Marti Alice Hearst is a professor in the School of Information at the University of California, Berkeley. She did early work in corpus-based computational linguistics, including some of the first work in automating sentiment analysis, and word sense disambiguation. She invented an algorithm that became known as "Hearst patterns" which applies lexico-syntactic patterns to recognize hyponymy (ISA) relations with high accuracy in large text collections, including an early application of it to WordNet; this algorithm is widely used in commercial text mining applications including ontology learning. Hearst also developed early work in automatic segmentation of text into topical discourse boundaries, inventing a now well-known approach called TextTiling. Hearst's research is on user interfaces for search engine technology and big data analytics. She did early work in user interfaces and information visualization for search user interfaces, inventing the TileBars query term visualization. Her Flamenco research project investigated and developed the now widely used faceted navigation approach for searching and browsing web sites and information collections. She wrote the first academic book on the topic of Search User Interfaces (Cambridge University Press, 2009). Hearst is an Edge Foundation contributing author and a member of the Usage panel of the American Heritage Dictionary of the English Language. Hearst received her B.A., M.S., and Ph.D. in computer science, all from Berkeley. In 2013 she became a fellow of the Association for Computing Machinery. She became a member of the CHI Academy in 2017, and has previously served as president of the Association for Computational Linguistics and on the advisory council of NSF's CISE Directorate. Additionally, she has been a member of the Web Board for CACM, the Usage Panel for the American Heritage Dictionary, the Edge.org panel of experts, the research staff at Xerox PARC, and the boards of ACM Transactions on the Web, Computational Linguistics, ACM Transactions on Information Systems, and IEEE Intelligent Systems. Hearst has received an NSF CAREER award, an IBM Faculty Award, and an Okawa Foundation Fellowship. Her work on user interfaces has had a profound impact on the industry, earning Hearst two Google Research Awards and four Excellence in Teaching Awards.} She has also led projects worth over $3.5M in research grants. Hearst’s publications date back to 1990, when ‘A Hybrid Approach to Restricted Text Interpretation’ was published in Stanford University’s AAAI Spring Symposium on Text Based Intelligent Systems in March of that year.
Tensor (machine learning)
In machine learning, the term tensor informally refers to two different concepts: (i) a way of organizing data and (ii) a multilinear (tensor) transformation. Data may be organized in a multidimensional array (M-way array), informally referred to as a "data tensor"; however, in the strict mathematical sense, a tensor is a multilinear mapping over a set of domain vector spaces to a range vector space. Observations, such as images, movies, volumes, sounds, and relationships among words and concepts, stored in an M-way array ("data tensor"), may be analyzed either by artificial neural networks or tensor methods. Tensor decomposition factors data tensors into smaller tensors. Operations on data tensors can be expressed in terms of matrix multiplication and the Kronecker product. The computation of gradients, a crucial aspect of backpropagation, can be performed using software libraries such as PyTorch and TensorFlow. Computations are often performed on graphics processing units (GPUs) using CUDA, and on dedicated hardware such as Google's Tensor Processing Unit or Nvidia's Tensor core. These developments have greatly accelerated neural network architectures, and increased the size and complexity of models that can be trained. == History == A tensor is by definition a multilinear map. In mathematics, this may express a multilinear relationship between sets of algebraic objects. In physics, tensor fields, considered as tensors at each point in space, are useful in expressing mechanics such as stress or elasticity. In machine learning, the exact use of tensors depends on the statistical approach being used. In 2001, the field of signal processing and statistics were making use of tensor methods. Pierre Comon surveys the early adoption of tensor methods in the fields of telecommunications, radio surveillance, chemometrics and sensor processing. Linear tensor rank methods (such as, Parafac/CANDECOMP) analyzed M-way arrays ("data tensors") composed of higher order statistics that were employed in blind source separation problems to compute a linear model of the data. He noted several early limitations in determining the tensor rank and efficient tensor rank decomposition. In the early 2000s, multilinear tensor methods crossed over into computer vision, computer graphics and machine learning with papers by Vasilescu or in collaboration with Terzopoulos, such as Human Motion Signatures, TensorFaces TensorTextures and Multilinear Projection. Multilinear algebra, the algebra of higher-order tensors, is a suitable and transparent framework for analyzing the multifactor structure of an ensemble of observations and for addressing the difficult problem of disentangling the causal factors based on second order or higher order statistics associated with each causal factor. Tensor (multilinear) factor analysis disentangles and reduces the influence of different causal factors with multilinear subspace learning. When treating an image or a video as a 2- or 3-way array, i.e., "data matrix/tensor", tensor methods reduce spatial or time redundancies as demonstrated by Wang and Ahuja. Yoshua Bengio, Geoff Hinton and their collaborators briefly