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Organization of the state space of a simple recurrent network before and after training on recursive linguistic structures.

Recurrent neural networks are often employed in the cognitive science community to process symbol sequences that represent various natural language structures. The aim is to study possible neural mechanisms of language processing and aid in development of artificial language processing systems. We used data sets containing recursive linguistic structures and trained the Elman simple recurrent network (SRN) for the next-symbol prediction task. Concentrating on neuron activation clusters in the recurrent layer of SRN we investigate the network state space organization before and after training. Given a SRN and a training stream, we construct predictive models, called neural prediction machines, that directly employ the state space dynamics of the network. We demonstrate two important properties of representations of recursive symbol series in the SRN. First, the clusters of recurrent activations emerging before training are meaningful and correspond to Markov prediction contexts. We show that prediction states that naturally arise in the SRN initialized with small random weights approximately correspond to states of Variable Memory Length Markov Models (VLMM) based on individual symbols (i.e. words). Second, we demonstrate that during training, the SRN reorganizes its state space according to word categories and their grammatical subcategories, and the next-symbol prediction is again based on the VLMM strategy. However, after training, the prediction is based on word categories and their grammatical subcategories rather than individual words. Our conclusion holds for small depths of recursions that are comparable to human performances. The methods of SRN training and analysis of its state space introduced in this paper are of a general nature and can be used for investigation of processing of any other symbol time series by means of SRN.

Artificial Intelligence↗

A natural language based search engine for ICD10 diagnosis encoding.

We have developed a multiple step process for implementing an ICD10 search engine. The complexity of the task has been shown and we recommend collecting adequate expertise before starting any implementation. Underestimation of the expert time and inadequate data resources are probable reasons for failure. We also claim that when all conditions are met in term of resource and availability of the expertise, the benefits of a responsive ICD10 search engine will be present and the investment will be successful.

Databases as Topic↗

Perspective in statements of quantity, with implications for consumer psychology.

We demonstrate that presentation of information about quantities, whether expressed in natural language or by using numbers, induces a perspective that influences subsequent processing. Experiment 1 shows this to be true for natural language quantifiers, with negative and positive expressions inducing different perspectives. In Experiment 2, we examined the application of this idea to the specific case of perspectives induced by describing products as containing x% fat or as being x% fat free. We found that the percentage-fat description appears to induce a perspective that is sensitive to the level offat being depicted, with products being judged as less healthy at higher amounts of fat. However, this effect was lessened (Experiment 2) or eliminated (Experiment 3) with the percentage-fat-free description. The experiments suggest the fat-free perspective blocks access to assumptions about healthy fat levels.

Adult↗

How native-like is non-native language processing?

Following several decades of research on native language (L1) processing, psycholinguists have more recently begun to investigate how non-native language (L2) speakers comprehend and process language in real time. Regarding the traditional assumption that L2 learners have 'difficulty with grammar', this new research has revealed some unexpected similarities and differences between L1 and L2 processing. Specifically, it appears that L2 processing can become native-like in some linguistic subdomains (including certain aspects of grammar) but that L1 and L2 processing differences persist in the domain of complex syntax, even in highly proficient L2 speakers. Thus, more subtle linguistic distinctions seem to be required to understand the nature of non-native language processing.

Brain Mapping↗

Combining decision support methodologies to diagnose pneumonia.

OBJECTIVE: To evaluate the performance of a computerized decision support system that combines two different decision support methodologies (a Bayesian network and a natural language understanding system) for the diagnosis of patients with pneumonia. DESIGN: Evaluation study using data from a prospective, clinical study. PATIENTS: All patients 18 years and older who presented to the emergency department of a tertiary care setting and whose chest x-ray report was available during the encounter. METHODS: The computerized decision support system calculated a probability of pneumonia using information provided by the two systems. Outcome measures were the area under the receiver operating characteristic curve, sensitivity, specificity, predictive values, likelihood ratios, and test effectiveness. RESULTS: During the 3-month study period there were 742 patients (45 with pneumonia). The area under the receiver operating characteristic curve was 0.881 (95% CI: 0.822, 0.925) for the Bayesian network alone and 0.916 (95% CI: 0.869, 0.949) for the Bayesian network combined with the natural language understanding system (p=0.01). CONCLUSION: Combining decision support methodologies that process information stored in different data formats can increase the performance of a computerized decision support system.

