Publications

Abstract

In a recent series of publications (Traxler et al. J Mem Lang 39:558–592, 1998; Van Gompel et al. J Mem Lang 52:284–307, 2005; see also Van Gompel et al. (In: Kennedy, et al.(eds) Reading as a perceptual process, Oxford, Elsevier pp 621–648, 2000); Van Gompel et al. J Mem Lang 45:225–258, 2001) eye tracking data are reported showing that globally ambiguous (GA) sentences are read faster than locally ambiguous (LA) counterparts. They argue that these data rule out “constraint-based” models where syntactic and conceptual processors operate concurrently and syntactic ambiguity resolution is accomplished by competition. Such models predict the opposite pattern of reading times. However, this argument against competition is valid only in conjunction with two standard assumptions in current constraint-based models of sentence comprehension: (1) that syntactic competitions (e.g., Which is the best attachment site of the incoming constituent?) are pooled together with conceptual competitions (e.g., Which attachment site entails the most plausible meaning?), and (2) that the duration of a competition is a function of the overall (pooled) quality score obtained by each competitor. We argue that it is not necessary to abandon competition as a successful basis for explaining parsing phenomena and that the above-mentioned reading time data can be accounted for by a parallel-interactive model with conceptual and syntactic processors that do not pool their quality scores together. Within the individual linguistic modules, decision-making can very well be competition-based.

Abstract

We introduce a novel computer implementation of the Unification-Space parser (Vosse & Kempen 2000) in the form of a localist neural network whose dynamics is based on interactive activation and inhibition. The wiring of the network is determined by Performance Grammar (Kempen & Harbusch 2003), a lexicalist formalism with feature unification as binding operation. While the network is processing input word strings incrementally, the evolving shape of parse trees is represented in the form of changing patterns of activation in nodes that code for syntactic properties of words and phrases, and for the grammatical functions they fulfill. The system is capable, at least in a qualitative and rudimentary sense, of simulating several important dynamic aspects of human syntactic parsing, including garden-path phenomena and reanalysis, effects of complexity (various types of clause embeddings), fault-tolerance in case of unification failures and unknown words, and predictive parsing (expectation-based analysis, surprisal effects). English is the target language of the parser described.

Abstract

Next to propositional content, speakers distribute information in their utterances in such a way that listeners can make a distinction between new (focused) and given (non-focused) information. This is referred to as information structure. We measured event-related potentials (ERPs) to explore the role of information structure in semantic processing. Following different questions in wh-question-answer pairs (e.g. What kind of vegetable did Ming buy for cooking today? /Who bought the vegetables for cooking today?), the answer sentences (e.g., Ming bought eggplant/beef to cook today.) contained a critical word, which was either semantically appropriate (eggplant) or inappropriate (beef), and either focus or non-focus. The results showed a full N400 effect only when the critical words were in focus position. In non-focus position a strongly reduced N400 effect was observed, in line with the well-known semantic illusion effect. The results suggest that information structure facilitates semantic processing by devoting more resources to focused information.

Abstract

We report detailed analyses of a very large database on timing of speech perception collected by Smits et al. (Smits, R., Warner, N., McQueen, J.M., Cutler, A., 2003. Unfolding of phonetic information over time: A database of Dutch diphone perception. J. Acoust. Soc. Am. 113, 563–574). Eighteen listeners heard all possible diphones of Dutch, gated in portions of varying size and presented without background noise. The present report analyzes listeners’ responses across gates in terms of phonological features (voicing, place, and manner for consonants; height, backness, and length for vowels). The resulting patterns for feature perception differ from patterns reported when speech is presented in noise. The data are also analyzed for effects of stress and of phonological context (neighboring vowel vs. consonant); effects of these factors are observed to be surprisingly limited. Finally, statistical effects, such as overall phoneme frequency and transitional probabilities, along with response biases, are examined; these too exercise only limited effects on response patterns. The results suggest highly accurate speech perception on the basis of acoustic information alone.

Abstract

Korean has a very complex phonology, with many interacting alternations. In a coronal-/i/ sequence, depending on the type of phonological boundary present, alternations such as palatalization, nasal insertion, nasal assimilation, coda neutralization, and intervocalic voicing can apply. This paper investigates how the phonological patterns of Korean affect processing of morphemes and words. Past research on languages such as English, German, Dutch, and Finnish has shown that listeners exploit syllable structure constraints in processing speech and segmenting it into words. The current study shows that in parsing speech, listeners also use much more complex patterns that relate the surface phonological string to various boundaries.