discuss the relationship between deep neural networks and tensor factor analysis beyond the use of M-way arrays ("data tensors") as inputs. One of the early uses of tensors for neural networks appeared in natural language processing. A single word can be expressed as a vector via Word2vec. Thus a relationship between two words can be encoded in a matrix. However, for more complex relationships such as subject-object-verb, it is necessary to build higher-dimensional networks. In 2009, the work of Sutskever introduced Bayesian Clustered Tensor Factorization to model relational concepts while reducing the parameter space. From 2014 to 2015, tensor methods become more common in convolutional neural networks (CNNs). Tensor methods organize neural network weights in a "data tensor", analyze and reduce the number of neural network weights. Lebedev et al. accelerated CNN networks for character classification (the recognition of letters and digits in images) by using 4D kernel tensors. == Definition == Let F {\displaystyle \mathbb {F} } be a field (such as the real numbers R {\displaystyle \mathbb {R} } or the complex numbers C {\displaystyle \mathbb {C} } ). A tensor T ∈ F I 1 × I 2 × … × I C {\displaystyle {\mathcal {T}}\in {\mathbb {F} }^{I_{1}\times I_{2}\times \ldots \times I_{C}}} is a multilinear transformation from a set of domain vector spaces to a range vector space: T : { F I 1 × F I 2 × … F I C } ↦ F I 0 {\displaystyle {\mathcal {T}}:\{{\mathbb {F} }^{I_{1}}\times {\mathbb {F} }^{I_{2}}\times \ldots {\mathbb {F} }^{I_{C}}\}\mapsto {\mathbb {F} }^{I_{0}}} Here, C {\displaystyle C} and I 0 , I 1 , … , I C {\displaystyle I_{0},I_{1},\ldots ,I_{C}} are positive integers, and ( C + 1 ) {\displaystyle (C+1)} is the number of modes of a tensor (also known as the number of ways of a multi-way array). The dimensionality of mode c {\displaystyle c} is I c {\displaystyle I_{c}} , for 0 ≤ c ≤ C {\displaystyle 0\leq c\leq C} . In statistics and machine learning, an image is vectorized when viewed as a single observation, and a collection of vectorized images is organized as a "data tensor". For example, a set of facial images { d i p , i e , i l , i v ∈ R I X } {\displaystyle \{{\mathbb {d} }_{i_{p},i_{e},i_{l},i_{v}}\in {\mathbb {R} }^{I_{X}}\}} with I X {\displaystyle I_{X}} pixels that are the consequences of multiple causal factors, such as a facial geometry i p ( 1 ≤ i p ≤ I P ) {\displaystyle i_{p}(1\leq i_{p}\leq I_{P})} , an expression i e ( 1 ≤ i e ≤ I E ) {\displaystyle i_{e}(1\leq i_{e}\leq I_{E})} , an illumination condition i l ( 1 ≤ i l ≤ I L ) {\displaystyle i_{l}(1\leq i_{l}\leq I_{L})} , and a viewing condition i v ( 1 ≤ i v ≤ I V ) {\displaystyle i_{v}(1\leq i_{v}\leq I_{V})} may be organized into a data tensor (ie. multiway array) D ∈ R I X × I P × I E × I L × V {\displaystyle {\mathcal {D}}\in {\mathbb {R} }^{I_{X}\times I_{P}\times I_{E}\times I_{L}\times V}} where I P {\displaystyle I_{P}} are the total number of facial geometries, I E {\displaystyle I_{E}} are the total number of expressions, I L {\displaystyle I_{L}} are the total number of illumination conditions, and I V {\displaystyle I_{V}} are the total number of viewing conditions. Tensor factorizations methods such as TensorFaces and multilinear (tensor) independent component analysis factorizes the data tensor into a set of vector spaces that span the causal factor representations, where an image is the result of tensor transformation T {\displaystyle {\mathcal {T}}} that maps a set of causal factor representations to the pixel space. Another approach to using tensors in machine learning is to embed various data types directly. For example, a grayscale image, commonly represented as a discrete 2-way array D ∈ R I R X × I C X {\displaystyle {\mathbf {D} }\in {\mathbb {R} }^{I_{RX}\times I_{CX}}} with dimensionality I R X × I C X {\displaystyle I_{RX}\times I_{CX}} where I R X {\displaystyle I_{RX}} are the number of rows and I C X {\displaystyle I_{CX}} are the number of columns. When an image is treated as 2-way array or 2nd order tensor (i.e. as a collection of column/row observations), tensor factorization methods compute the image column space, the image row space and the normalized PCA coefficients or the ICA coefficients. Similarly, a color image with RGB channels, D ∈ R N × M × 3 . {\displaystyle {\mathcal {D}}\in \mathbb {R} ^{N\times M\times 3}.} may be viewed as a 3rd order data tensor or 3-way array.-------- In natural language processing, a word might be expressed as a vector v {\displaystyle v} via the Word2vec algorithm. Thus v {\displaystyle v} becomes a mode-1 tensor v ↦ A ∈ R N . {\displaystyle v\mapsto {\mathcal {A}}\in \mathbb {R} ^{N}.} The embedding of subject-object-verb semantics requires embedding relationships among three words. Because a word is itself a vector, subject-object-verb semantics could be expressed using mode-3 tensors v a × v b × v c ↦ A ∈ R N × N × N . {\displaystyle v_{a}\times v_{b}\times v_{c}\mapsto {\mathcal {A}}\in \mathbb {R} ^{N\times N\times N}.} In practice the neural network designer is primarily concerned with the specification of embeddings, the connection of tensor layers, and the operations performed on them in a network. Modern machine learning frameworks manage the optimization, tensor factorization and backpropagation automatically. === As unit values === Tensors may be used as the unit values of neural networks which extend the concept of scalar, vector and matrix values to multiple dimensions. The output value of single layer unit y m {\displaystyle y_{m}} is the sum-product of its input units and the connection weights filtered through the activation function f {\displaystyle f} : y m = f ( ∑ n x n u m , n ) , {\displaystyle y_{m}=f\left(\sum _{n}x_{n}u_{m,n}\right),} where y m ∈ R .