Adult↗

A natural language parsing system for encoding admitting diagnoses.

Free-text or natural language documents make up an increasing part of the computerized medical record. While they do provide accessible clinical information to health care personnel, they fail to support processes that require clinical data coded according to a shared lexicon and data structure. We have developed a natural language parser that converts free-text admitting diagnoses into a coded form. This application has proven acceptably accurate in the experimental laboratory to warrant a test in the target clinical environment. Here we describe an approach to moving this research application into a production environment where it can contribute to the efforts of the Health Information Services Department. This transition is essential if the products of natural language understanding research are to contribute to patient care in a routine and sustainable way.

Diagnosis-Related Groups↗

[A data processing system for bacteriological and chemical water analysis].

Using the "Natural" computer language a menu-guided system for cataloguing, processing and evaluating bacteriological and chemical water analyses was designed. The program can be employed to different blocs of analyses, e.g. "TrinkwV"-analyses, standard-analyses, those on volatile chlorinated hydrocarbons and bacteriological water analyses as well. For each water sample the actual, the last and the next to the last value, also arithmetical means, minimal and maximal are stored and can be retrieved. The evaluation of the bacteriological analyses and those of the volatile chlorinated hydrocarbons is carried out by a choice of text variants, whereas the TVO- and standard-analyses are interpreted automatically. Managing laboratory data has become much easier during our three years experience using this system for information storage, search and retrieval in water research and routine; even untrained users are able to handle it after a short period of tuition.

Bacteria↗

Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation.

MOTIVATION: Many bioinformatics data resources not only hold data in the form of sequences, but also as annotation. In the majority of cases, annotation is written as scientific natural language: this is suitable for humans, but not particularly useful for machine processing. Ontologies offer a mechanism by which knowledge can be represented in a form capable of such processing. In this paper we investigate the use of ontological annotation to measure the similarities in knowledge content or 'semantic similarity' between entries in a data resource. These allow a bioinformatician to perform a similarity measure over annotation in an analogous manner to those performed over sequences. A measure of semantic similarity for the knowledge component of bioinformatics resources should afford a biologist a new tool in their repertoire of analyses. RESULTS: We present the results from experiments that investigate the validity of using semantic similarity by comparison with sequence similarity. We show a simple extension that enables a semantic search of the knowledge held within sequence databases. AVAILABILITY: Software available from http://www.russet.org.uk.

Artificial Intelligence↗

A personal case history of transient anomia.

The article presents a first-person account of a transient anomia or word-finding deficit; the assumption is that such an account, reported by someone with a professional background in memory, cognition, and language processes, may shed additional light on the nature of an anomic episode and on the subjective experience of memory and language disruption due to brain-related abnormalities. During the 45-min episode, I was unable to retrieve and use specific content words and terms ("data," "experiment," "printout") in overt speech. I was completely conscious of these target concepts, although not of their names, and was aware of my inability to find the words. Neither word finding for "everyday" words nor ongoing thought processes were particularly disrupted. The nature and quality of my thoughts during the episode indicate no loss of awareness of circumstances or "presence of mind," but no genuine awareness of the seriousness of the episode. I briefly consider the implications of my experience and the similarities to another published case history.

Adult↗

NLP techniques associated with the OpenGALEN ontology for semi-automatic textual extraction of medical knowledge: abstracting and mapping equivalent linguistic and logical constructs.

This research project presents methodological and theoretical issues related to the inter-relationship between linguistic and conceptual semantics, analysing the results obtained by the application of a NLP parser to a set of radiology reports. Our objective is to define a technique for associating linguistic methods with domain specific ontologies for semi-automatic extraction of intermediate representation (IR) information formats and medical ontological knowledge from clinical texts. We have applied the Edinburgh LTG natural language parser to 2810 clinical narratives describing radiology procedures. In a second step, we have used medical expertise and ontology formalism for identification of semantic structures and abstraction of IR schemas related to the processed texts. These IR schemas are an association of linguistic and conceptual knowledge, based on their semantic contents. This methodology aims to contribute to the elaboration of models relating linguistic and logical constructs based on empirical data analysis. Advance in this field might lead to the development of computational techniques for automatic enrichment of medical ontologies from real clinical environments, using descriptive knowledge implicit in large text corpora sources.

