Defuzzification is the process of producing a quantifiable result in crisp logic, given fuzzy sets and corresponding membership degrees. It is the process that maps a fuzzy set to a crisp set. It is typically needed in fuzzy control systems. These systems will have a number of rules that transform a number of variables into a fuzzy result, that is, the result is described in terms of membership in fuzzy sets. For example, rules designed to decide how much pressure to apply might result in "Decrease Pressure (15%), Maintain Pressure (34%), Increase Pressure (72%)". Defuzzification is interpreting the membership degrees of the fuzzy sets into a specific decision or real value. The simplest but least useful defuzzification method is to choose the set with the highest membership, in this case, "Increase Pressure" since it has a 72% membership, and ignore the others, and convert this 72% to some number. The problem with this approach is that it loses information. The rules that called for decreasing or maintaining pressure might as well have not been there in this case. A common and useful defuzzification technique is center of gravity. First, the results of the rules must be added together in some way. The most typical fuzzy set membership function has the graph of a triangle. Now, if this triangle were to be cut in a straight horizontal line somewhere between the top and the bottom, and the top portion were to be removed, the remaining portion forms a trapezoid. The first step of defuzzification typically "chops off" parts of the graphs to form trapezoids (or other shapes if the initial shapes were not triangles). For example, if the output has "Decrease Pressure (15%)", then this triangle will be cut 15% the way up from the bottom. In the most common technique, all of these trapezoids are then superimposed one upon another, forming a single geometric shape. Then, the centroid of this shape, called the fuzzy centroid, is calculated. The x coordinate of the centroid is the defuzzified value. == Methods == There are many different methods of defuzzification available, including the following: AI (adaptive integration) BADD (basic defuzzification distributions) BOA (bisector of area) CDD (constraint decision defuzzification) COA (center of area) COG (center of gravity) ECOA (extended center of area) EQM (extended quality method) FCD (fuzzy clustering defuzzification) FM (fuzzy mean) FOM (first of maximum) GLSD (generalized level set defuzzification) ICOG (indexed center of gravity) IV (influence value) LOM (last of maximum) MeOM (mean of maxima) MOM (middle of maximum) QM (quality method) RCOM (random choice of maximum) SLIDE (semi-linear defuzzification) WFM (weighted fuzzy mean) The maxima methods are good candidates for fuzzy reasoning systems. The distribution methods and the area methods exhibit the property of continuity that makes them suitable for fuzzy controllers.
Curse of dimensionality
The curse of dimensionality refers to various phenomena that arise when analyzing and organizing data in high-dimensional spaces that do not occur in low-dimensional settings such as the three-dimensional physical space of everyday experience. The expression was coined by Richard E. Bellman when considering problems in dynamic programming. The curse generally refers to issues that arise when the number of datapoints is small (in a suitably defined sense) relative to the intrinsic dimension of the data. Dimensionally cursed phenomena occur in domains such as numerical analysis, sampling, combinatorics, machine learning, data mining and databases. The common theme of these problems is that when the dimensionality increases, the volume of the space increases so fast that the available data becomes sparse. In order to obtain a reliable result, the amount of data needed often grows exponentially with the dimensionality. Also, organizing and searching data often relies on detecting areas where objects form groups with similar properties; in high dimensional data, however, all objects appear to be sparse and dissimilar in many ways, which prevents common data organization strategies from being efficient. == Domains == === Combinatorics === In some problems, each variable can take one of several discrete values, or the range of possible values is divided to give a finite number of possibilities. Taking the variables together, a huge number of combinations of values must be considered. This effect is also known as the combinatorial explosion. Even in the simplest case of d {\displaystyle d} binary variables, the number of possible combinations already is 2 d {\displaystyle 2^{d}} , exponential in the dimensionality. Naively, each additional dimension doubles the effort needed to try all combinations. === Sampling === There is an exponential increase in volume associated with adding extra dimensions to a mathematical space. For example, 102 = 100 evenly spaced sample points suffice to sample a unit interval (try to visualize a "1-dimensional" cube, i.e. a line) with no more than 10−2 = 0.01 distance between points; an equivalent sampling of a 10-dimensional unit hypercube with a lattice that has a spacing of 10−2 = 0.01 between adjacent points would require 1020 = [(102)10] sample points. In general, with