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PubMed2026

A token-pruning framework enables efficient representation of the human genome for RNA modification analysis.

MOTIVATION: Modelling long genomic sequences remains challenging due to extreme sequence length, high redundancy, and the need for biological interpretability. Although Transformer-based architectures have achieved strong performance across genomic tasks, their high computational cost and reliance on fixed tokenization strategies limit their scalability and ability to focus on biologically informative regions. RESULTS: We propose ATSFormer, a token-pruning Transformer framework for efficient and biologically informed genomic sequence modelling. ATSFormer incorporates an attention-guided and parameter-free Adaptive Token Sampling (ATS) module into Transformer layers. Guided by attention-derived importance scores, ATS dynamically retains informative tokens while probabilistically discarding redundant ones, thereby reducing sequence length, FLOPs, and memory usage without introducing additional learnable parameters or extra training procedures. Importantly, the retained tokens correspond to key contributors to model predictions, enabling ATSFormer to highlight biologically meaningful sites and sequence motifs. We evaluated ATSFormer on four benchmark RNA modification datasets derived from RMVar 2.0, covering A-to-I, m1A, m5C, and m7G. Experimental results show that ATSFormer consistently outperforms existing state-of-the-art methods while achieving substantial computational savings. Furthermore, structural analysis using AlphaFold3 supports the biological relevance of the motifs identified by ATSFormer. AVAILABILITY AND IMPLEMENTATION: The source data and code are freely available at GitHub (https://github.com/1gao2/ATSFormer) and Zenodo (https://doi.org/10.5281/zenodo.21813541).

Humans↗
PubMed2005

Pitch shifts for complex tones with unresolved harmonics and the implications for models of pitch perception.

Complex tone bursts were bandpass filtered, 22nd-30th harmonic, to produce waveforms with five regularly occurring envelope peaks ("pitch pulses") that evoked pitches associated with their repetition period. Two such tone bursts were presented sequentially and separated by an interpulse interval (IPI). When the IPI was varied, the pitch of the whole sequence was shifted by between +2% and -5%. When the IPI was greater than one period, little effect was seen. This is consistent with a pitch mechanism employing a long integration time for continuous stimuli that resets in response to temporal discontinuities of greater than about one period of the waveform. Similar pitch shifts were observed for fundamental frequencies from 100 to 250 Hz. The pitch shifts depended on the IPI duration relative to the period of the complex, not on the absolute IPI duration. The pitch shifts are inconsistent with the autocorrelation model of Meddis and O'Mard [J. Acoust. Soc. Am. 102, 1811-1820 (1997)], although a modified version of the weighted mean-interval model of Carlyon et al. [J. Acoust. Soc. Am. 112, 621-633 (2002)] was successful. The pitch shifts suggest that, when two pulses occur close together, one of the pulses is ignored on a probabilistic basis.

Acoustic Stimulation↗
PubMed1999

Estimating uncertainty ranges for costs by the bootstrap procedure combined with probabilistic sensitivity analysis.

When an economic evaluation incorporates patient-level data, there are two types of uncertainty over the results: uncertainty due to variation in the sampled data, and uncertainty over the choice of modelling parameters and assumptions. Previously statistical methods have been used to estimate the extent of the former, and sensitivity analysis to estimate the extent of the latter. Ideally interval estimates for economic variables should reflect both types of uncertainty. This paper describes a method for combining bootstrapping with probabilistic sensitivity analysis to estimate a total 'uncertainty range' for incremental costs. The approach is illustrated using cost data from a randomized controlled trial of endoscopy for Helicobactor pylori negative young dyspeptic patients. The trial failed to demonstrate any clinical benefit from endoscopy, which was on average pound 395 more costly. The combined 95% uncertainty range for incremental costs (-pound 236 to pound 931) was wider than 95% intervals estimated by either probabilistic sensitivity analysis (pound 43 to pound 592) or the non-parametric bootstrap method (-pound 95 to pound 667) alone. The method can easily be extended to the calculation of uncertainty ranges for incremental cost-effectiveness ratios.

Confidence Intervals↗
PubMed2003

The use of decision models in mental health economic evaluation: challenges and opportunities.

A number of reasons have been suggested for the increased use of decision-analytic modelling in assessing the cost-effectiveness of mental health interventions: (1) the need to rapidly assess the value-for-money of new pharmaceuticals; (2) the short time horizon of clinical trials in mental health; (3) the lack of head-to-head comparisons between alternative treatment strategies; and (4) the necessity to generalise the study results. As simulation exercises become more widely accepted and used to inform policy making decisions, a trend towards more sophisticated modelling structures is starting to emerge. This paper undertakes a structured critical appraisal of cost-effectiveness modelling studies, using published examples relating to available drug treatments for schizophrenia and Alzheimer's disease (AD). The models identified display some methodological heterogeneity in terms of the choice of comparator, costing methodology, timeframe and perspective of the analysis, target population and model structure. The use of 'state-of-the-art' techniques, such as value-of-information analysis and probabilistic-sensitivity analysis has been somewhat limited. Health service researchers need to make sure that the best available techniques are employed to maximise the use of the information already available.

Cost-Benefit Analysis↗
PubMed1999

The cost-effectiveness of a new chlorhexidine delivery system in the treatment of adult periodontitis.

