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Detecting adverse drug events in discharge summaries using variations on the simple Bayes model.

Detection and prevention of adverse events and, in particular, adverse drug events (ADEs), is an important problem in health care today. We describe the implementation and evaluation of four variations on the simple Bayes model for identifying ADE-related discharge summaries. Our results show that these probabilistic techniques achieve an ROC curve area of up to 0.77 in correctly determining which patient cases should be assigned an ADE-related ICD-9-CM code. These results suggest a potential for these techniques to contribute to the development of an automated system that helps identify ADEs, as a step toward further understanding and preventing them.

Abstracting and Indexing↗

Probabilistic quantum memories.

Typical address-oriented computer memories cannot recognize incomplete or noisy information. Associative (content-addressable) memories solve this problem but suffer from severe capacity shortages. I propose a model of a quantum memory that solves both problems. The storage capacity is exponential in the number of qbits and thus optimal. The retrieval mechanism for incomplete or noisy inputs is probabilistic, with postselection of the measurement result. The output is determined by a probability distribution on the memory which is peaked around the stored patterns closest in Hamming distance to the input.

Journal Article↗

Mathematical analysis of transport and consumption of molecules in heterogeneous brain tissue (methodology).

A computer model of metabolite transport and consumption in heterogeneous brain tissue, using a combination of probabilistic and deterministic techniques is being developed. The metabolites are put into two separate classes: (I) those that have reached a membrane for the first time during a small time step, delta t, and (II) those that have not yet reached a cell membrane for the first time during that time step. The time dependent spatial distribution of class (I) molecules is determined using random walk theory, which takes into account the actual paths of the molecules. The variation of the spatial distribution of class (II) molecules with time is determined using the time dependent diffusion equation with a boundary condition of zero concentration on the enclosing membrane boundaries.

Biological Transport, Active↗

[Thoughts upon the construction of requirements of disinfection procedures concerning contaminated hands - an analysis (author's transl)].

The construction of detailed test methods for the evaluation of disinfection procedures has primarily to be based upon requirements which have to be formulated in advance. A recently proposed test model is being discussed on the basis of 5 conceivable formulations of possible requirements. Essentially, they may be allotted to two types: the one implies the comparison of the disinfection procedure to be tested as against an hypothetical procedure. The other makes use of the simple comparison with a concrete standard procedure and is preferable to the first possibility for several reasons. The presented, mathematical formulations of the structure describing the proposed model represents a first approximation in order to permit the comparison of disinfection effects on the hands under assistance of probabilistic methods and eliminating other effects inherent ot a test method.

Disinfection↗

The ethology of saccades: a non-cognitive model.

It is proposed that there is a low-level automatic component of visual scanning in which saccades are triggered probabilistically in time by non-foveal stimulus features. By ignoring cognitive factors and memory, a first-order Markov approach is taken, which is tractable for spatially homogeneous stimuli. The predicted distributions of saccade magnitude, fixation duration, fixation position, and how they are related to stimulus size are in good agreement with empirical observations by Bahill et al. (1975), Enoch (1959), and Harris et al. (1988). Ways in which this low-level process could be modulated by cognitive factors are discussed.

Eye Movements↗

Engineering risk analysis of a hospital oxygen supply system.

Reports from the Food and Drug Administration (FDA) and the Joint Commission on Accreditation of Healthcare Organizations (JCAHO) have emphasized the potential for injury to patients caused by failures in oxygen supply systems. This article presents a model of patient risk related to the process of supplying oxygen at a single university hospital. One of the goals of the article is to illustrate how probabilistic risk analysis (PRA) can be used by hospitals to assess and mitigate risk and, therefore, to meet JCAHO requirements. PRA techniques are useful to 1) model the reliability of a complex system and 2) assess the cost-effectiveness of different risk mitigation measures. The authors focus on the risk estimation step, describing in detail their modeling of the oxygen supply system and analysis of the results. For the hospital that the authors study (20,000 admissions yearly), the total expected number of fatalities from oxygen system failure is 44 over a 30-year time horizon. The greatest contribution to the risk (94% of the expected number of fatalities) comes from problems that involve the supply network (e.g., damage to structure and poisoning) as opposed to incidents that occur inside patient rooms. Although the threat to patient safety is not dramatic, health care organizations should be concerned about potential failures of their oxygen system because improving this system could avoid low-probability, high-consequence failures at a low cost.

California↗

Visualizing the function computed by a feedforward neural network.