K-nearest neighbors algorithm
In statistics, the k-nearest neighbors algorithm (k-NN) is a non-parametric supervised learning method. It was first developed by Evelyn Fix and Joseph Hodges in 1951, and later expanded by Thomas Cover. In classification, a new example is assigned a label based on the labels of its k nearest training examples; in regression, the prediction is computed from the values of those neighbors. Most often, it is used for classification, as a k-NN classifier, the output of which is a class membership. An object is classified by a plurality vote of its neighbors, with the object being assigned to the class most common among its k nearest neighbors (k is a positive integer, typically small). If k = 1, then the object is simply assigned to the class of that single nearest neighbor. The k-NN algorithm can also be generalized for regression. In k-NN regression, also known as nearest neighbor smoothing, the output is the property value for the object. This value is the average of the values of k nearest neighbors. If k = 1, then the output is simply assigned to the value of that single nearest neighbor, also known as nearest neighbor interpolation. For both classification and regression, a useful technique can be to assign weights to the contributions of the neighbors, so that nearer neighbors contribute more to the average than distant ones. For example, a common weighting scheme consists of giving each neighbor a weight of 1/d, where d is the distance to the neighbor. The input consists of the k closest training examples in a data set. The neighbors are taken from a set of objects for which the class (for k-NN classification) or the object property value (for k-NN regression) is known. This can be thought of as the training set for the algorithm, though no explicit training step is required. A peculiarity (sometimes even a disadvantage) of the k-NN algorithm is its sensitivity to the local structure of the data. In k-NN classification the function is only approximated locally and all computation is deferred until function evaluation. Since this algorithm relies on distance, if the features represent different physical units or come in vastly different scales, then feature-wise normalizing of the training data can greatly improve its accuracy. == Statistical setting == Suppose we have pairs ( X 1 , Y 1 ) , ( X 2 , Y 2 ) , … , ( X n , Y n ) {\displaystyle (X_{1},Y_{1}),(X_{2},Y_{2}),\dots ,(X_{n},Y_{n})} taking values in R d × { 1 , 2 } {\displaystyle \mathbb {R} ^{d}\times \{1,2\}} , where Y is the class label of X, so that X | Y = r ∼ P r {\displaystyle X|Y=r\sim P_{r}} for r = 1 , 2 {\displaystyle r=1,2} (and probability distributions P r {\displaystyle P_{r}} ). Given some norm ‖ ⋅ ‖ {\displaystyle \|\cdot \|} on R d {\displaystyle \mathbb {R} ^{d}} and a point x ∈ R d {\displaystyle x\in \mathbb {R} ^{d}} , let ( X ( 1 ) , Y ( 1 ) ) , … , ( X ( n ) , Y ( n ) ) {\displaystyle (X_{(1)},Y_{(1)}),\dots ,(X_{(n)},Y_{(n)})} be a reordering of the training data such that ‖ X ( 1 ) − x ‖ ≤ ⋯ ≤ ‖ X ( n ) − x ‖ {\displaystyle \|X_{(1)}-x\|\leq \dots \leq \|X_{(n)}-x\|} . == Algorithm == The training examples are vectors in a multidimensional feature space, each with a class label. The training phase of the algorithm consists only of storing the feature vectors and class labels of the training samples. In the classification phase, k is a user-defined constant, and an unlabeled vector (a query or test point) is classified by assigning the label which is most frequent among the k training samples nearest to that query point. A commonly used distance metric for continuous variables is Euclidean distance. For discrete variables, such as for text classification, another metric can be used, such as the overlap metric (or Hamming distance). In the context of gene expression microarray data, for example, k-NN has been employed with correlation coefficients, such as Pearson and Spearman, as a metric. Often, the classification accuracy of k-NN can be improved significantly if the distance metric is learned with specialized algorithms such as large margin nearest neighbor or neighborhood components analysis. A drawback of the basic "majority voting" classification occurs when the class distribution is skewed. That is, examples of a more frequent class tend to dominate the prediction of the new example, because they tend to be common among the k nearest