Electronic Data Processing↗

How to build a baby: II. Conceptual primitives.

A mechanism of perceptual analysis by which infants derive meaning from perceptual activity is described. Infants use this mechanism to redescribe perceptual information into image-schematic format. Image-schemas create conceptual structure from the spatial structure of objects and their movements, resulting in notions such as animacy, inanimacy, agency, and containment. These earliest meanings are nonpropositional, analogical representations grounded in the perceptual world of the infant. In contrast with most perceptual processing, which is not analyzed in this fashion, redescription into image-schematic format simplifies perceptual information and makes it potentially accessible for purposes of concept formation and thought. In addition to enabling preverbal thought, image-schemas provide a foundation for language acquisition by creating an interface between the continuous processes of perception and the discrete nature of language.

Child↗

In search of the elusive nature of clinical psychoanalytic theory.

Two case vignettes illustrating different ways of listening to clinical material are presented. The author discusses some limitations of clinical psychoanalytic theory that stem from the fact that primary unconscious processes are, by their very nature, impossible to describe in a language regulated by secondary processes. Hegelian dialectics, first addressed in psychoanalysis by Lacan and later elaborated in the work of Green, as well as the use of paradox by Winnicott and the formalistic approaches of Matte Blanco and Bion, are briefly reviewed as alternative formulas. As psychoanalysts, we are condemned to live with doubt, and neither clinical theories nor metapsychology offer escape from this reality.

Adult↗

Broken agreement.

The subjects and verbs of English sentences agree in number. This superficially simple syntactic operation is regularly implemented by speakers, but occasionally derails in sentences such as The cost of the improvements have not yet been estimated. We examined whether the incidence of such errors was related to the presence of subject-like semantic features in the immediate preverbal nouns, in light of current questions about the semantic versus syntactic nature of sentence subjects and the interactivity of language processing. In three experiments, speakers completed sentence fragments designed to elicit erroneous agreement. We varied the number and animacy of the head noun and the immediate preverbal (local) noun, as well as the amount of material separating the head noun from the verb. The plurality of the local noun phrase had a large and reliable effect on the incidence of agreement errors, but neither its animacy nor its length affected their occurrence. The latter findings suggest, respectively, that the semantic features of sentence subjects are of minimal relevance to the syntactic and morphological processes that implement agreement, and that agreement features are specified at a point in processing where the eventual length of sentential constituents has little effect on syntactic planning. Both results follow naturally from explanations of language production that emphasize the segregation of sentence formulation processes into relatively autonomous components.

Adult↗

Speech motor development: Integrating muscles, movements, and linguistic units.

UNLABELLED: A fundamental problem for those interested in human communication is to determine how ideas and the various units of language structure are communicated through speaking. The physiological concepts involved in the control of muscle contraction and movement are theoretically distant from the processing levels and units postulated to exist in language production models. A review of the literature on adult speakers suggests that they engage complex, parallel processes involving many units, including sentence, phrase, syllable, and phoneme levels. Infants must develop multilayered interactions among language and motor systems. This discussion describes recent studies of speech motor performance relative to varying linguistic goals during the childhood, teenage, and young adult years. Studies of the developing interactions between speech motor and language systems reveal both qualitative and quantitative differences between the developing and the mature systems. These studies provide an experimental basis for a more comprehensive theoretical account of how mappings between units of language and units of action are formed and how they function. LEARNING OUTCOMES: Readers will be able to: (1) understand the theoretical differences between models of speech motor control and models of language processing, as well as the nature of the concepts used in the two different kinds of models, (2) explain the concept of coarticulation and state why this phenomenon has confounded attempts to determine the role of linguistic units, such as syllables and phonemes, in speech production, (3) describe the development of speech motor performance skills and specify quantitative and qualitative differences between speech motor performance in children and adults, and (4) describe experimental methods that allow scientists to study speech and limb motor control, as well as compare units of action used to study non-speech and speech movements.

Adolescent↗

The role of meaning in inflection: why the past tense does not require a rule.