Abstract

Natural, spontaneous speech (and even quite careful speech) often shows extreme reduction in many speech segments, even resulting in apparent deletion of consonants. Where the flap ([(sic)]) allophone of /t/ and /d/ is expected in American English, one frequently sees an approximant-like or even vocalic pattern, rather than a clear flap. Still, the /t/ or /d/ is usually perceived, suggesting the acoustic characteristics of a reduced flap are sufficient for perception of a consonant. This paper identifies several acoustic characteristics of reduced flaps based on previous acoustic research (size of intensity dip, consonant duration, and F4 valley) and presents phonetic identification data for continua that manipulate these acoustic characteristics of reduction. The results indicate that the most obvious types of acoustic variability seen in natural flaps do affect listeners' percept of a consonant, but not sufficiently to completely account for the percept. Listeners are affected by the acoustic characteristics of consonant reduction, but they are also very skilled at evaluating variability along the acoustic dimensions that realize reduction.

Abstract

This article addresses revitalization of a dormant language whose prospective speakers live in scattered geographical areas. In comparison to increasing the usage of an endangered language, revitalizing a dormant language (one with no living speakers) requires different methods to gain knowledge of the language. Language teaching for a dormant language with a scattered community presents different problems from other teaching situations. In this article, we discuss the types of tasks that must be accomplished for dormant-language revitalization, with particular focus on development of teaching materials. We also address the role of computer technologies, arguing that each use of technology should be evaluated for how effectively it increases fluency. We discuss methods for achieving semi-fluency for the first new speakers of a dormant language, and for spreading the language through the community.

Abstract

An event-related brain potential experiment was carried out to investigate on-line thematic role assignment during sentence–picture matching in patients with Broca's aphasia. Subjects were presented with a picture that was followed by an auditory sentence. The sentence either matched the picture or mismatched the visual information depicted. Sentences differed in complexity, and ranged from simple active semantically irreversible sentences to passive semantically reversible sentences. ERPs were recorded while subjects were engaged in sentence–picture matching. In addition, reaction time and accuracy were measured. Three groups of subjects were tested: Broca patients (N = 10), non-aphasic patients with a right hemisphere (RH) lesion (N = 8), and healthy aged-matched controls (N = 15). The results of this study showed that, in neurologically unimpaired individuals, thematic role assignment in the context of visual information was an immediate process. This in contrast to patients with Broca's aphasia who demonstrated no signs of on-line sensitivity to the picture–sentence mismatches. The syntactic contribution to the thematic role assignment process seemed to be diminished given the reduction and even absence of P600 effects. Nevertheless, Broca patients showed some off-line behavioral sensitivity to the sentence–picture mismatches. The long response latencies of Broca's aphasics make it likely that off-line response strategies were used.

Abstract

An event-related brain potential experiment was carried out to investigate on-line syntactic processing in patients with Broca’s aphasia. Subjects were visually presented with sentences that were either syntactically correct or contained violations of word-category. Three groups of subjects were tested: Broca patients (N=11), non-aphasic patients with a right hemisphere (RH) lesion (N=9), and healthy aged-matched controls (N=15). Both control groups appeared sensitive to the violations of word-category as shown by clear P600/SPS effects. The Broca patients displayed only a very reduced and delayed P600/SPS effect. The results are discussed in the context of a lexicalist parsing model. It is concluded that Broca patients are hindered to detect on-line violations of word-category, if word class information is incomplete or delayed available.

Abstract

This dissertation focuses on syntactic comprehension problems in patients with Broca's aphasia from an electrophysiological perspective. The central objective of this dissertation was to further explore what syntax-related event-related brain potential (ERP) effects can reveal about the nature of the deficit that underlies syntactic comprehension problems in patients with Broca's aphasia. Chapter two to four describe experiments in which event-related brain potentials were recorded while subjects (Broca patients, non-aphasic patients with a right-hemisphere lesion, and healthy elderly controls) were presented with sentences that contained either violations of syntactic constraints or were syntactically correct. Chapter two investigates ERP effects of subject-verb agreement violations in the different subject groups, and seeks to answer the following questions: Do agrammatic comprehenders show sensitivity to subject-verb agreement violations as indicated by a syntax-related ERP effect? In addition, does the severity of the syntactic comprehension impairment in the Broca patients affect the ERP responses? Chapter three describes an investigation of whether Broca patients show sensitivity to violations of word order as indicated by a syntax-related ERP effect, and whether the ERP responses in the Broca patients are affected by the severity of their syntactic comprehension impairment. Chapter four reports on ERP effects of violations of word-category. In addition, also a semantic violation condition was added to track possible dissociations in the sensitivity to semantic and syntactic information in the Broca patients. Chapter five describes the development of a paradigm in which the electrophysiological approach and the classical sentence-picture matching approach are combined. In this chapter, the ERP method is applied to study on-line thematic role assignment in Broca patients during sentence-picture matching. Also the relation between ERP effects and behavioral responses is pursued. Finally, Chapter 6 provides a summary of the main findings of the experiments and a general discussion.