neighbors due to their large number. One way to overcome this problem is to weight the classification, taking into account the distance from the test point to each of its k nearest neighbors. The class (or value, in regression problems) of each of the k nearest points is multiplied by a weight proportional to the inverse of the distance from that point to the test point. Another way to overcome skew is by abstraction in data representation. For example, in a self-organizing map (SOM), each node is a representative (a center) of a cluster of similar points, regardless of their density in the original training data. k-NN can then be applied to the SOM. == Parameter selection == The best choice of k depends upon the data; generally, larger values of k reduces effect of the noise on the classification, but make boundaries between classes less distinct. A good k can be selected by various heuristic techniques (see hyperparameter optimization). The special case where the class is predicted to be the class of the closest training sample (i.e. when k = 1) is called the nearest neighbor algorithm. The accuracy of the k-NN algorithm can be severely degraded by the presence of noisy or irrelevant features, or if the feature scales are not consistent with their importance. Much research effort has been put into selecting or scaling features to improve classification. A particularly popular approach is the use of evolutionary algorithms to optimize feature scaling. Another popular approach is to scale features by the mutual information of the training data with the training classes. In binary (two class) classification problems, it is helpful to choose k to be an odd number as this avoids tied votes. One popular way of choosing the empirically optimal k in this setting is via bootstrap method. == The 1-nearest neighbor classifier == The most intuitive nearest neighbour type classifier is the one nearest neighbour classifier that assigns a point x to the class of its closest neighbour in the feature space, that is C n 1 n n ( x ) = Y ( 1 ) {\displaystyle C_{n}^{1nn}(x)=Y_{(1)}} . As the size of training data set approaches infinity, the one nearest neighbour classifier guarantees an error rate of no worse than twice the Bayes error rate (the minimum achievable error rate given the distribution of the data). == The weighted nearest neighbour classifier == The k-nearest neighbour classifier can be viewed as assigning the k nearest neighbours a weight 1 / k {\displaystyle 1/k} and all others 0 weight. This can be generalised to weighted nearest neighbour classifiers. That is, where the ith nearest neighbour is assigned a weight w n i {\displaystyle w_{ni}} , with ∑ i = 1 n w n i = 1 {\textstyle \sum _{i=1}^{n}w_{ni}=1} . An analogous result on the strong consistency of weighted nearest neighbour classifiers also holds. Let C n w n n {\displaystyle C_{n}^{wnn}} denote the weighted nearest classifier with weights { w n i } i = 1 n {\displaystyle \{w_{ni}\}_{i=1}^{n}} . Subject to regularity conditions, which in asymptotic theory are conditional variables which require assumptions to differentiate among parameters with some criteria. On the class distributions the excess risk has the following asymptotic expansion R R ( C n w n n ) − R R ( C Bayes ) = ( B 1 s n 2 + B 2 t n 2 ) { 1 + o ( 1 ) } , {\displaystyle {\mathcal {R}}_{\mathcal {R}}(C_{n}^{wnn})-{\mathcal {R}}_{\mathcal {R}}(C^{\text{Bayes}})=\left(B_{1}s_{n}^{2}+B_{2}t_{n}^{2}\right)\{1+o(1)\},} for constants B 1 {\displaystyle B_{1}} and B 2 {\displaystyle B_{2}} where s n 2 = ∑ i = 1 n w n i 2 {\displaystyle s_{n}^{2}=\sum _{i=1}^{n}w_{ni}^{2}} and t n = n − 2 / d ∑ i = 1 n w n i { i 1 + 2 / d − ( i − 1 ) 1 + 2 / d } {\displaystyle t_{n}=n^{-2/d}\sum _{i=1}^{n}w_{ni}\left\{i^{1+2/d}-(i-1)^{1+2/d}\right\}} . The optimal weighting scheme { w n i ∗ } i = 1 n {\displaystyle \{w_{ni}^{}\}_{i=1}^{n}} , that balances the two terms in the display above, is given as follows: set k ∗ = ⌊ B n 4 d + 4 ⌋ {\displaystyle k^{}=\lfloor Bn^{\frac {4}{d+4}}\rfloor } , w n i ∗ = 1 k ∗ [ 1 + d 2 − d 2 k ∗ 2 / d { i 1 + 2 / d − ( i − 1 ) 1 + 2 / d } ] {\displaystyle w_{ni}^{}={\frac {1}{k^{}}}\left[1+{\frac {d}{2}}-{\frac {d}{2{k^{}}^{2/d}}}\{i^{1+2/d}-(i-1)^{1+2/d}\}\right]} for i = 1 , 2 , … , k ∗ {\displaystyle i=1,2,\dots ,k^{}} and w n i ∗ = 0 {\displaystyle w_{ni}^{}=0} for i = k ∗ + 1 , … , n {\displaystyle i=k^{}+1,\dots ,n} . With optimal weights the dominant term in the asymptotic expansion of the excess risk is O ( n − 4 d + 4 ) {\displaystyle {\mathcal {O}}(n^{-{\frac {4}{d+4}}})}