A method for visualizing the function computed by a feedforward neural network is presented. It is most suitable for models with continuous inputs and a small number of outputs, where the output function is reasonably smooth, as in regression and probabilistic classification tasks. The visualization makes readily apparent the effects of each input and the way in which the functions deviate from a linear function. The visualization can also assist in identifying interactions in the fitted model. The method uses only the input-output relationship and thus can be applied to any predictive statistical model, including bagged and committee models, which are otherwise difficult to interpret. The visualization method is demonstrated on a neural network model of how the risk of lung cancer is affected by smoking and drinking.

Alcohol Drinking↗

Mathematical modeling of the mastitis infection process.

Mastitis infection is a biological process with a serial structure and stochastic in nature. A mathematical model for this process was developed from Markov chain theory. The unit of the process was an individual quarter; and four infection processes for first, second, third, fourth or higher lactation were described. Two Markov matrices which probabilistically determine the transitions between seven mutually exclusive states at each stage of the process were defined. After its validation, the model was used to determine the lactational consequences of the mastitis infection by calculating expected milk-yield productivity. Expected milk-yield productivity for an individual quarter was .93, .88, .85, and .84 for first, second, third, and fourth or higher lactation. The expected milk yield productivity of a quarter as a function of its state at the beginning of the process also was calculated. The quarters infected but not clinical have the lowest productivity.

Animals↗

The FDG/PET methodology for early detection of disease onset: a statistical model.

The development of appropriate statistical methodologies for neuroimaging studies is dependent upon the research question of interest. Often studies are analyzed with techniques that may not be appropriate for the research question but are accepted owing to convention, familiarity, or apparent statistical sophistication. Neuroimaging data are particularly complex owing to (a) the high number of potential dependent variables (i.e., regions of interest) coupled with the practical limitations on sample size; (b) the known physical properties of scanners (e.g., resolution) interacting with the intricate and variable structure of the human brain; and (c) mathematical properties introduced into the data by the physiological model for quantification. In this article, a statistical model will be discussed for addressing a particular problem in clinical studies. Given that there is a characteristic abnormality in regional glucose metabolism in a specific disease, can a probabilistic statement be made with confidence regarding the likelihood of an individual scan being similar to those from the disease group or normal subjects? The model capitalizes on known statistical aspects of normal regional glucose metabolism. To illustrate the model, data will be presented on normal subjects, patients with confirmed Huntington's disease, and subjects at risk for the disease. Reliability and clinical validity of the model will be discussed.

Adult↗

Probing universality classes in solid-on-solid deposition.

We consider several stochastic processes corresponding to the same physical solid-on-solid deposition problem. Simplified models presenting the same (conditional) mean and variance for each process are also introduced as well as generalizations in terms of the deposition of blobs and probabilistic deposition rules. We compare the evolution of the roughness as a function of time for a three-parameter family that includes as limit cases the Family model and the Edwards-Wilkinson equation, showing that in all cases the derived models with the same mean and variance are indistinguishable from the originating models in terms of the evolution of the roughness. Finally, we show that although all the models studied belong to the same universality class, some relevant features such as the final surface roughness are reproduced only for models within a restricted class determined by sharing the same (conditional) mean and variance.

Journal Article↗

The statistical structure of natural light patterns determines perceived light intensity.

The same target luminance in different contexts can elicit markedly different perceptions of brightness, a fact that has long puzzled vision scientists. Here we test the proposal that the visual system encodes not luminance as such but rather the statistical relationship of a particular luminance to all possible luminance values experienced in natural contexts during evolution. This statistical conception of vision was validated by using a database of natural scenes in which we could determine the probability distribution functions of co-occurring target and contextual luminance values. The distribution functions obtained in this way predict target brightness in response to a variety of challenging stimuli, thus explaining these otherwise puzzling percepts. That brightness is determined by the statistics of natural light patterns implies that the relevant neural circuitry is specifically organized to generate these probabilistic responses.

Biometry↗

Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities.

BACKGROUND: Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily. RESULTS: We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends. CONCLUSION: Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at http://biozon.org.

Abstracting and Indexing↗

Ion and transmitter movements during spreading cortical depression.