Abstract

Recent studies using phoneme detection tasks have shown that spoken-language processing is neither facilitated nor interfered with by optional assimilation, but is inhibited by violation of obligatory assimilation. Interpretation of these results depends on an assessment of their generality, specifically, whether they also obtain when listeners are processing nonnative language. Two separate experiments are presented in which native listeners of German and native listeners of Dutch had to detect a target fricative in legal monosyllabic Dutch nonwords. All of the nonwords were correct realisations in standard Dutch. For German listeners, however, half of the nonwords contained phoneme strings which violate the German fricative assimilation rule. Whereas the Dutch listeners showed no significant effects, German listeners detected the target fricative faster when the German fricative assimilation was violated than when no violation occurred. The results might suggest that violation of assimilation rules does not have to make processing more difficult per se.

Abstract

A longstanding question in bilingualism is whether syntactic information is shared between the two language processing systems. We used an fMRI repetition suppression paradigm to investigate syntactic priming in reading comprehension in German–English late-acquisition bilinguals. In comparison to conventional subtraction analyses in bilingual experiments, repetition suppression has the advantage of being able to detect neuronal populations that are sensitive to properties that are shared by consecutive stimuli. In this study, we manipulated the syntactic structure between prime and target sentences. A sentence with a passive sentence structure in English was preceded either by a passive or by an active sentence in English or German. We looked for repetition suppression effects in left inferior frontal, left precentral and left middle temporal regions of interest. These regions were defined by a contrast of all non-target sentences in German and English versus the baseline of sentence-format consonant strings. We found decreases in activity (repetition suppression effects) in these regions of interest following the repetition of syntactic structure from the first to the second language and within the second language.
Moreover, a separate behavioural experiment using a word-by-word reading paradigm similar to the fMRI experiment showed faster reading times for primed compared to unprimed English target sentences regardless of whether they were preceded by an English or a German sentence of the same structure.
We conclude that there is interaction between the language processing systems and that at least some syntactic information is shared between a bilingual's languages with similar syntactic structures.

Abstract

Lexical recognition is typically slower in L2 than in L1. Part of the difficulty comes from a not precise enough processing of L2 phonemes. Consequently, L2 listeners fail to eliminate candidate words that L1 listeners can exclude from competing for recognition. For instance, the inability to distinguish /r/ from /l/ in rocket and locker makes for Japanese listeners both words possible candidates when hearing their onset (e.g., Cutler, Weber, and Otake, 2006). The L2 disadvantage can, however, be dispelled: For L2 listeners, but not L1 listeners, L2 speech from a non-native talker with the same language background is known to be as intelligible as L2 speech from a native talker (e.g., Bent and Bradlow, 2003). A reason for this may be that L2 listeners have ample experience with segmental deviations that are characteristic for their own accent. On this account, only phonemic deviations that are typical for the listeners’ own accent will cause spurious lexical activation in L2 listening (e.g., English magic pronounced as megic for Dutch listeners). In this talk, I will present evidence from cross-modal priming studies with a variety of L2 listener groups, showing how the processing of phonemic deviations is accent-specific but withstands fine phonetic differences.

Abstract

In a visual-world study, we examined spoken-wordrecognition in Spanish. Spanish listeners followed spoken instructions to click on pictures while their eye movements were monitored. When instructed to click on the picture of a door (puerta), they experienced interference from the picture of a pig (p u e r c o ). The same interference from phonologically related items was observed when the displays contained printed names or a combination of pictures with their names printed underneath, although the effect was strongest for displays with printed names. Implications of the finding that the interference effect can be induced with standard pictorial displays as well as with orthographic displays are discussed.