Operational taxonomic unit
An operational taxonomic unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "operational taxonomic unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopic organisms. For several years, OTUs have been the most commonly used units of diversity, especially when analysing small subunit 16S (for prokaryotes) or 18S rRNA (for eukaryotes) marker gene sequence datasets. == Molecular OTU by clustering of marker gene sequences == In the approach represented by DNA barcoding, a particular locus is chosen to be used as the marker gene for classification. This locus should be universally present in the scope selected, variable enough to be different among close-related species, and be flanked by conservative sequences that allow for easy amplification and detection. There are databases containing sequences for such marker genes from many different species, allowing for comparison. (Sometimes only using one locus does not provide sufficient resolution, so multiple marker genes are used. This is the case for plants, where rbcL+matK is common.) Sequences obtained this way can be clustered according to their similarity to one another, and operational taxonomic units are defined based on the similarity threshold set by the researcher. The exact threshold depends on the taxa in question and the mutational rates of the selected locus in the taxon. 97–99% are commonly used, but "it is now recognized to be somewhat arbitrary as sequence variation within and among species varies across taxa". 100% similarity (fully identical) is also common, also known as single variants. It remains debatable how well this commonly used method recapitulates true microbial species phylogeny or ecology. Although OTUs can be calculated differently when using different algorithms or thresholds, research by Schmidt et al. (2014) demonstrated that 16S-derived microbial OTUs were generally ecologically consistent across habitats and several clustering approaches. The number of OTUs defined may be inflated due to errors in DNA sequencing. === OTU clustering approaches === There are three main approaches to clustering OTUs: De novo, for which the clustering is based on similarities between sequencing reads. Closed-reference, for which the clustering is performed against a reference database of sequences. Open-reference, where clustering is first performed against a reference database of sequences, then any remaining sequences that could not be mapped to the reference are clustered de novo. Using a reference provides taxonomic context for the OTUs found. Alternatively, taxonomic context can be found after the construction of clusters by comparing representative sequences from clusters against a reference database. There are also specialized classifiers for this purpose which are much faster than naive comparison using BLAST. === OTU clustering algorithms === Hierarchical clustering algorithms (HCA): uclust & cd-hit & ESPRIT Bayesian clustering: CROP == Molecular OTU by other methods == In addition to similarity-based grouping, marker gene sequences can be sorted into OTUs using molecular phylogeny, k-mer composition, or hybrid methods combining these methods with similarity. There are also Bayesian tree-less methods and machine learning approaches. Using phylogeny often involves manually assigning terminal clades or single nodes to an OTU, so this is usually only done for refinement. Genome skimming can be used to obtain high-copy DNA without the need to choose marker genes or to design PCR primers for the chosen genes. It can provide fairly good coverage of organelle DNA and repetitive elements such as ribosomal DNA, both of which can be used like marker genes in OTU analysis. Whole-genome sequencing is more expensive and involves the production and processing of more data. By considering the entire genome, many (sometimes over 100) marker genes can be used at the same time, producing highly resolved phylogenies that correctly identify problematic taxa. It is also possible to use entire genomes for OTU assignment. For example, genomes from different bacterial species almost always have an average nucleotide identity lower than 95%, a fact that can be used to define new OTUs (and likely new species).
