}\right|-1\right]} and rounded. For the rotation, k {\displaystyle k} is determined similarly to the distance d {\displaystyle d} , but the value 0 {\displaystyle 0} is forbidden. For the inversion, note that i ≠ j {\displaystyle i\neq j} must hold, so for d {\displaystyle d} the value 0 {\displaystyle 0} must be excluded.

Fluency Voice Technology

Fluency Voice Technology was a company that developed and sold packaged speech recognition solutions for use in call centers. Fluency's Speech Recognition solutions are used by call centers worldwide to improve customer service and significantly reduce costs and are available on-premises and hosted. == History == 1998 – Fluency was created as a spin-off from the Voice Research & Development team of a company called netdecisions. This R&D operation was established in Cambridge UK. The focus of the development was speech recognition systems based on the VXML standard. 2001 – Fluency became a separate entity in May 2001. Fluency began the creation of a software development platform specifically aimed at automating call center activities. This platform became Fluency's VoiceRunner. 2002 to 2004 – Fluency establishes accomplishes many successful deployments in customer sites such as National Express and Barclaycard. 2003 – Fluency expanded into the USA. Fluency also acquires Vocalis of Cambridge, UK in August 2003. 2004 – Fluency receives £6 million investment from leading European Venture Capitalists and establishes a global OEM partnership with Avaya, and the acquisition of SRC Telecom. 2008 – Fluency is acquired by Syntellect Ltd == Customers == Call Centers around the world use Fluency to improve service and reduce costs. They include Travelodge, Standard Life Bank, Sutton and East Surrey Water, Pizza Hut, CWT, Barclays, Powergen, First Choice, OutRight, J D Williams, Capital Blue Cross, Chelsea Building Society, EDF, bss, TV Licensing and Capita Software Services.