Abstract

Many explanations of the difficulties associated with interpreting object relative clauses appeal to the demands that object relatives make on working memory. MacDonald and Christiansen [MacDonald, M. C., & Christiansen, M. H. (2002). Reassessing working memory: Comment on Just and Carpenter (1992) and Waters and Caplan (1996). Psychological Review, 109, 35-54] pointed to variations in reading experience as a source of differences, arguing that the unique word order of object relatives makes their processing more difficult and more sensitive to the effects of previous experience than the processing of subject relatives. This hypothesis was tested in a large-scale study manipulating reading experiences of adults over several weeks. The group receiving relative clause experience increased reading speeds for object relatives more than for subject relatives, whereas a control experience group did not. The reading time data were compared to performance of a computational model given different amounts of experience. The results support claims for experience-based individual differences and an important role for statistical learning in sentence comprehension processes.

Abstract

Three experiments examined the time course of phonological encoding in speech production. A new methodology is introduced in which subjects are required to monitor their internal speech production for prespecified target segments and syllables. Experiment 1 demonstrated that word initial target segments are monitored significantly faster than second syllable initial target segments. The addition of a concurrent articulation task (Experiment 1b) had a limited effect on performance, excluding the possibility that subjects are monitoring a subvocal articulation of the carrier word. Moreover, no relationship was observed between the pattern of monitoring latencies and the timing of the targets in subjects′ overt speech. Subjects are not, therefore, monitoring an internal phonetic representation of the carrier word. Experiment 2 used the production monitoring task to replicate the syllable monitoring effect observed in speech perception experiments: responses to targets were faster when they corresponded to the initial syllable of the carrier word than when they did not. We conclude that subjects are monitoring their internal generation of a syllabified phonological representation. Experiment 3 provides more detailed evidence concerning the time course of the generation of this representation by comparing monitoring latencies to targets within, as well as between, syllables. Some amendments to current models of phonological encoding are suggested in light of these results.

Abstract

Field data are drawn from a particular speech community at a certain place and time. The intent of this survey is to enrich understanding of the various socio-cultural contexts in which linguistic and “cognitive” data may have been collected, so that we can explore the role which societal, cultural and contextual factors may play in this material. The questionnaire gives guidelines concerning types of ethnographic information that are important to cross-cultural and cross-linguistic enquiry, and will be especially useful to researchers who do not have specialised training in anthropology.

Abstract

How do languages encode different kinds of movement, and what features do people pay attention to when describing motion events? This document outlines topics concerning the investigation of “enter” and “exit” events. It helps contextualise research tasks that examine this domain (see 'Motion Elicitation' and 'Enter/Exit animation') and gives some pointers about what other questions can be explored.

Abstract

Pointing gestures are recognised to be a primary manifestation of human social cognition and communicative capacity. The goal of this task is to collect empirical descriptions of pointing practices in different cultural settings.

Abstract

How do languages encode different kinds of movement, and what features do people pay attention to when describing motion events? This task investigates the expression of “enter” and “exit” activities, that is, events involving motion in(to) and motion out (of) container-like items. The researcher first uses particular stimuli (a ball, a cup, rice, etc.) to elicit descriptions of enter/exit events from one consultant, and then asks another consultant to demonstrate the event based on these descriptions. See also the related entries Enter/Exit Animation and Background Questions for Enter/Exit Research.

Abstract

The purpose of this paper is to question some of the basic assumpiions concerning motion verbs. In particular, it examines the assumption that "come" and "go" are lexical universals which manifest a universal deictic Opposition. Against the background offive working hypotheses about the nature of'come" and ''go", this study presents a comparative investigation of t wo unrelated languages—Mparntwe Arrernte (Pama-Nyungan, Australian) and Longgu (Oceanic, Austronesian). Although the pragmatic and deictic "suppositional" complexity of"come" and "go" expressions has long been recognized, we argue that in any given language the analysis of these expressions is much more semantically and systemically complex than has been assumed in the literature. Languages vary at the lexical semantic level äs t o what is entailed by these expressions, äs well äs differing äs t o what constitutes the prototype and categorial structure for such expressions. The data also strongly suggest that, ifthere is a lexical universal "go", then this cannof be an inherently deictic expression. However, due to systemic Opposition with "come", non-deictic "go" expressions often take on a deictic Interpretation through pragmatic attribution. Thus, this crosslinguistic investigation of "come" and "go" highlights the need to consider semantics and pragmatics äs modularly separate.