Jpred
Jpred v.4 is the latest version of the JPred Protein Secondary Structure Prediction Server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction, that has existed since 1998 in different versions. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 134 000 jobs per month and has carried out over 2 million predictions in total for users in 179 countries. == JPred 2 == The static HTML pages of JPred 2 are still available for reference. == JPred 3 == The JPred v3 followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References). This release added new functionality and fixed many bugs. The highlights are: New, friendlier user interface Retrained and optimised version of Jnet (v2) - mean secondary structure prediction accuracy of >81% Batch submission of jobs Better error checking of input sequences/alignments Predictions now (optionally) returned via e-mail Users may provide their own query names for each submission JPred now makes a prediction even when there are no PSI-BLAST hits to the query PS/PDF output now incorporates all the predictions == JPred 4 == The current version of JPred (v4) has the following improvements and updates incorporated: Retrained on the latest UniRef90 and SCOPe/ASTRAL version of Jnet (v2.3.1) - mean secondary structure prediction accuracy of >82%. Upgraded the Web Server to the latest technologies (Bootstrap framework, JavaScript) and updating the web pages – improving the design and usability through implementing responsive technologies. Added RESTful API and mass-submission and results retrieval scripts - resulting in peak throughput above 20,000 predictions per day. Added prediction jobs monitoring tools. Upgraded the results reporting – both, on the web-site, and through the optional email summary reports: improved batch submission, added results summary preview through Jalview results visualization summary in SVG and adding full multiple sequence alignments into the reports. Improved help-pages, incorporating tool-tips, and adding one-page step-by-step tutorials. Sequence residues are categorised or assigned to one of the secondary structure elements, such as alpha-helix, beta-sheet and coiled-coil. Jnet uses two neural networks for its prediction. The first network is fed with a window of 17 residues over each amino acid in the alignment plus a conservation number. It uses a hidden layer of nine nodes and has three output nodes, one for each secondary structure element. The second network is fed with a window of 19 residues (the result of first network) plus the conservation number. It has a hidden layer with nine nodes and has three output nodes.
Outline of natural language processing
Natural language processing is computer activity in which computers are entailed to analyze, understand, alter, or generate natural language. This includes the automation of any or all linguistic forms, activities, or methods of communication, such as conversation, correspondence, reading, written composition, dictation, publishing, translation, lip reading, and so on. Natural-language processing is also the name of the branch of computer science, artificial intelligence, and linguistics concerned with enabling computers to engage in communication using natural language(s) in all forms, including but not limited to speech, print, writing, and signing. The following outline is provided as an overview of and topical guide to natural-language processing: == Natural-language processing == Natural-language processing can be described as all of the following: A field of science – systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe. An applied science – field that applies human knowledge to build or design useful things. A field of computer science – scientific and practical approach to computation and its applications. A branch of artificial intelligence – intelligence of machines and robots and the branch of computer science that aims to create it. A subfield of computational linguistics – interdisciplinary field dealing with the statistical or rule-based modeling of natural language from a computational perspective. An application of engineering – science, skill, and profession of acquiring and applying scientific, economic, social, and practical knowledge, in order to design and also build structures, machines, devices, systems, materials and processes. An application of software engineering – application of a systematic, disciplined, quantifiable approach to the design, development, operation, and maintenance of software, and the study of these approaches; that is, the application of engineering to software. A subfield of computer programming – process of designing, writing, testing, debugging, and maintaining the source code of computer programs. This source code is written in one or more programming languages (such as Java, C++, C#, Python, etc.). The purpose of programming is to create a set of instructions that computers use to perform specific operations or to exhibit desired behaviors. A subfield of artificial intelligence programming – A type of system – set of interacting or interdependent components forming an integrated whole or a set of elements (often called 'components' ) and relationships which are different from relationships of the set or its elements to other elements or sets. A system that includes software – software is a collection of computer programs and related data that provides the instructions for telling a computer what to do and how to do it. Software refers to one or more computer programs and data held in the storage of the computer. In other words, software is a set of programs, procedures, algorithms and its documentation concerned with the operation of a data processing system. A type of technology – making, modification, usage, and knowledge of tools, machines, techniques, crafts, systems, methods of organization, in order to solve a problem, improve a preexisting solution to a problem, achieve a goal, handle an applied input/output relation or perform a specific function. It can also refer to the collection of such tools, machinery, modifications, arrangements and procedures. Technologies significantly affect human as well as other animal species' ability to control and adapt to their natural environments. A form of computer technology – computers and their application. NLP makes use of computers, image scanners, microphones, and many types of software programs. Language technology – consists of natural-language processing (NLP) and computational linguistics (CL) on the one hand, and speech technology on