Apache cTAKES: clinical Text Analysis and Knowledge Extraction System is an open-source Natural Language Processing (NLP) system that extracts clinical information from electronic health record unstructured text. It processes clinical notes, identifying types of clinical named entities — drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures. Each named entity has attributes for the text span, the ontology mapping code, context (family history of, current, unrelated to patient), and negated/not negated. cTAKES was built using the UIMA Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit. == Components == Components of cTAKES are specifically trained for the clinical domain, and create rich linguistic and semantic annotations that can be utilized by clinical decision support systems and clinical research. These components include: Named Section identifier Sentence boundary detector Rule-based tokenizer Formatted list identifier Normalizer Context dependent tokenizer Part-of-speech tagger Phrasal chunker Dictionary lookup annotator Context annotator Negation detector Uncertainty detector Subject detector Dependency parser patient smoking status identifier Drug mention annotator == History == Development of cTAKES began at the Mayo Clinic in 2006. The development team, led by Dr. Guergana Savova and Dr. Christopher Chute, included physicians, computer scientists and software engineers. After its deployment, cTAKES became an integral part of Mayo's clinical data management infrastructure, processing more than 80 million clinical notes. When Dr. Savova's moved to Boston Children's Hospital in early 2010, the core development team grew to include members there. Further external collaborations include: University of Colorado Brandeis University University of Pittsburgh University of California at San Diego Such collaborations have extended cTAKES' capabilities into other areas such as Temporal Reasoning, Clinical Question Answering, and coreference resolution for the clinical domain. In 2010, cTAKES was adopted by the i2b2 program and is a central component of the SHARP Area 4. In 2013, cTAKES released their first release as an Apache Software Foundation incubator project: cTAKES 3.0. In March 2013, cTAKES became an Apache Software Foundation Top Level Project (TLP).
Landweber iteration
The Landweber iteration or Landweber algorithm is an algorithm to solve ill-posed linear inverse problems, and it has been extended to solve non-linear problems that involve constraints. The method was first proposed in the 1950s by Louis Landweber, and it can be now viewed as a special case of many other more general methods. == Basic algorithm == The original Landweber algorithm attempts to recover a signal x from (noisy) measurements y. The linear version assumes that y = A x {\displaystyle y=Ax} for a linear operator A. When the problem is in finite dimensions, A is just a matrix. When A is nonsingular, then an explicit solution is x = A − 1 y {\displaystyle x=A^{-1}y} . However, if A is ill-conditioned, the explicit solution is a poor choice since it is sensitive to any noise in the data y. If A is singular, this explicit solution doesn't even exist. The Landweber algorithm is an attempt to regularize the problem, and is one of the alternatives to Tikhonov regularization. We may view the Landweber algorithm as solving: min x ‖ A x − y ‖ 2 2 / 2 {\displaystyle \min _{x}\|Ax-y\|_{2}^{2}/2} using an iterative method. The algorithm is given by the update x k + 1 = x k − ω A ∗ ( A x k − y ) . {\displaystyle x_{k+1}=x_{k}-\omega A^{}(Ax_{k}-y).} where the relaxation factor ω {\displaystyle \omega } satisfies 0 < ω < 2 / σ 1 2 {\displaystyle 0<\omega <2/\sigma _{1}^{2}} . Here σ 1 {\displaystyle \sigma _{1}} is the largest singular value of A {\displaystyle A} . If we write f ( x ) = ‖ A x − y ‖ 2 2 / 2 {\displaystyle f(x)=\|Ax-y\|_{2}^{2}/2} , then the update can be written in terms of the gradient x k + 1 = x k − ω ∇ f ( x k ) {\displaystyle x_{k+1}=x_{k}-\omega \nabla f(x_{k})} and hence the algorithm is a special case of gradient descent. For ill-posed problems, the iterative method needs to be stopped at a suitable iteration index, because it semi-converges. This means that the iterates approach a regularized solution during the first iterations, but become unstable in further iterations. The reciprocal of the iteration index 1 / k {\displaystyle 1/k} acts as a regularization parameter. A suitable parameter is found, when the mismatch ‖ A x k − y ‖ 2 2 {\displaystyle \|Ax_{k}-y\|_{2}^{2}} approaches the noise level. Using the Landweber iteration as a regularization algorithm has been discussed in the literature. == Nonlinear extension == In general, the updates generated by x k + 1 = x k − τ ∇ f ( x k ) {\displaystyle x_{k+1}=x_{k}-\tau \nabla f(x_{k})} will generate a sequence f ( x k ) {\displaystyle f(x_{k})} that converges to a minimizer of f whenever f is convex and the stepsize τ {\displaystyle \tau } is chosen such that 0 < τ < 2 / ( ‖ ∇ f ‖ 2 ) {\displaystyle 0<\tau <2/(\|\nabla f\|^{2})} where ‖ ⋅ ‖ {\displaystyle \|\cdot \|} is the spectral norm. Since this is special type of gradient descent, there currently is not much benefit to analyzing it on its own as the nonlinear Landweber, but such analysis was performed historically by many communities not aware of unifying frameworks. The nonlinear Landweber problem has been studied in many papers in many communities; see, for example. == Extension to constrained problems == If f is a convex function and C is a convex set, then the problem min x ∈ C f ( x ) {\displaystyle \min _{x\in C}f(x)} can be solved by the constrained, nonlinear Landweber iteration, given by: x k + 1 = P C ( x k − τ ∇ f ( x k ) ) {\displaystyle x_{k+1}={\mathcal {P}}_{C}(x_{k}-\tau \nabla f(x_{k}))} where P {\displaystyle {\mathcal {P}}} is the projection onto the set C. Convergence is guaranteed when 0 < τ < 2 / ( ‖ A ‖ 2 ) {\displaystyle 0<\tau <2/(\|A\|^{2})} . This is again a special case of projected gradient descent (which is a special case of the forward–backward algorithm) as discussed in. == Applications == Since the method has been around since the 1950s, it has been adopted and rediscovered by many scientific communities, especially those studying ill-posed problems. In X-ray computed tomography it is called simultaneous iterative reconstruction technique (SIRT). It has also been used in the computer vision community and the signal restoration community. It is also used in image processing, since many image problems, such as deconvolution, are ill-posed. Variants of this method have been used also in sparse approximation problems and compressed sensing settings.
Collocation
In corpus linguistics, a collocation is a series of words or terms that co-occur more often than would be expected by chance. In phraseology, a collocation is a type of compositional phraseme, meaning that it can be understood from the words that make it up. This contrasts with an idiom, where the meaning of the whole cannot be inferred from its parts, and may be completely unrelated. There are about seven main types of collocations: adjective + noun, noun + noun (such as collective nouns), noun + verb, verb + noun, adverb + adjective, verbs + prepositional phrase (phrasal verbs), and verb + adverb. Collocation extraction is a computational technique that finds collocations in a document or corpus, using various computational linguistics elements resembling data mining. == Expanded definition == Collocations are partly or fully fixed expressions that become established through repeated context-dependent use. Such terms as crystal clear, middle management, nuclear family, and cosmetic surgery are examples of collocated pairs of words. Collocations can be in a syntactic relation (such as verb–object: make and decision), lexical relation (such as antonymy), or they can be in no linguistically defined relation. Knowledge of collocations is vital for the competent use of a language: a grammatically correct sentence will stand out as awkward if collocational preferences are violated. This makes collocation a common focus for language teaching. Corpus linguists specify a key word in context (KWIC) and identify the words immediately surrounding them, to illustrate the way words are used in practice. The processing of collocations involves a number of parameters, the most important of which is the measure of association, which evaluates whether the co-occurrence is purely by chance or statistically significant. Due to the non-random nature of language, most collocations are classed as significant, and the association scores are simply used to rank the results. Commonly used measures of association include mutual information, t scores, and log-likelihood. Rather than select a single definition, Gledhill proposes that collocation involves at least three different perspectives: co-occurrence, a statistical view, which sees collocation as the recurrent appearance in a text