Abstract

Although generally studied in isolation, language and action often co-occur in everyday life. Here we investigated one particular form of simultaneous language and action, namely speech and gestures that speakers use in everyday communication. In a functional magnetic resonance imaging study, we identified the neural networks involved in the integration of semantic information from speech and gestures. Verbal and/or gestural content could be integrated easily or less easily with the content of the preceding part of speech. Premotor areas involved in action observation (Brodmann area [BA] 6) were found to be specifically modulated by action information "mismatching" to a language context. Importantly, an increase in integration load of both verbal and gestural information into prior speech context activated Broca's area and adjacent cortex (BA 45/47). A classical language area, Broca's area, is not only recruited for language-internal processing but also when action observation is integrated with speech. These findings provide direct evidence that action and language processing share a high-level neural integration system.

Abstract

If motor imagery uses neural structures involved in action execution, then the neural correlates of imagining an action should differ between individuals who tend to execute the action differently. Here we report fMRI data showing that motor imagery is influenced by the way people habitually perform motor actions with their particular bodies; that is, motor imagery is ‘body-specific’ (Casasanto, 2009). During mental imagery for complex hand actions, activation of cortical areas involved in motor planning and execution was left-lateralized in right-handers but right-lateralized in left-handers. We conclude that motor imagery involves the generation of an action plan that is grounded in the participant’s motor habits, not just an abstract representation at the level of the action’s goal. People with different patterns of motor experience form correspondingly different neurocognitive representations of imagined actions.

Abstract

Several studies indicate that both posterior superior temporal sulcus/middle temporal gyrus (pSTS/MTG) and left inferior frontal gyrus (LIFG) are involved in integrating information from different modalities. Here we investigated the respective roles of these two areas in integration of action and language information. We exploited the fact that the semantic relationship between language and different forms of action (i.e. co-speech gestures and pantomimes) is radically different. Speech and co-speech gestures are always produced together, and gestures are not unambiguously understood without speech. On the contrary, pantomimes are not necessarily produced together with speech and can be easily understood without speech. We presented speech together with these two types of communicative hand actions in matching or mismatching combinations to manipulate semantic integration load. Left and right pSTS/MTG were only involved in semantic integration of speech and pantomimes. Left IFG on the other hand was involved in integration of speech and co-speech gestures as well as of speech and pantomimes. Effective connectivity analyses showed that depending upon the semantic relationship between language and action, LIFG modulates activation levels in left pSTS.

This suggests that integration in pSTS/MTG involves the matching of two input streams for which there is a relatively stable common object representation, whereas integration in LIFG is better characterized as the on-line construction of a new and unified representation of the input streams. In conclusion, pSTS/MTG and LIFG are differentially involved in multimodal integration, crucially depending upon the semantic relationship between the input streams.

Abstract

Co-speech gestures embody a form of manual action that is tightly coupled to the language system. As such, the co-occurrence of speech and co-speech gestures is an excellent example of the interplay between language and action. There are, however, other ways in which language and action can be thought of as closely related. In this paper we will give an overview of studies in cognitive neuroscience that examine the neural underpinnings of links between language and action. Topics include neurocognitive studies of motor representations of speech sounds, action-related language, sign language and co-speech gestures. It will be concluded that there is strong evidence on the interaction between speech and gestures in the brain. This interaction however shares general properties with other domains in which there is interplay between language and action.

Abstract

It has been argued that we map observed actions onto our own motor system. Here we added to this issue by investigating whether hand preference influences the neural correlates of action observation of simple, essentially meaningless hand actions. Such an influence would argue for an intricate neural coupling between action production and action observation, which goes beyond effects of motor repertoire or explicit motor training, as has been suggested before. Indeed, parts of the human motor system exhibited a close coupling between action production and action observation. Ventral premotor and inferior and superior parietal cortices showed differential activation for left- and right-handers that was similar during action production as well as during action observation. This suggests that mapping observed actions onto the observer's own motor system is a core feature of action observation - at least for actions that do not have a clear goal or meaning. Basic differences in the way we act upon the world are not only reflected in neural correlates of action production, but can also influence the brain basis of action observation.

Abstract

About 5,000 languages are spoken in the world today. More than half of them have less than 10,000 speakers, a quarter of them even fewer than 1,000. The majority of these “small” languages will not live to see the end of this century; some estimates predict that no more than a dozen languages will still be spoken by the turn of the next millennium. This collection of papers approaches the subject of language extinction through five major topics: general aspects of language death, case studies, endangered subsystems, language protection and revitalization, language ecology. In 24 articles, the authors address the causes, manifestations, and consequences of language endangerment and extinction as well as the linguistic and social changes associated with it, drawing examples from a large number of languages.