the other. It also includes many application oriented aspects of these. It is often called human language technology (HLT). == Prerequisite technologies == The following technologies make natural-language processing possible: Communication – the activity of a source sending a message to a receiver Language – Speech – Writing – Computing – Computers – Computer programming – Information extraction – User interface – Software – Text editing – program used to edit plain text files Word processing – piece of software used for composing, editing, formatting, printing documents Input devices – pieces of hardware for sending data to a computer to be processed Computer keyboard – typewriter style input device whose input is converted into various data depending on the circumstances Image scanners – == Subfields of natural-language processing == Information extraction (IE) – field concerned in general with the extraction of semantic information from text. This covers tasks such as named-entity recognition, coreference resolution, relationship extraction, etc. Ontology engineering – field that studies the methods and methodologies for building ontologies, which are formal representations of a set of concepts within a domain and the relationships between those concepts. Speech processing – field that covers speech recognition, text-to-speech and related tasks. Statistical natural-language processing – Statistical semantics – a subfield of computational semantics that establishes semantic relations between words to examine their contexts. Distributional semantics – a subfield of statistical semantics that examines the semantic relationship of words across a corpora or in large samples of data. == Related fields == Natural-language processing contributes to, and makes use of (the theories, tools, and methodologies from), the following fields: Automated reasoning – area of computer science and mathematical logic dedicated to understanding various aspects of reasoning, and producing software which allows computers to reason completely, or nearly completely, automatically. A sub-field of artificial intelligence, automatic reasoning is also grounded in theoretical computer science and philosophy of mind. Linguistics – scientific study of human language. Natural-language processing requires understanding of the structure and application of language, and therefore it draws heavily from linguistics. Applied linguistics – interdisciplinary field of study that identifies, investigates, and offers solutions to language-related real-life problems. Some of the academic fields related to applied linguistics are education, linguistics, psychology, computer science, anthropology, and sociology. Some of the subfields of applied linguistics relevant to natural-language processing are: Bilingualism / Multilingualism – Computer-mediated communication (CMC) – any communicative transaction that occurs through the use of two or more networked computers. Research on CMC focuses largely on the social effects of different computer-supported communication technologies. Many recent studies involve Internet-based social networking supported by social software. Contrastive linguistics – practice-oriented linguistic approach that seeks to describe the differences and similarities between a pair of languages. Conversation analysis (CA) – approach to the study of social interaction, embracing both verbal and non-verbal conduct, in situations of everyday life. Turn-taking is one aspect of language use that is studied by CA. Discourse analysis – various approaches to analyzing written, vocal, or sign language use or any significant semiotic event. Forensic linguistics – application of linguistic knowledge, methods and insights to the forensic context of law, language, crime investigation, trial, and judicial procedure. Interlinguistics – study of improving communications between people of different first languages with the use of ethnic and auxiliary languages (lingua franca). For instance by use of intentional international auxiliary languages, such as Esperanto or Interlingua, or spontaneous interlanguages known as pidgin languages. Language assessment – assessment of first, second or other language in the school, college, or university context; assessment of language use in the workplace; and assessment of language in the immigration, citizenship, and asylum contexts. The assessment may include analyses of listening, speaking, reading, writing or cultural understanding, with respect to understanding how the language works theoretically and the ability to use the language practically. Language pedagogy – science and art of language education, including approaches and methods of language teaching and study. Natural-language processing is used in programs designed to teach language, including first- and second-language training. Language planning – Language policy – Lexicography – Literacies – Pragmatics – Second-language acquisition – Stylistics – Translation – Comp
VITAL (machine learning software)
VITAL (Validating Investment Tool for Advancing Life Sciences) was a Board Management Software machine learning proprietary software developed by Aging Analytics, a company registered in Bristol (England) and dissolved in 2017. Andrew Garazha (the firm's Senior Analyst) declared that the project aimed "through iterative releases and updates to create a piece of software capable of making autonomous investment decisions." According to Nick Dyer-Witheford, VITAL 1.0 was a "basic algorithm". On 13 May 2014, Deep Knowledge Ventures, a Hong Kong venture capital firm, claimed to have appointed VITAL to its board of directors in order to prove that artificial intelligence could be an instrument for investment decision-making. The announcement received great press coverage despite the fact commentators consider this a publicity stunt. Fortune reported in 2019 that VITAL is no longer used. == Criticism == Academics and journalists viewed VITAL's board appointment with skepticism. University of Sheffield computer science professor Noel Sharkey called it "a publicity hype". Michael Osborne, a University of Oxford associate professor in machine learning, found it is "a gimmick to call that an actual board member". Simon Sharwood of The Register, wrote there is "a strong whiff of stunt and/or promotion about this". In a 2019 speech, the Chief Scientist of Australia, Alan Finkel, commented, "At the time, most of us probably dismissed Vital as a PR exercise. I admit, I used her story three years ago to get a laugh in one of my speeches." Florian