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Selectional constraints: an information-theoretic model and its computational realization.

A new, information-theoretic model of selectional constraints is proposed. The strategy adopted here is a minimalist one: how far can one get making as few assumptions as possible? In keeping with that strategy, the proposed model consists of only two components: first, a fairly generic taxonomic representation of concepts, and, second, a probabilistic formalization of selectional constraints defined in terms of that taxonomy, computed on the basis of simple, observable frequencies of co-occurrence between predicates and their arguments. Unlike traditional selection restrictions, the information-theoretic approach avoids empirical problems associated with definitional theories of word meaning, accommodates the observation that semantic anomaly often appears to be a matter of degree, and provides an account of how selectional constraints can be learned. A computational implementation of the model "learns" selectional constraints from collections of naturally occurring text; the predictions of the implemented model are evaluated against judgments elicited from adult subjects, and used to explore the way that arguments are syntactically realized for a class of English verbs. The paper concludes with a discussion of the role of selectional constraints in the acquisition of verb meaning.

Adult↗

Multicue HMM-UKF for real-time contour tracking.

We propose an HMM model for contour detection based on multiple visual cues in spatial domain and improve it by joint probabilistic matching to reduce background clutter. It is further integrated with unscented Kalman filter to exploit object dynamics in nonlinear systems for robust contour tracking.

Algorithms↗

The role of "evidence" in recovery from mental illness.

Evidence-based practice (EBP), a derivative of evidence-based medicine (EBM), is ascendant in the United States' mental health system; the findings of randomized controlled trials and other experimental research are widely considered authoritative in mental health practice and policy. The concept of recovery from mental illness is similarly pervasive in mental health programming and advocacy, and it emphasizes consumer expertise and self-determination. What is the relationship between these two powerful and potentially incompatible forces for mental health reform? This paper identifies four attempts, in the mental health literature, to delineate the role of "evidence" in recovery. One is the strong version of evidence-based practice-an applied science model-and three others address weaknesses in the first by limiting the authority of probabilistic findings. The paper also offers a fifth version, based on the concept of communicative accountability, which is derived from Habermas' work on communicative action. The fifth version responds to the other four and emphasizes learning, disclosure and respect in clinical and other helping relationships.

Evidence-Based Medicine↗

Sensorless freehand 3-D ultrasound using regression of the echo intensity.

In freehand 3-D ultrasound (US), a position sensor is attached to the probe of a 2-D US machine. The resulting 3-D data permit flexible visualisation and more accurate volume measurement than can be achieved using 2-D B-scans alone; however, the use of the position sensor can be inconvenient for the clinician. The objective is, thus, to replace the sensor with a technique for estimating the probe trajectory based on the B-scan images, themselves. One such technique exists, based on decorrelation algorithms. This paper presents an alternative approach based on linear regression of the echo-envelope intensity signal. A probabilistic analysis of the speckle characteristics of the US signal leads to a linear model, on which the regression algorithm is based. The gradient parameter of this model is shown to be directly related to probe motion. The viability of the new approach is demonstrated through simulations and in vitro and in vivo experiments.

Algorithms↗

Using guide trees to construct multiple-sequence evolutionary HMMs.

MOTIVATION: Score-based progressive alignment algorithms do dynamic programming on successive branches of a guide tree. The analogous probabilistic construct is an Evolutionary HMM. This is a multiple-sequence hidden Markov model (HMM) made by combining transducers (conditionally normalised Pair HMMs) on the branches of a phylogenetic tree. METHODS: We present general algorithms for constructing an Evolutionary HMM from any Pair HMM and for doing dynamic programming to any Multiple-sequence HMM. RESULTS: Our prototype implementation, Handel, is based on the Thorne-Kishino-Felsenstein evolutionary model and is benchmarked using structural reference alignments.

Algorithms↗

Time to failure of hierarchical load-transfer models of fracture.

The time to failure, T, of dynamical models of fracture for a hierarchical load-transfer geometry is studied. Using a probabilistic strategy and juxtaposing hierarchical structures of height n, we devise an exact method to compute T, for structures of height n+1. Bounding T, for large n, we are able to deduce that the time to failure tends to a nonzero value when n tends to infinity. This numerical conclusion is deduced for both power law and exponential breakdown rules.