Abstract

Brain processing depends on the interactions between neuronal groups. Those interactions are governed by the pattern of anatomical connections and by yet unknown mechanisms that modulate the effective strength of a given connection. We found that the mutual influence among neuronal groups depends on the phase relation between rhythmic activities within the groups. Phase relations supporting interactions between the groups preceded those interactions by a few milliseconds, consistent with a mechanistic role. These effects were specific in time, frequency, and space, and we therefore propose that the pattern of synchronization flexibly determines the pattern of neuronal interactions.

Abstract

Set is widely used as a kind of basic data structure. However, when it is used for large scale data set the cost of storage, search and transport is overhead. The bloom filter uses a fixed size bit string to represent elements in a static set, which can reduce storage space and search cost that is a fixed constant. The time-space efficiency is achieved at the cost of a small probability of false positive in membership query. However, for many applications the space savings and locating time constantly outweigh this drawback. Dynamic bloom filter (DBF) can support concisely representation and approximate membership queries of dynamic set instead of static set. It has been proved that DBF not only possess the advantage of standard bloom filter, but also has better features when dealing with dynamic set. This paper proposes a time-dependent multiple bit-strings bloom filter (TMBF) which roots in the DBF and targets on dynamic incremental set. TMBF uses multiple bit-strings in time order to present a dynamic increasing set and uses backward searching to test whether an element is in a set. Based on the system logs from a real P2P file sharing system, the evaluation shows a 20% reduction in searching cost compared to DBF.

Abstract

This article reports on several sub-projects of research and development related to the use of Indian Sign Language in educational settings. In many countries around the world, sign languages are now recognised as the legitimate, full-fledged languages of the deaf communities that use them. In India, the development of sign language resources and their application in educational contexts, is still in its initial stages. The work reported on here, is the first principled and comprehensive effort of establishing educational programmes in Indian Sign Language at a national level. Programmes are of several types: a) Indian Sign Language instruction for hearing people; b) sign language teacher training programmes for deaf people; and c) educational materials for use in schools for the Deaf. The conceptual approach used in the programmes for deaf students is known as bilingual education, which emphasises the acquisition of a first language, Indian Sign Language, alongside the acquisition of spoken languages, primarily in their written form.

Abstract

In response to DNA damage or replication stress, the protein kinase ATR is activated and subsequently transduces genotoxic signals to cell cycle control and DNA repair machinery through phosphorylation of a number of downstream substrates. Very little is known about the molecular mechanism by which ATR is activated in response to genotoxic insults. In this report, we demonstrate that protein phosphatase 5 (PP5) is required for the ATR-mediated checkpoint activation. PP5 forms a complex with ATR in a genotoxic stress-inducible manner. Interference with the expression or the activity of PP5 leads to impairment of the ATR-mediated phosphorylation of hRad17 and Chk1 after UV or hydroxyurea treatment. Similar results are obtained in ATM-deficient cells, suggesting that the observed defect in checkpoint signaling is the consequence of impaired functional interaction between ATR and PP5. In cells exposed to UV irradiation, PP5 is required to elicit an appropriate S-phase checkpoint response. In addition, loss of PP5 leads to premature mitosis after hydroxyurea treatment. Interestingly, reduced PP5 activity exerts differential effects on the formation of intranuclear foci by ATR and replication protein A, implicating a functional role for PP5 in a specific stage of the checkpoint signaling pathway. Taken together, our results suggest that PP5 plays a critical role in the ATR-mediated checkpoint activation.

Abstract

Genome-wide association studies using thousands to hundreds of thousands of single nucleotide polymorphism (SNP) markers and region-wide association studies using a dense panel of SNPs are already in use to identify disease susceptibility genes and to predict disease risk in individuals. Because these tasks become increasingly important, three different data sets were provided for the Genetic Analysis Workshop 15, thus allowing examination of various novel and existing data mining methods for both classification and identification of disease susceptibility genes, gene by gene or gene by environment interaction. The approach most often applied in this presentation group was random forests because of its simplicity, elegance, and robustness. It was used for prediction and for screening for interesting SNPs in a first step. The logistic tree with unbiased selection approach appeared to be an interesting alternative to efficiently select interesting SNPs. Machine learning, specifically ensemble methods, might be useful as pre-screening tools for large-scale association studies because they can be less prone to overfitting, can be less computer processor time intensive, can easily include pair-wise and higher-order interactions compared with standard statistical approaches and can also have a high capability for classification. However, improved implementations that are able to deal with hundreds of thousands of SNPs at a time are required.

Abstract

The Corpus NGT