of a node and its collocates; construction, which sees collocation either as a correlation between a lexeme and a lexical-grammatical pattern, or as a relation between a base and its collocative partners; and expression, a pragmatic view of collocation as a conventional unit of expression, regardless of form. These different perspectives contrast with the usual way of presenting collocation in phraseological studies. Traditionally speaking, collocation is explained in terms of all three perspectives at once, in a continuum: == In dictionaries == In 1933, Harold Palmer's Second Interim Report on English Collocations highlighted the importance of collocation as a key to producing natural-sounding language, for anyone learning a foreign language. Thus from the 1940s onwards, information about recurrent word combinations became a standard feature of monolingual learner's dictionaries. As these dictionaries became "less word-centred and more phrase-centred", more attention was paid to collocation. This trend was supported, from the beginning of the 21st century, by the availability of large text corpora and intelligent corpus-querying software, making it possible to provide a more systematic account of collocation in dictionaries. Using these tools, dictionaries such as the Macmillan English Dictionary and the Longman Dictionary of Contemporary English included boxes or panels with lists of frequent collocations. There are also a number of specialized dictionaries devoted to describing the frequent collocations in a language. These include (for Spanish) Redes: Diccionario combinatorio del español contemporaneo (2004), (for French) Le Robert: Dictionnaire des combinaisons de mots (2007), and (for English) the LTP Dictionary of Selected Collocations (1997) and the Macmillan Collocations Dictionary (2010). == Statistically significant collocation == Student's t-test can be used to determine whether the occurrence of a collocation in a corpus is statistically significant. For a bigram w 1 w 2 {\displaystyle w_{1}w_{2}} , let P ( w 1 ) = # w 1 N {\displaystyle P(w_{1})={\frac {\#w_{1}}{N}}} be the unconditional probability of occurrence of w 1 {\displaystyle w_{1}} in a corpus with size N {\displaystyle N} , and let P ( w 2 ) = # w 2 N {\displaystyle P(w_{2})={\frac {\#w_{2}}{N}}} be the unconditional probability of occurrence of w 2 {\displaystyle w_{2}} in the corpus. The t-score for the bigram w 1 w 2 {\displaystyle w_{1}w_{2}} is calculated as: where x ¯ = # w i w j N {\displaystyle {\bar {x}}={\frac {\#w_{i}w_{j}}{N}}} is the sample mean of the occurrence of w 1 w 2 {\displaystyle w_{1}w_{2}} , # w 1 w 2 {\displaystyle \#w_{1}w_{2}} is the number of occurrences of w 1 w 2 {\displaystyle w_{1}w_{2}} , μ = P ( w i ) P ( w j ) {\displaystyle \mu =P(w_{i})P(w_{j})} is the probability of w 1 w 2 {\displaystyle w_{1}w_{2}} under the null-hypothesis that w 1 {\displaystyle w_{1}} and w 2 {\displaystyle w_{2}} appear independently in the text, and s 2 = x ¯ ( 1 − x ¯ ) ≈ x ¯ {\displaystyle s^{2}={\bar {x}}(1-{\bar {x}})\approx {\bar {x}}} is the sample variance. With a large N {\displaystyle N} , the t-test is equivalent to a Z-test.
Stochastic grammar
A stochastic grammar (statistical grammar) is a grammar framework with a probabilistic notion of grammaticality: Stochastic context-free grammar Statistical parsing Data-oriented parsing Hidden Markov model (or stochastic regular grammar) Estimation theory The grammar is realized as a language model. Allowed sentences are stored in a database together with the frequency how common a sentence is. Statistical natural language processing uses stochastic, probabilistic and statistical methods, especially to resolve difficulties that arise because longer sentences are highly ambiguous when processed with realistic grammars, yielding thousands or millions of possible analyses. Methods for disambiguation often involve the use of corpora and Markov models. "A probabilistic model consists of a non-probabilistic model plus some numerical quantities; it is not true that probabilistic models are inherently simpler or less structural than non-probabilistic models." == Examples == A probabilistic method for rhyme detection is implemented by Hirjee & Brown in their study in 2013 to find internal and imperfect rhyme pairs in rap lyrics. The concept is adapted from a sequence alignment technique using BLOSUM (BLOcks SUbstitution Matrix). They were able to detect rhymes undetectable by non-probabilistic models.