Journal Article↗

Probabilistic tomography maps chemical heterogeneities throughout the lower mantle.

We obtained likelihoods in the lower mantle for long-wavelength models of bulk sound and shear wave speed, density, and boundary topography, compatible with gravity constraints, from normal mode splitting functions and surface wave data. Taking into account the large uncertainties in Earth's thermodynamic reference state and the published range of mineral physics data, we converted the tomographic likelihoods into probability density functions for temperature, perovskite, and iron variations. Temperature and composition can be separated, showing that chemical variations contribute to the overall buoyancy and are dominant in the lower 1000 kilometers of the mantle.

Journal Article↗

[Behavioral tactics of schizophrenic patients and psychopathic personalities in a probabilistic setting].

In experiments on structural disturbances of prognostication in psychopathic personalities and schizophrenic patients with psychopathlike disorders on the model of "probable prognosis" the study of 2 situations was attempted: the prognosis made by the examinee of changes in the environment and the prognosis in conditions of interaction with the "opponent". The studies demonstrated the influence of different tasks on the activity and varying degree of motivation on the tactics of behaviour in probable situations. The data obtained permit to evaluate in a new light the hypotheses of disturbed probable structures of the past experience. It is concluded that at least 3 determinants should be analyzed: tasks of activity, motivation and probable characteristics of events. New facts have been obtained, concerning the disturbed prognostication in psychopathic personalities under conditions of increased significance of signals.

Antisocial Personality Disorder↗

Thurstonian and Brunswikian origins of uncertainty in judgment: a sampling model of confidence in sensory discrimination.

As a preliminary step towards the presentation of a model of confidence in sensory discrimination, the authors propose a distinction between 2 different origins of uncertainty named after 2 of the great probabilists in the history of psychology, L.L. Thurstone and Egon Brunswik. The authors review data that suggest that there are empirical as well as conceptual differences between the 2 modes of uncertainty and thus that separate models of confidence are needed in tasks dominated by Thurstonian and Brunswikian uncertainty. The article presents a computational model for 1 class of tasks dominated by Thurstonian uncertainty: sensory discrimination with pair comparisons. The sensory sampling model predicts decisions, confidence assessments, and the complex pattern of response times in simple psychophysical discrimination tasks (J.V. Baranski and W.M. Petrusic, 1994). The model also accounts for the disposition towards underconfidence often observed in sensory discrimination with pair comparisons.

Adult↗

[A probabilistic method for the calculation of energy of hydrophobic interactions].

A theoretical approach to the quantitative estimation of the energy of hydrophobic interactions on the molecular level has been developed. The model is based on the fundamental relationship between the probability of shaping of a cavity of the excluded volume in liquid water that results from fluctuations of density and free energy of prime hydrophobic solvates, hard spheres. This probability was estimated with the use of the probabilistic method in combination with experimentally observed data on density and radial distribution function of allocation. Free energy of hydrophobic interactions for a complex consisting of several hard spheres was determined. The critical value of the particles included in the complex was estimated.

Hydrophobic and Hydrophilic Interactions↗

ExonHunter: a comprehensive approach to gene finding.

MOTIVATION: We present ExonHunter, a new and comprehensive gene finding system that outperforms existing systems and features several new ideas and approaches. Our system combines numerous sources of information (genomic sequences, expressed sequence tags and protein databases of related species) into a gene finder based on a hidden Markov model in a novel and systematic way. In our framework, various sources of information are expressed as partial probabilistic statements about positions in the sequence and their annotation. We then combine these into the final prediction via a quadratic programming method, which we show to be an extension of existing methods. Allowing only partial statements is key to our transparent handling of missing information and coping with the heterogeneous character of individual sources of information. In addition, we give a new method for modeling the length distribution of intergenic regions in hidden Markov models. RESULTS: On a commonly used test set, ExonHunter performs significantly better than the existing gene finders ROSETTA, SLAM and TWINSCAN, with more than two-thirds of genes predicted completely correctly. AVAILABILITY: Supplementary material available at http://www.bioinformatics.uwaterloo.ca/supplements/05eh/

Animals↗

Optimizing, diagnostic, and therapeutic strategies using decision-theoretic planning: principles and applications.