a spacing distance of 10−n the 10-dimensional hypercube appears to be a factor of 10n(10−1) = [(10n)10/(10n)] "larger" than the 1-dimensional hypercube, which is the unit interval. In the above example n = 2: when using a sampling distance of 0.01 the 10-dimensional hypercube appears to be 1018 "larger" than the unit interval. This effect is a combination of the combinatorics problems above and the distance function problems explained below. === Optimization === When solving dynamic optimization problems by numerical backward induction, the objective function must be computed for each combination of values. This is a significant obstacle when the dimension of the "state variable" is large. === Machine learning === In machine learning problems that involve learning a "state-of-nature" from a finite number of data samples in a high-dimensional feature space with each feature having a range of possible values, typically an enormous amount of training data is required to ensure that there are several samples with each combination of values. In an abstract sense, as the number of features or dimensions grows, the amount of data we need to generalize accurately grows exponentially. A typical rule of thumb is that there should be at least 5 training examples for each dimension in the representation. In machine learning and insofar as predictive performance is concerned, the curse of dimensionality is used interchangeably with the peaking phenomenon, which is also known as Hughes phenomenon. This phenomenon states that with a fixed number of training samples, the average (expected) predictive power of a classifier or regressor first increases as the number of dimensions or features used is increased but beyond a certain dimensionality it starts deteriorating instead of improving steadily. Nevertheless, in the context of a simple classifier (e.g., linear discriminant analysis in the multivariate Gaussian model under the assumption of a common known covariance matrix), Zollanvari et al. showed both analytically and empirically that as long as the relative cumulative efficacy of an additional feature set (with respect to features that are already part of the classifier) is greater (or less) than the size of this additional feature set, the expected error of the classifier constructed using these additional features will be less (or greater) than the expected error of the classifier constructed without them. In other words, both the size of additional features and their (relative) cumulative discriminatory effect are important in observing a decrease or increase in the average predictive power. In metric learning, higher dimensions can sometimes allow a model to achieve better performance. After normalizing embeddings to the surface of a hypersphere, FaceNet achieves the best performance using 128 dimensions as opposed to 64, 256, or 512 dimensions in one ablation study. A loss function for unitary-invariant dissimilarity between word embeddings was found to be minimized in high dimensions. === Data mining === In data mining, the curse of dimensionality refers to a data set with too many features. Consider the first table, which depicts 200 individuals and 2000 genes (features) with a 1 or 0 denoting whether or not they have a genetic mutation in that gene. A data mining application to this data set may be finding the correlation between specific genetic mutations and creating a classification algorithm such as a decision tree to determine whether an individual has cancer or not. A common practice of data mining in this domain would be to create association rules between genetic mutations that lead to the development of cancers. To do this, one would have to loop through each genetic mutation of each individual and find other genetic mutations that occur over a desired threshold and create pairs. They would start with pairs of two, then three, then four until they result in an empty set of pairs. The complexity of this algorithm can lead to calculating all permutations of gene pairs for each individual or row. Given the formula for calculating the permutations of n items with a group size of r is: n ! ( n − r ) ! {\displaystyle {\frac {n!}{(n-r)!}}} , calculating the number of three pair permutations of any given individual would be 7988004000 different pairs of genes to evaluate for each individual. The number of pairs created will grow by an order of factorial as the size of the pairs increase. The growth is depicted in the permutation table (see right). As we can see from the permutation table above, one of the major problems data miners face regarding the curse of dimensionality is that the space of possible parameter values grows exponentially or factorially as the number of features in the data set grows. This problem critically affects both computational time and space when searching for associations or optimal features to consider. Another problem data miners may face when dealing with too many features is that the number of false predictions or classifications tends to increase as the number of features grows in the data set. In terms of the classification problem discussed above, keeping every data point could lead to a higher number of false positives and false negatives in the model. This