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Open information extraction
In natural language processing, open information extraction (OIE) is the task of generating a structured, machine-readable representation of the information in text, usually in the form of triples or n-ary propositions. == Overview == A proposition can be understood as truth-bearer, a textual expression of a potential fact (e.g., "Dante wrote the Divine Comedy"), represented in an amenable structure for computers [e.g., ("Dante", "wrote", "Divine Comedy")]. An OIE extraction normally consists of a relation and a set of arguments. For instance, ("Dante", "passed away in" "Ravenna") is a proposition formed by the relation "passed away in" and the arguments "Dante" and "Ravenna". The first argument is usually referred as the subject while the second is considered to be the object. The extraction is said to be a textual representation of a potential fact because its elements are not linked to a knowledge base. Furthermore, the factual nature of the proposition has not yet been established. In the above example, transforming the extraction into a full fledged fact would first require linking, if possible, the relation and the arguments to a knowledge base. Second, the truth of the extraction would need to be determined. In computer science transforming OIE extractions into ontological facts is known as relation extraction. In fact, OIE can be seen as the first step to a wide range of deeper text understanding tasks such as relation extraction, knowledge-base construction, question answering, semantic role labeling. The extracted propositions can also be directly used for end-user applications such as structured search (e.g., retrieve all propositions with "Dante" as subject). OIE was first introduced by TextRunner developed at the University of Washington Turing Center headed by Oren Etzioni. Other methods introduced later such as Reverb, OLLIE, ClausIE or CSD helped to shape the OIE task by characterizing some of its aspects. At a high level, all of these approaches make use of a set of patterns to generate the extractions. Depending on the particular approach, these patterns are either hand-crafted or learned. == OIE systems and contributions == Reverb suggested the necessity to produce meaningful relations to more accurately capture the information in the input text. For instance, given the sentence "Faust made a pact with the devil", it would be erroneous to just produce the extraction ("Faust", "made", "a pact") since it would not be adequately informative. A more precise extraction would be ("Faust", "made a pact with", "the devil"). Reverb also argued against the generation of overspecific relations. OLLIE stressed two important aspects for OIE. First, it pointed to the lack of factuality of the propositions. For instance, in a sentence like "If John studies hard, he will pass the exam", it would be inaccurate to consider ("John", "will pass", "the exam") as a fact. Additionally, the authors indicated that an OIE system should be able to extract non-verb mediated relations, which account for significant portion of the information expressed in natural language text. For instance, in the sentence "Obama, the former US president, was born in Hawaii", an OIE system should be able to recognize a proposition ("Obama", "is", "former US president"). ClausIE introduced the connection between grammatical clauses, propositions, and OIE extractions. The authors stated that as each grammatical clause expresses a proposition, each verb mediated proposition can be identified by solely recognizing the set of clauses expressed in each sentence. This implies that to correctly recognize the set of propositions in an input sentence, it is necessary to understand its grammatical structure. The authors studied the case in the English language that only admits seven clause types, meaning that the identification of each proposition only requires defining seven grammatical patterns. The finding also established a separation between the recognition of the propositions and its materialization. In a first step, the proposition can be identified without any consideration of its final form, in a domain-independent and unsupervised way, mostly based on linguistic principles. In a second step, the information can be represented according to the requirements of the underlying application, without conditioning the identification phase. Consider the sentence "Albert Einstein was born in Ulm and died in Princeton". The first step will recognize the two propositions ("Albert Einstein", "was born", "in Ulm") and ("Albert Einstein", "died", "in Princeton"). Once the information has been correctly identified, the propositions can take the particular form required by the underlying application [e.g., ("Albert Einstein", "was born in", "Ulm") and ("Albert Einstein", "died in", "Princeton")]. CSD introduced the idea of minimality in OIE. It considers that computers can make better use of the extractions if they are expressed in a compact way. This is especially important in sentences with subordinate clauses. In these cases, CSD suggests the generation of nested extractions. For example, consider the sentence "The Embassy said that 6,700 Americans were in Pakistan". CSD generates two extractions [i] ("6,700 Americans", "were", "in Pakistan") and [ii] ("The Embassy", "said", "that [i]"). This is usually known as reification.