OBJECTIVE: Decision-theoretic planning is a new technique for selecting optimal actions. The authors sought to determine whether decision-theoretic planning could be applied to medical decision making to identify optimal strategies for diagnosis and therapy. METHODS: An existing model of acute deep venous thrombosis (DVT) of the lower extremities--in which 24 management strategies were compared--was converted into a set of conditional-probabilistic actions for use by the DRIPS decision-theoretic planning system. Actions were grouped into an abstraction/decomposition hierarchy. A utility function was defined in accordance with the existing DVT management model to incorporate the costs and risks of the diagnostic tests and treatments. RESULTS: From 18 primitive actions (such as "perform venography" and "treat if venography shows thigh DVT"), a total of 312 possible concrete plans were encoded within the abstraction/decomposition hierarchy. The DRIPS planning system used abstraction techniques to eliminate 136 possible plans (44%) from consideration. It determined that, given the parameters specified, the most cost-effective management strategy was "no tests, no treatment." This result differed from the published result of "perform ultrasonography, treat if positive." In reviewing the original article, it was determined that DRIPS had revealed an error in the manually constructed decision trees used in that manuscript. At values of $75,000 and greater for the cost of death, the optimal strategy became "impedance plethysmography (IPG), don't wait, perform venography if IPG is positive, and treat only if venography shows thigh DVT." CONCLUSION: Decision-theoretic planning is applicable to medical decision making and may be an extremely useful technique for complex decisions. The use of inheritance abstraction makes the technique computationally tractable for complex planning problems, and the modular nature of the data entry may help eliminate errors that appear in manually encoded decision trees.

Computer Simulation↗

[Patient involvement in medical care].

Models of doctor-patient relationship may be broadly classified as "paternalistic"(doctor decides, patient complies) and "shared decisions" (doctor informs patient and considers patient's preferences). During recent decades there has been increasing emphasis on respect for the patient's autonomy. Physicians agree that clinical decisions require understanding of how patients view alternative treatment outcomes, and that when they can and wish to do so, patients should participate in the choice of management options. However, involving patients in medical decisions is difficult. Although population surveys have indicated an almost unanimous rejection of the paternalistic model, they have not yielded consistent results on the proportion of patients who want to participate in decision making, and of those who would prefer information and guidance, with a view to following the doctor's advice. A second difficulty relates to method: how should the various options be explained to those who want to participate in decision making? Framing, order of presentation of data and amount of data to be presented have all been shown to affect the way patients perceive aand respond to probabilistic information on treatment outcome. Therefore, there is considerable doubt regarding the applicability of the shared decision model in an unselected patient population. Further research will hopefully identify ways to elicit patient preferences and to communicate information about treatment outcomes, such as life expectancy, morbidity, burdens of taking medication and economic costs. For the present, there seems to be no substitute for the compassionate physician who treats patients with respect and who tries to understand their needs.

Decision Making↗

Towards a neural model of timing.

This paper describes a neural model of interval timing, which reproduces the duration discrimination experiments of Wearden, J.H., 1992, J. Exp. Psychol. 18, 134-144. The model comprises three layers of neural units. The units in the first layer represent clusters of neurons with probabilistic internal feedback that maintains self-sustained (short-term memory) activity for a random time. The unit in the second layer is a spiking neuron that fires as long as a sufficient number of input clusters are active. The unit in the third layer detects the offset of firing in the previous layer by producing a short burst of spikes. Analysis and simulation of the model shows spikes produced at random times with a distribution determined by the number of units in the first layer, their survival time constant, and the threshold of the unit in layer 2. Interval times can be learned with any of these parameters but lead to different Weber law relations. A variable threshold in layer 2 predicts S-shaped Weber curves, a variable number of units in layer 1 leads to a saturation of the Weber curve (decreasing Weber fraction) and a variable time constant in layer 1 causes a linear Weber curve.

Models, Neurological↗

A decision chart for assessing and improving the transferability of economic evaluation results between countries.