may seem counterintuitive, but consider the genetic mutation table from above, depicting all genetic mutations for each individual. Each genetic mutation, whether they correlate with cancer or not, will have some input or weight in the model that guides the decision-making process of the algorithm. There may be mutations that are outliers or ones that dominate the overall distribution of genetic mutations when in fact they do not correlate with cancer. These features may be working against one's model, making it more difficult to obtain optimal results. This problem is up to the data miner to solve, and there is no universal solution. The first step any data miner should take is to explore the data, in an attempt to gain an understanding of how it can be used to solve the problem. One must first understand what the data means, and what they are trying to discover before they can decide if anything must be removed from the data set. Then they can create or use a feature selection or dimensionality reduction algorithm to remove samples or features from the data set if they deem it necessary. One example of such methods is the interquartile range method, used to remove outliers in a data set by calculating the standard deviation of a feature or occurrence. === Distance function === When a measure such as a Euclidean distance is defined using many coordinat
Multiple sequence alignment
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations (single amino acid or nucleotide changes), insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides. Multiple sequence alignments require more sophisticated methodologies than pairwise alignments, as they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. However, heuristic methods generally cannot guarantee high-quality solutions and have been shown to fail to yield near-optimal solutions on benchmark test cases. == Problem statement == Given m {\displaystyle m} sequences S i {\displaystyle S_{i}} , i = 1 , ⋯ , m {\displaystyle i=1,\cdots ,m} similar to the form below: S := { S 1 = ( S 11 , S 12 , … , S 1 n 1 ) S 2 = ( S 21 , S 22 , ⋯ , S 2 n 2 ) ⋮ S m = ( S m 1 , S m 2 , … , S m n m ) {\displaystyle S:={\begin{cases}S_{1}=(S_{11},S_{12},\ldots ,S_{1n_{1}})\\S_{2}=(S_{21},S_{22},\cdots ,S_{2n_{2}})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S_{m}=(S_{m1},S_{m2},\ldots ,S_{mn_{m}})\end{cases}}} A multiple sequence alignment is taken of this set of sequences S {\displaystyle S} by inserting any amount of gaps needed into each of the S i {\displaystyle S_{i}} sequences of S {\displaystyle S} until the modified sequences, S i ′ {\displaystyle S'_{i}} , all conform to length L ≥ max { n i ∣ i = 1 , … , m } {\displaystyle L\geq \max\{n_{i}\mid i=1,\ldots ,m\}} and no values in the sequences of S {\displaystyle S} of the same column consists of only gaps. The mathematical form of an MSA of the above sequence set is shown below: S ′ := { S 1 ′ = ( S 11 ′ , S 12 ′ , … , S 1 L ′ ) S 2 ′ = ( S 21 ′ , S 22 ′ , … , S 2 L ′ ) ⋮ S m ′ = ( S m 1 ′ , S m 2 ′ , … , S m L ′ ) {\displaystyle S':={\begin{cases}S'_{1}=(S'_{11},S'_{12},\ldots ,S'_{1L})\\S'_{2}=(S'_{21},S'_{22},\ldots ,S'_{2L})\\\,\,\,\,\,\,\,\,\,\,\vdots \\S'_{m}=(S'_{m1},S'_{m2},\ldots ,S'_{mL})\end{cases}}} To return from each particular sequence S i ′ {\displaystyle S'_{i}} to S i {\displaystyle S_{i}} , remove all gaps. == Graphing approach == A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. When finding alignments via graph, a complete alignment is created in a weighted graph that contains a set of vertices and a set of edges. Each of the graph edges has a weight based on a certain heuristic that helps to score each alignment or subset of the original graph. === Tracing alignments === When determining the best suited alignments for each MSA, a trace is usually generated. A trace is a set of realized, or corresponding and aligned, vertices that has a specific weight based on the edges that are selected between corresponding vertices. When choosing traces for a set of sequences it is necessary to choose a trace with a maximum weight to get the best alignment of the sequences. == Alignment methods == There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. Each is usually based on a certain heuristic with an insight into the evolutionary process. Most try to replicate evolution to get the most realistic alignment possible to best predict relations between sequences. === Dynamic programming === A direct method for producing an MSA uses the dynamic programming technique to identify the globally optimal alignment solution. For proteins, this method usually involves two sets of parameters: a gap penalty and a substitution matrix assigning scores or probabilities to the alignment of each possible pair of amino acids based on the similarity of the amino acids' chemical properties and the evolutionary probability of the mutation. For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. The search space thus increases exponentially with increasing n and is also strongly dependent on sequence length. Expressed with the big O notation commonly used to measure computational complexity, a naïve MSA takes O(LengthNseqs) time to produce. To find the global optimum for n sequences this