Charge based boundary element fast multipole method

The charge-based formulation of the boundary element method (BEM) is a dimensionality reduction numerical technique that is used to model quasistatic electromagnetic phenomena in highly complex conducting media (targeting, e.g., the human brain) with a very large (up to approximately 1 billion) number of unknowns. The charge-based BEM solves an integral equation of the potential theory written in terms of the induced surface charge density. This formulation is naturally combined with fast multipole method (FMM) acceleration, and the entire method is known as charge-based BEM-FMM. The combination of BEM and FMM is a common technique in different areas of computational electromagnetics and, in the context of bioelectromagnetism, it provides improvements over the finite element method. == Historical development == Along with more common electric potential-based BEM, the quasistatic charge-based BEM, derived in terms of the single-layer (charge) density, for a single-compartment medium has been known in the potential theory since the beginning of the 20th century. For multi-compartment conducting media, the surface charge density formulation first appeared in discretized form (for faceted interfaces) in the 1964 paper by Gelernter and Swihart. A subsequent continuous form, including time-dependent and dielectric effects, appeared in the 1967 paper by Barnard, Duck, and Lynn. The charge-based BEM has also been formulated for conducting, dielectric, and magnetic media, and used in different applications. In 2009, Greengard et al. successfully applied the charge-based BEM with fast multipole acceleration to molecular electrostatics of dielectrics. A similar approach to realistic modeling of the human brain with multiple conducting compartments was first described by Makarov et al. in 2018. Along with this, the BEM-based multilevel fast multipole method has been widely used in radar and antenna studies at microwave frequencies as well as in acoustics. == Physical background - surface charges in biological media == The charge-based BEM is based on the concept of an impressed (or primary) electric field E i {\displaystyle \mathbf {E} ^{i}} and a secondary electric field E s {\displaystyle \mathbf {E} ^{s}} . The impressed field is usually known a priori or is trivial to find. For the human brain, the impressed electric field can be classified as one of the following: A conservative field E i {\displaystyle \mathbf {E} ^{i}} derived from an impressed density of EEG or MEG current sources in a homogeneous infinite medium with the conductivity σ {\displaystyle \sigma } at the source location; An instantaneous solenoidal field E i {\displaystyle \mathbf {E} ^{i}} of an induction coil obtained from Faraday's law of induction in a homogeneous infinite medium (air), when transcranial magnetic stimulation (TMS) problems are concerned; A surface field E i {\displaystyle \mathbf {E} ^{i}} derived from an impressed surface current density J i = σ E i {\displaystyle \mathbf {J} ^{i}=\sigma \mathbf {E} ^{i}} of current electrodes injecting electric current at a boundary of a compartment with conductivity σ {\displaystyle \sigma } when transcranial direct-current stimulation (tDCS) or deep brain stimulation (DBS) are concerned; A conservative field E i {\displaystyle \mathbf {E} ^{i}} of charges deposited on voltage electrodes for tDCS or DBS. This specific problem requires a coupled treatment since these charges will depend on the environment; In application to multiscale modeling, a field E i {\displaystyle \mathbf {E} ^{i}} obtained from any other macroscopic numerical solution in a small (mesoscale or microscale) spatial domain within the brain. For example, a constant field can be used. When the impressed field is "turned on", free charges located within a conducting volume D immediately begin to redistribute and accumulate at the boundaries (interfaces) of regions of different conductivity in D. A surface charge density ρ ( r ) {\displaystyle \rho (\mathbf {r} )} appears on the conductivity interfaces. This charge density induces a secondary conservative electric field E s {\displaystyle \mathbf {E} ^{s}} following Coulomb's law. One example is a human under a direct current powerline with the known field E i {\displaystyle \mathbf {E} ^{i}} directed down. The superior surface of the human's conducting body will be charged negatively while its inferior portion is charged positively. These surface charges create a secondary electric field that effectively cancels or blocks the primary field everywhere in the body so that no current will flow within the body under DC steady state conditions. Another example is a human head with electrodes attached. At any conductivity interface with a normal vector n {\displaystyle \mathbf {n} } pointing from an "inside" (-) compartment of conductivity σ − {\displaystyle \sigma ^{-}} to an "outside" (+) compartment of conductivity σ + {\displaystyle \sigma ^{+}} , Kirchhoff's current law requires continuity of the normal component of the electric current density. This leads to the interfacial boundary condition in the form for every facet at a triangulated interface. As long as σ ± {\displaystyle \sigma ^{\pm }} are different from each other, the two normal components of the electric field, E ± ⋅ n {\displaystyle \mathbf {E} ^{\pm }\cdot \mathbf {n} } , must also be different. Such a jump across the interface is only possible when a sheet of surface charge exists at that interface. Thus, if an electric current or voltage is applied, the surface charge density follows. The goal of the numerical analysis is to find the unknown surface charge distribution and thus the total electric field E = E i + E s {\displaystyle \mathbf {E} =\mathbf {E} ^{i}+\mathbf {E} ^{s}} (and the total electric potential if required) anywhere in space. == System of equations for surface charges == Below, a derivation is given based on Gauss's law and Coulomb's law. All conductivity interfaces, denoted by S, are discretized into planar triangular facets t m {\displaystyle t_{m}} with centers r m {\displaystyle \mathbf {r} _{m}} . Assume that an m-th facet with the normal vector n m {\displaystyle \mathbf {n} _{m}} and area A m {\displaystyle A_{m}} carries a uniform surface charge density ρ m {\displaystyle \rho _{m}} . If a volumetric tetrahedral mesh were present, the charged facets would belong to tetrahedra with different conductivity values. We first compute the electric field E m + {\displaystyle \mathbf {E} _{m}^{+}} at the point r m + δ n m {\displaystyle \mathbf {r} _{m}+\delta \mathbf {n} _{m}} , for δ → 0 + {\displaystyle \delta \rightarrow 0^{+}} i.e., just outside facet 𝑚 at its center. This field contains three contributions: The continuous impressed electric field E i {\displaystyle \mathbf {E} ^{i}} itself; An electric field of the m-th charged facet itself. Very close to the facet, it can be approximated as the electric field of an infinite sheet of uniform surface charge ρ m {\displaystyle \rho _{m}} . By Gauss's law, it is given by + ρ m / 2 ε 0 ⋅ n m {\displaystyle +\rho _{m}/2\varepsilon _{0}\cdot \mathbf {n} _{m}} where ε 0 {\displaystyle \varepsilon _{0}} is a background electrical permittivity; An electric field generated by all other facets t n {\displaystyle t_{n}} , which we approximate as point charges of charge A n ρ n {\displaystyle A_{n}\rho _{n}} at each center r n {\displaystyle \mathbf {r} _{n}} . A similar treatment holds for the electric field E m − {\displaystyle \mathbf {E} _{m}^{-}} just inside facet 𝑚, but the electric field of the flat sheet of charge changes its sign. Using Coulomb's law to calculate the contribution of facets different from t m {\displaystyle t_{m}} , we find From this equation, we see that the normal component of the electric field indeed undergoes a jump through the charged interface. This is equivalent to a jump relation of the potential theory. As a second step, the two expressions for E m ± {\displaystyle \mathbf {E} _{m}^{\pm }} are substituted into the interfacial boundary condition σ − E m − ⋅ n m = σ + E m + ⋅ n m {\displaystyle \sigma ^{-}\mathbf {E} _{m}^{-}\cdot \mathbf {n} _{m}=\sigma ^{+}\mathbf {E} _{m}^{+}\cdot \mathbf {n} _{m}} , applied to every facet 𝑚. This operation leads to a system of linear equations for unknown charge densities ρ m {\displaystyle \rho _{m}} which solves the problem: where K m = σ − − σ + σ − + σ + {\displaystyle K_{m}={\frac {\sigma ^{-}-\sigma ^{+}}{\sigma ^{-}+\sigma ^{+}}}} is the electric conductivity contrast at the m-th facet. The normalization constant ε 0 {\displaystyle \varepsilon _{0}} will cancel out after the solution is substituted in the expression for E s {\displaystyle \mathbf {E} ^{s}} and becomes redundant. == Application of fast multipole method == For modern characterizations of brain topologies with ever-increasing levels of complexity, the above system of equations for ρ m {\displaystyle \rho _{m}} is very large; it is t