OBJECTIVE: To develop a user-friendly tool for managing the transfer of economic evaluation results. METHODS: Factors that may influence the transfer of health economic study results were systematically identified and the way they impact on transferability was investigated. A transferability decision chart was developed that includes: knock-out criteria; a checklist based on the transferability factors; and methods for improving transferability and for assessing the uncertainty of transferred results. This approach was tested on various international cost-effectiveness studies in the areas of interventional cardiology, vaccination and screening. RESULTS: The transfer of study results is possible pending the outcomes of the transferability check and necessary adjustments. Transferability factors can be grouped into areas of methodological, healthcare system and population characteristics. Different levels of effort are required for analysis of factors, ranging from very low (e.g. discount rate) to very high (e.g. practice variation). The impact of differences of most transferability factors can be estimated via the key health economic determinants: capacity utilisation, effectiveness, productivity loss and returns to scale. Depending on the outcomes of the transferability check a correction of the study results for inflation and for differences related to currencies or purchasing power might be sufficient. Otherwise, modelling-based adjustments might be necessary, requiring the (re-)building and sometimes structural modification of the study model. For determination of the most essential adjustments, a univariate sensitivity analysis seems appropriate. If not all relevant study parameters can be substituted with country-specific ones, multivariate or probabilistic sensitivity analysis seems to be a promising way to quantify the uncertainty associated with a transfer. If study results cannot be transferred, the transfer of study models or designs should be investigated as this can significantly save time when conducting a new study. CONCLUSIONS: Our transferability decision chart is a transparent and user-friendly tool for assessing and improving the transferability of economic evaluation results. A state of the art description of the methodology in a study, providing detailed components for calculation, is not only essential for determining its transferability but also for improving it via modelling adjustments.

Cost-Benefit Analysis↗

Phasing via SAD/MAD data: the method of the joint probability distribution functions.

The method of the joint probability distribution functions is applied to derive a probabilistic formula which is able to phase reflections in the MAD case accurately, under the condition that the anomalous-scatterer substructure has been defined previously. The mathematical approach takes into account both measurement and model errors, which are treated as primitive random variables, as well as the atomic positions defining the unknown part of the crystal structure. The probabilistic formula has the classical tangent expression. All the parameters influencing the phase estimation are immediately interpretable in terms of experimental quantities: i.e. anomalous and dispersive differences, magnitude of the errors and normalized structure-factor moduli. The formula has been applied to several practical cases: a procedure has also been designed which is able to refine the phases and lead to easily interpretable electron-density maps.

Crystallography, X-Ray↗

Towards automatic clustering of protein sequences.

Analyzing protein sequence data becomes increasingly important recently. Most previous work on this area has mainly focused on building classification models. In this paper, we investigate in the problem of automatic clustering of unlabeled protein sequences. As a widely recognized technique in statistics and computer science, clustering has been proven very useful in detecting unknown object categories and revealing hidden correlations among objects. One difficulty that prevents clustering from being performed directly on protein sequence is the lack of an effective similarity measure that can be computed efficiently. Therefore, we propose a novel model for protein sequence cluster by exploring significant statistical properties possessed by the sequences. The concept of imprecise probabilities are introduced to the original probabilistic suffix tree to monitor the convergence of the empirical measurement and to guide the clustering process. It has been demonstrated that the proposed method can successfully discover meaningful families without the necessity of learning models of different families from pre-labeled "training data".

Algorithms↗

Hypermedia and randomized algorithms for medical expert systems.

KNET is an environment for constructing probabilistic, knowledge-intensive systems within the axiomatic framework of decision theory. The KNET architecture defines a complete separation between the hypermedia user interface on the one hand, and the representation and management of expert opinion on the other. KNET offers a choice of algorithms for probabilistic inference. We and our coworkers have used KNET to build consultation systems for lymph-node pathology, bone-marrow transplantation therapy, clinical epidemiology, and alarm management in the intensive-care unit. Most important, KNET contains a randomized approximation scheme (RAS) for the difficult and almost certainly intractable problem of Bayesian inference. Our algorithm can, in many circumstances, perform efficient approximate inference in large and richly interconnected models of medical diagnosis. In this article, we describe the architecture of KNET, construct a randomized algorithm for probabilistic inference, and analyze the algorithm's performance. Finally, we characterize our algorithms' empiric behavior and explore its potential for parallel speedups. From design to implementation, then, KNET demonstrates the crucial interaction between theoretical computer science and medical informatics.

Algorithms↗