A reaction--diffusion system of equations whose components are the extracellular concentrations of K+, Ca++, Na+, Cl-, an excitatory neurotransmitter and an inhibitory neurotransmitter, is developed in order to model the movements of these substances through various kinds of membrane in brain structures. Expressions are derived from probabilistic arguments for the conductances induced in subsynaptic membrane by transmitter substances at various concentrations, for one-way active transport rates and for an exchange pump rate. These expressions are employed in the reaction terms of the system. The meaning of the many constants is explained and, with appropriate choices for their values, the model predicts subthreshold responses to small enough local elevations of KCl or glutamate and stable propagating SD waves if the local elevations of these chemicals is sufficient. The SD waves consist of elevated K+ and transmitter substances and diminished Ca++, Na+ and Cl-, the velocity of propagation in cortex being about 0.6 mm/min. This is in the experimental range, the K+-amplitude being 17 mM relative to a baseline of 3 mM, as the model developed ignores the effects of action potentials. There is no SD response to either NaCl or GABA. The effects of no K+ and no glutamate diffusion are investigated, both being manifest as a failure in propagation of the stable SD waves. The wave solutions are analysed in terms of phase portraits. The roles of various amino acid uptake and release processes by neurons and glia are discussed, as are the complications with regard to their incorporation in a model for SD. The roles of neurons and glia are analysed and the six basic fluxes of K+ are outlined. It is postulated that under some circumstances, in cortex treated with TTX, there may be practically no transmitter release, but SD may propagate if TTX does not completely abolish gNa for nonsynaptic membrane, a corresponding system of model equations being developed. The data and ideas of K+-based and glutamate-based SD of Van Harreveld are discussed and interpreted in terms of which reaction terms are operative in the K+ equation. An appendix contains the values of the parameters used in the numerical calculations.

Animals↗

Probabilistic interpretation of population codes.

We present a general encoding-decoding framework for interpreting the activity of a population of units. A standard population code interpretation method, the Poisson model, starts from a description as to how a single value of an underlying quantity can generate the activities of each unit in the population. In casting it in the encoding-decoding framework, we find that this model is too restrictive to describe fully the activities of units in population codes in higher processing areas, such as the medial temporal area. Under a more powerful model, the population activity can convey information not only about a single value of some quantity but also about its whole distribution, including its variance, and perhaps even the certainty the system has in the actual presence in the world of the entity generating this quantity. We propose a novel method for forming such probabilistic interpretations of population codes and compare it to the existing method.

Data Interpretation, Statistical↗

Broadening the Tests of Learning Models.

For many years psychological studies of the learning process have used a simulated medical diagnosis task in which symptom configurations are probabilistically related to diseases. Participants are given a set of symptoms and asked to indicate which disease is present, and feedback is given on each trial. We enrich this standard laboratory task in four different ways. First, the symptoms have four possible values (low, medium low, medium high, and high) rather than just two. Second, symptom configurations are generated from an expanded factorial design rather than a simple factorial design. Third, subjects are asked to make a continuous judgment indicating their confidence in the diagnosis, rather than simply a binary judgment. Fourth, cumulated performance scores, payoffs, and the availability of a historical summary of the outcomes are varied in order to assess how these treatments modulate performance. These enrichments provide a broader data set and more challenging tests of the models. Using 123 subjects each in 480 trials, we compare five existing learning models plus several variants, including the well-known Bayesian, fuzzy logic, connectionist, exemplar, and ALCOVE models. We find that the subjects do learn to distinguish the symptom configurations, that subjects are quite heterogeneous in their response to the task, and that only a small part of the variation across subjects arises from the differences in treatments. The most striking finding is that the model that best predicts subjects' behavior is a simple Bayesian model with a single fitted parameter for prior precision to capture individual differences. We use rolling regression techniques to elucidate the behavior of this model over time and find some evidence of over-response to current stimuli. Copyright 1998 Academic Press.

Journal Article↗

Prediction of overall persistence and long-range transport potential with multimedia fate models: robustness and sensitivity of results.

The hazard indicators persistence (P) and long-range transport potential (LRTP) are used in chemicals assessment to characterize chemicals with regard to the temporal and spatial extent of their environmental exposure. They are often calculated based on the results of multimedia fate models. The environmental and substance-specific input parameters of such models are subject to a range of methodological uncertainties and also influenced by natural variability. We employed probabilistic uncertainty analysis to quantify variance in P and LRTP predictions for chemicals with different partitioning and transport behavior. Variance found in the results is so large that it prevents a clear distinction between chemicals. Additionally, only small improvements are observed when evaluating the results relative to a benchmark chemical. This can be explained by the dominance of substance-specific parameters and the only small direct influence of environmental parameters on P and LRTP as model outcomes. The findings underline the importance of learning how environmental conditions cause variability in substance behavior for improved substance ranking and classification.

Air Movements↗