Steve Omohundro
Stephen Malvern Omohundro (born 1959) is an American computer scientist whose areas of research include Hamiltonian physics, dynamical systems, programming languages, machine learning, machine vision, and the social implications of artificial intelligence. His current work uses rational economics to develop safe and beneficial intelligent technologies for better collaborative modeling, understanding, innovation, and decision making. == Education == Omohundro has degrees in physics and mathematics from Stanford University (Phi Beta Kappa) and a Ph.D. in physics from the University of California, Berkeley. == Learning algorithms == Omohundro started the "Vision and Learning Group" at the University of Illinois, which produced 4 Masters and 2 Ph.D. theses. His work in learning algorithms included a number of efficient geometric algorithms, the manifold learning task and various algorithms for accomplishing this task, other related visual learning and modelling tasks, the best-first model merging approach to machine learning (including the learning of Hidden Markov Models and Stochastic Context-free Grammars), and the Family Discovery Learning Algorithm, which discovers the dimension and structure of a parameterized family of stochastic models. == Self-improving artificial intelligence and AI safety == Omohundro started Self-Aware Systems in Palo Alto, California to research the technology and social implications of self-improving artificial intelligence. He is an advisor to the Machine Intelligence Research Institute on artificial intelligence. He argues that rational systems exhibit problematic natural "drives" that will need to be countered in order to build intelligent systems safely. His papers, talks, and videos on AI safety have generated extensive interest. He has given many talks on self-improving artificial intelligence, cooperative technology, AI safety, and connections with biological intelligence. == Programming languages == At Thinking Machines Corporation, Cliff Lasser and Steve Omohundro developed Star Lisp, the first programming language for the Connection Machine. Omohundro joined the International Computer Science Institute (ICSI) in Berkeley, California, where he led the development of the open source programming language Sather. Sather is featured in O'Reilly's History of Programming Languages poster. == Physics and dynamical systems theory == Omohundro's book Geometric Perturbation Theory in Physics describes natural Hamiltonian symplectic structures for a wide range of physical models that arise from perturbation theory analyses. He showed that there exist smooth partial differential equations which stably perform universal computation by simulating arbitrary cellular automata. The asymptotic behavior of these PDEs is therefore logically undecidable. With John David Crawford he showed that the orbits of three-dimensional period doubling systems can form an infinite number of topologically distinct torus knots and described the structure of their stable and unstable manifolds. == Mathematica and Apple tablet contest == From 1986 to 1988, he was an Assistant Professor of Computer science at the University of Illinois at Urbana-Champaign and cofounded the Center for Complex Systems Research with Stephen Wolfram and Norman Packard. While at the University of Illinois, he worked with Stephen Wolfram and five others to create the symbolic mathematics program Mathematica. He and Wolfram led a team of students that won an Apple Computer contest to design "The Computer of the Year 2000." Their design entry "Tablet" was a touchscreen tablet with GPS and other features that finally appeared when the Apple iPad was introduced 22 years later. == Other contributions == Subutai Ahmad and Steve Omohundro developed biologically realistic neural models of selective attention. As a research scientist at the NEC Research Institute, Omohundro worked on machine learning and computer vision, and was a co-inventor of U.S. Patent 5,696,964, "Multimedia Database Retrieval System Which Maintains a Posterior Probability Distribution that Each Item in the Database is a Target of a Search." === Pirate puzzle === Omohundro developed an extension to the game theoretic pirate puzzle featured in Scientific American. == Outreach == Omohundro has sat on the Machine Intelligence Research Institute board of advisors. He has written extensively on artificial intelligence, and has warned that "an autonomous weapons arms race is already taking place" because "military and economic pressures are driving the rapid development of autonomous systems".