way has been shown to be an NP-complete problem. In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. In this approach pairwise dynamic programming alignments are performed on each pair of sequences in the query set, and only the space near the n-dimensional intersection of these alignments is searched for the n-way alignment. The MSA program optimizes the sum of all of the pairs of characters at each position in the alignment (the so-called sum of pair score) and has been implemented in a software program for constructing multiple sequence alignments. In 2019, Hosseininasab and van Hoeve showed that by using decision diagrams, MSA may be modeled in polynomial space complexity. === Progressive alignment construction === The most widely used approach to multiple sequence alignments uses a heuristic search known as progressive technique (also known as the hierarchical or tree method) developed by Da-Fei Feng and Doolittle in 1987. Progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related. All progressive alignment methods require two stages: a first stage in which the relationships between the sequences are represented as a phylogenetic tree, called a guide tree, and a second step in which the MSA is built by adding the sequences sequentially to the growing MSA according to the guide tree. The initial guide tree is determined by an efficient clustering method such as neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA), and may use distances based on the number of identical two-letter sub-sequences (as in FASTA rather than a dynamic programming alignment). Progressive alignments are not guaranteed to be globally optimal. The primary problem is that when errors are made at any stage in growing the MSA, these errors are then propagated through to the final result. Performance is also particularly bad when all of the sequences in the set are rather distantly related. Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors to individual members of the query set in a nonlinear fashion based on their phylogenetic distance from their nearest neighbors. This corrects for non-random selection of the sequences given to the alignment program. Progressive alignment methods are efficient enough to implement on a large scale for many (100s to 1000s) sequences. A popular progressive alignment method has been the Clustal family. ClustalW is used extensively for phylogenetic tree construction, in spite of the author's explicit warnings that unedited alignments should not be used in such studies and as input for protein structure prediction by homology modeling. European Bioinformatics Institute (EMBL-EBI) announced that CLustalW2 will expire in August 2015. They recommend Clustal Omega which performs based on seeded guide trees and HMM profile-profile techniques for protein alignments. An alternative tool for progressive DNA alignments is multiple alignment using fast Fourier transform (MAFFT). Another common progressive alignment method named T-Coffee is slower than Clustal and its derivatives but generally produces more accurate alignments for distantly related sequence sets. T-Coffee calculates pairwise alignments by combining the direct alignment of the pair with indirect alignments that aligns each sequence of the pair to a third sequence. It uses the output from Clustal as well as another local alignment program LALIGN, which finds multiple regions of local alignment between two sequences. The resulting alignment and phylogenetic tree are used as a guide to produce new and more accurate w
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Phrase structure grammar
The term phrase structure grammar was originally introduced by Noam Chomsky as the term for grammar studied previously by Emil Post and Axel Thue (Post canonical systems). Some authors, however, reserve the term for more restricted grammars in the Chomsky hierarchy: context-sensitive grammars or context-free grammars. In a broader sense, phrase structure grammars are also known as constituency grammars. The defining character of phrase structure grammars is thus their adherence to the constituency relation, as opposed to the dependency relation of dependency grammars. == History == In 1956, Chomsky wrote, "A phrase-structure grammar is defined by a finite vocabulary (alphabet) Vp, and a finite set Σ of initial strings in Vp, and a finite set F of rules of the form: X → Y, where X and Y are strings in Vp." == Constituency relation == In linguistics, phrase structure grammars are all those grammars that are based on the constituency relation, as opposed to the dependency relation associated with dependency grammars; hence, phrase structure grammars are also known as constituency grammars. Any of several related theories for the parsing of natural language qualify as constituency grammars, and most of them have been developed from Chomsky's work, including Government and binding theory Generalized phrase structure grammar Head-driven phrase structure grammar Lexical functional grammar The minimalist program Nanosyntax Further grammar frameworks and formalisms also qualify as constituency-based, although they may not think of themselves as having spawned from Chomsky's work, e.g. Arc pair grammar, and Categorial grammar.