Möslein, a law professor at the University of Marburg, wrote in 2018 that "Vital has widely been acknowledged as the 'world's first artificial intelligence company director'". Vice journalist Jason Koebler suggested that the software did not have any article intelligence capabilities and concluded "VITAL can’t talk, and it can’t hear, and it can’t be a real, functional executive of a company." Sharwood of The Register noted that because VITAL was not a natural person, it could not be a board member under Hong Kong's corporate governance laws. However, in a 2017 interview to The Nikkei, Dmitry Kaminskiy, managing partner of Deep Knowledge Ventures, stated that VITAL had observer status on the board and no voting rights. University of Sheffield computer science professor Noel Sharkey said of VITAL, "On first sight, it looks like a futuristic idea but on reflection it is really a little bit of publicity hype." Vice journalist Jason Koebler said "this is a gimmick" and said "There is literally nothing to suggest that VITAL has any sort of capabilities beyond any other proprietary analysis software". Michael Osborne, a University of Oxford associate professor in machine learning, found VITAL's appointment to be noncredible, saying it is "a bit of a gimmick to call that an actual board member". Osborne said that a core duty of board members to converse with each other, which the algorithm is incapable of doing, so its more likely functionality is to serve as a springboard for conversation among other board members. In a 2019 speech, the Chief Scientist of Australia, Alan Finkel, commented, "At the time, most of us probably dismissed Vital as a PR exercise. I admit, I used her story three years ago to get a laugh in one of my speeches." == Machine intelligence as board member == VITAL was created by a group of programmers employed by Aging Analytics According to Andrew Garazh, Aging Analytics Senior Analyst, VITAL was not a machine learning algorithm as the necessary datasets on investment rounds, intellectual property and clinical trial outcomes are generally not disclosed. Rather, VITAL used fuzzy logic based on 50 parameters to assess risk factors. Aging Analytics licensed the software to Deep Knowledge Ventures. It was used to help the human board members of Deep Knowledge Venture make investment decisions in biotechnology companies. For instance, it supported investments in Insilico Medicine, which creates ways for computers to help find drugs in research into aging. VITAL also supported investing in Pathway Pharmaceuticals, which uses the OncoFinder algorithm to choose and appraise cancer treatments. According to Dmitry Kaminskiy, managing partner of Deep Knowledge Ventures, the motivation for using VITAL was the large number of failed investments in the biotechnology sector and the desire to avoid investing in companies likely to fail. == Ethical and legal implications == Scholars addressed questions around the safety, privacy, accountability transparency and bias in algorithms. Writing in the philosophical journal Multitudes, the academic Ariel Kyrou raised questions about the consequences of a mistake made by an algorithm recommending a dangerous investment. He raised the hypothetical where VITAL was able to persuade the board to invest in a startup that had the facade of doing research into treatment for age-associated ills, but in actuality was run by terrorists who were raising funds. Kyrou raised a series of questions about who society would fault for VITAL's mistake. As the owner of VITAL, should Deep Knowledge Ventures be held accountable, or rather should the companies that supplied data to VITAL or the people who created VITAL be held liable? Simon Sharwood of The Register wrote that because the appointment of a software program to the board directors is not legally feasible in Hong Kong, there is "a strong whiff of stunt and/or promotion about this". Quoting a Thomson Reuters website describing Hong Kong legislation related to corporate governance, Sharwood pointed out that in Hong Kong "the board comprises all of the directors of the company" and "a director must normally be a natural person, except that a private company may have a body corporate as its director if the company is not a member of a listed group." He concluded that since VITAL cannot be considered a "natural person", it is merely a "cosmetic" appointment to the board and that "this software is no more a Board member than Caligula's horse was a senator". Sharwood further argued that corporations frequently purchase directors and officers liability insurance but that it would be practically impossible to get such insurance for VITAL. Sharwood also wrote that were VITAL to be hacked, any misinformation it outputs could be considered "false and misleading communications". In the book Research Handbook on the Law of Artificial Intelligence, Florian Mölein wrote that VITAL could not become a director as defined in Hong Kong's corporate laws, so the other directors just were approaching it as "a member of [the] board with observer status". Lin Shaowei raised concerns in a Journal of East China University of Political Science and Law article about how the software's appearance inspired a complex question about the relationship between corporate law and artificial intelligence. VITAL could be considered either a board director who has voting rights or an observer who does not. Lin said either choice raised questions about whether VITAL is subject to corporate law and who would be held accountable if VITAL recommends a choice that turns out to be damaging to the company. David Theo Goldberg in the Critical Times, a peer reviewed journal in Critical Global Theory, argues that VITAL processed a dataset to predict the most remunerative investment opportunities. Drawing his analysis on an article from Business Insider, Goldberg describes VITAL's decision-making predictiveness based "on surface pattern recognition and the identification of regularities and/or irregularities". In other words, Goldberg asserts that "the normativity of the surface" explains algorithmic knowledge of a "product" like VITAL. In Homo Deus, Yuval Noah Harari mentions VITAL as an example of the future risks that humankind faces. Harari argues that the human mind is being replaced by a world in which algorithms and data make the decisions. Specifically, it is argued that "as algorithms push humans out of the job market," executive boards driven by artificial intelligence are more likely to give priority to algorithms over the humans.