How do we produce the past tenses of verbs? For the last 20 years this question has been the focal domain for conflicting theories of language, knowledge representation, and cognitive processing. On one side of the debate have been similarity-based or single-route approaches that propose that all past tenses are formed simply through phonological analogies to existing past tenses stored in memory. On the other side of the debate are rule-based or dual-route approaches which agree that phonological analogy is important for producing irregular past tenses (e.g., think-->thought), but argue that regular past tenses (e.g., walk-->walked) are generated via a +ed rule and that a principled account of regular inflection can only be given by recourse to explicit rules. This debate has become a crucial battleground for arguments concerning the necessity and importance of abstract mental rules, embracing not only language processing, but also the of nature cognition itself. However, in centering on the roles of phonological similarity and rules, the past tense debate has largely ignored the possible role of semantics in determining inflection. This paper presents five studies that demonstrate a striking and decisive role of semantic similarity in inflection. In fact, semantic factors appear to be more important in inflection than the grammatical considerations put forward by the dual-route account. Further, these new findings provide a new way of discriminating between the claims of single-route (similarity-based) and dual-route (rule-based) approaches. It appears that inflection is carried out through analogical reminding based on semantic and phonological similarity and that a rule-based route is not necessary to account for past tense inflection.

Humans↗

[Value of automated medical indexing of an image database and a digital radiological library].

We indexed the contents of a radiology server on the web to facilitate access to research documents and to link reference texts to images contained in radiology databases. Indexation also allows case reports to be transformed with no supplementary work into formats compatible with computer-assisted training. Indexation was performed automatically by ADM-Index, the aim being to identify the medical concepts expressed within each medical text. Two types of texts were indexed: medical imaging reference books (Edicerf) and case reports with illustrations and captions (Iconocerf). These documents are now available on a web server with HTML format for Edicerf and on an Oracle database for Iconocerf. When the user consults a chapter of a book or a case report, the indexed terms are displayed in the heading; all reference texts and case reports containing the indexed terms can then be called up instantaneously. The user can express his search in natural language. Indexation follows the same process allowing instantaneous recall of all reference texts and case reports where the same concept appears in the diagnosis or clinical context. By using the context of the case reports as the search index, all case reports involving a common medical concept can be found. The context is interpreted as a question. When the user responds to this question, ADM-Index compares this response with the answer furnished by the reference texts and case reports. Correct or erroneous responses can thus be identified, converting the system into a computer-assisted training tool.

Abstracting and Indexing↗

Generation of a large gene/protein lexicon by morphological pattern analysis.

The identification of gene/protein names in natural language text is an important problem in named entity recognition. In previous work we have processed MEDLINE documents to obtain a collection of over two million names of which we estimate that perhaps two thirds are valid gene/protein names. Our problem has been how to purify this set to obtain a high quality subset of gene/protein names. Here we describe an approach which is based on the generation of certain classes of names that are characterized by common morphological features. Within each class inductive logic programming (ILP) is applied to learn the characteristics of those names that are gene/protein names. The criteria learned in this manner are then applied to our large set of names. We generated 193 classes of names and ILP led to criteria defining a select subset of 1,240,462 names. A simple false positive filter was applied to remove 8% of this set leaving 1,145,913 names. Examination of a random sample from this gene/protein name lexicon suggests it is composed of 82% (+/-3%) complete and accurate gene/protein names, 12% names related to genes/proteins (too generic, a valid name plus additional text, part of a valid name, etc.), and 6% names unrelated to genes/proteins. The lexicon is freely available at ftp.ncbi.nlm.nih.gov/pub/tanabe/Gene.Lexicon.

Algorithms↗

Toward a mechanistic psychology of dialogue.

Traditional mechanistic accounts of language processing derive almost entirely from the study of monologue. Yet, the most natural and basic form of language use is dialogue. As a result, these accounts may only offer limited theories of the mechanisms that underlie language processing in general. We propose a mechanistic account of dialogue, the interactive alignment account, and use it to derive a number of predictions about basic language processes. The account assumes that, in dialogue, the linguistic representations employed by the interlocutors become aligned at many levels, as a result of a largely automatic process. This process greatly simplifies production and comprehension in dialogue. After considering the evidence for the interactive alignment model, we concentrate on three aspects of processing that follow from it. It makes use of a simple interactive inference mechanism, enables the development of local dialogue routines that greatly simplify language processing, and explains the origins of self-monitoring in production. We consider the need for a grammatical framework that is designed to deal with language in dialogue rather than monologue, and discuss a range of implications of the account.

Humans↗