Roni Rosenfeld
Roni Rosenfeld (Hebrew: רוני רוזנפלד) is an Israeli-American computer scientist and computational epidemiologist, currently serving as the head of the Machine Learning Department at Carnegie Mellon University. He is an international expert in machine learning, infectious disease forecasting, statistical language modeling and artificial intelligence. == Education == Rosenfeld received his B.Sc. in mathematics and physics from Tel Aviv University in 1985. He received his Ph.D. in computer science from Carnegie Mellon University in 1994. While a graduate student, he developed and open-sourced a statistical language-modeling toolkit to allow anyone to create statistical language models from their own corpora and experiment with and extend the toolkit's capabilities. The toolkit has been used by more than 100 NLP laboratories in more than 20 countries. Rosenfeld's Ph.D. thesis, A Maximum Entropy Approach to Adaptive Statistical Language Modeling, was advised by Raj Reddy and Xuedong Huang and won the 2001 Computer, Speech and Language award for "Most Influential Paper in the Last 5 Years." == Career == Shortly after receiving his Ph.D., Rosenfeld joined the faculty of the Carnegie Mellon School of Computer Science as an assistant professor. He was promoted to the rank of associate professor in 1999 and received tenure in 2001. In 2005 he was promoted to professor of language technologies, machine learning computer science and computational biology in the School of Computer Science at Carnegie Mellon University. Rosenfeld also holds adjunct appointments at the University of Pittsburgh School of Medicine, department of computational and systems biology. From 2002 to 2003, Rosenfeld was a visiting professor at the University of Hong Kong. Rosenfeld is the director of Carnegie Mellon's Machine Learning for Social Good (ML4SG) program. He has held educational leadership positions in a variety of programs, including the M.S. in computational finance (1997–1999), graduate computational and statistical learning (2001–2003), M.S. in machine learning (2017) and undergraduate minor in machine learning. Rosenfeld was appointed Head of Carnegie Mellon's Machine Learning Department in 2018. == Research == Rosenfeld's research interests include epidemiological forecasting, information and communication technologies for development (ICT4D), and machine learning for social good. === Epidemiological forecasting === Rosenfeld is a world expert in epidemiological forecasting. He founded and directs the Delphi research group, which has won most of the epidemiological forecasting challenges organized by the U.S. CDC and other U.S. government agencies. In December 2016, the CDC named his group the "Most Accurate Forecaster" for 2015–2016, and in October 2017, the Delphi group's two systems took the top two spots in the 2016-2017 flu forecasting challenge. The CDC recognized Rosenfeld's Delphi group at Carnegie Mellon University as having contributed the most accurate national-, regional-, and state-level influenza-like illness forecasts and national-level hospitalization forecasts to the site. In 2019, the CDC recognized forecasts provided by the Delphi group at Carnegie Mellon as having been the most accurate for five seasons in a row, and named the Delphi group an Influenza Forecasting Center of Excellence, a five-year designation that includes $3 million in research funding. Rosenfeld describes his forecasting research goal as "to make epidemiological forecasting as universally accepted and useful as weather forecasting is today." His recent work in the area has focused on selecting high value epidemiological forecasting targets (e.g. Influenza and Dengue); creating baseline forecasting methods for them; establishing metrics for measuring and tracking forecasting accuracy; estimating the limits of forecastability for each target; and identifying new sources of data that could be helpful to the forecasting goal. == Honors and awards == 2017 Joel and Ruth Spira Teaching Award 2017 CDC Influenza Forecasting Challenge "Most Accurate Forecaster" 1992 Allen Newell Medal for Research Excellence