BACKGROUND: Periodontal treatment is costly. The authors assessed the potential economic impact of a new periodontal chemotherapeutic, testing the hypothesis that its adjunctive use would result in reduced periodontal surgical needs. METHODS: An economic model estimated treatment needs following two clinical trials of the adjunctive use of a chlorhexidine, or CHX, -containing chip compared with scaling and root planing, or SRP, alone. Needs were based on periodontal status at nine months and a probabilistic algorithm; costs were assigned on the basis of a national dental survey and an average wholesale price of the CHX chip. RESULTS: The base case model projected significantly more maintenance procedures and significantly fewer periodontal surgical procedures for patients treated with SRP and the CHX chip compared with patients who were treated with SRP alone (54.4 percent vs. 46.4 percent, P = .014; 29.2 percent vs. 35.5 percent, P = .015, respectively). Average total costs of care for patients treated with SRP and CHX chip were $737 +/- $244 compared with $734 +/- $239 for patients treated with SRP alone. Sensitivity analyses to account for variations in practice patterns did not appreciably alter the results. When data were analyzed after only three or six months of treatment, the significant differences in treatment needs disappeared. CONCLUSIONS: The CHX chip is a new, apparently cost-effective treatment option for non-surgical periodontal therapy. Adjunctive use of the CHX chip could reduce periodontal surgical needs significantly at little or no additional cost. CLINICAL IMPLICATIONS: Results suggest that incorporating the CHX chip into routine practice requires a new algorithm for management of periodontal disease. To obtain full clinical benefit, treatment needs to be continued for nine months.

Adult↗
PubMed1981

Probability aspects of supernumerary production in the regenerating limbs of the axolotl, Ambystoma mexicanum.

The applicability of deterministic models, and in particular the polar co-ordinate model of French, Bryant & Bryant (1976), to the regenerative process has been investigated by performing ipsilateral blastemal rotations of varying angle on the fore and hind limbs of the axolotl. The results show that the frequency of supernumerary production rises with increasing angle to reach a peak at 180 degree and then falls off more rapidly, giving rise to an asymmetric distribution curve. The position of supernumerary outgrowth als suggests a probabilistic event, there being no consistent relationship between this parameter and the angle of rotation. The polar co-ordinate model is incapable of explaining these results and the work suggests that the determinism of current regeneration models may have to be abandoned in favour of a more stochastic theory.

Ambystoma mexicanum↗
PubMed2006

Ecology of microbial invasions: amplification allows virus carriers to invade more rapidly when rare.

Locally adapted residents present a formidable barrier to invasion . One solution for invaders is to kill residents . Here, we explore the comparative ecological dynamics of two distinct microbial mechanisms of killing competitors, via the release of chemicals (e.g., bacteriocins ) and via the release of parasites (e.g., temperate phage ). We compared the short-term population dynamics of susceptible E. coli K12 and isogenic carriers of phage varphi80 in experimental cultures to that anticipated by mathematical models using independently derived experimental parameters. Whereas phages are a direct burden to their carriers because of probabilistic host lysis, by killing competitor bacteria they can indirectly benefit bacterial kin made immune by carrying isogenic phage. This is similar to previously described bacteriocin-mediated effects. However, unlike chemical killing, viable phage trigger an epidemic among susceptible competitors, which become factories producing more phage. Amplification makes phage carriers able to invade well-mixed susceptibles even faster when rare, whereas chemical killers can only win in a well-mixed environment when sufficiently abundant. We demonstrate that for plausible parameters, the release of chemical toxins is superior as a resident strategy to repel invasions, whereas the release of temperate phage is superior as a strategy of invasion.

Bacteriocins↗
PubMed2000

Statistical support for uncertainty in radiological diagnosis.

Radiological interpretation and diagnosis involves the comparison and classification of complex medical images and is typical of the categorisation tasks that have been the subject of observational studies in Cognitive Science. This paper considers the affinity between statistical modelling and theories of categorisation for naturally occurring categories. Statistical based measures of similarity and typicality with a probabilistic interpretation are derived. The utilisation of these measures in the support of diagnosis under uncertainty via interactive overview plots is described. The application of the methodology to magnetic resonance imaging of the head is considered. The methods detailed have application to other fields involving archiving and retrieving of image data.

Decision Support Techniques↗
PubMed1985

Diagnostic value of computerized exercise testing in men without previous myocardial infarction. A multivariate, compartmental and probabilistic approach.

The value of exercise testing for the diagnosis of coronary artery disease is disputed but very few studies have taken advantage of all recent improvements, namely computer averaging of the ECG signals, multivariate analysis of the data, a compartmental diagnostic approach and probabilistic interpretation of the results. These methods were tested in a group of 387 men who had a computer-assisted multistage maximal exercise test; none had a history of myocardial infarction. In 284 symptomatic patients, the diagnosis was made by arteriography; 103 ostensibly healthy men were also included. The computer-averaged ECG signals (X, Y, Z) recorded at maximal exercise, maximal heart rate, blood pressure and workload, and the onset of angina pectoris during exercise were submitted to a multivariate stepwise discriminant analysis. The pretest likelihood for CAD was calculated from age and history; the post-test likelihood was calculated from Bayes' theorem and the average information content of several diagnostic methods was assessed in categorical and compartmental models. By multivariate analysis, 5 variables collected at maximal exercise were selected, namely the heart-rate, the ST60 segment level, the onset of angina during the test, the workload and the slope of the ST segment in lead X. The average information content of the analysis using 5 variables was 44% in a categorical model versus 55% in a compartmental model (P less than 0.001). For comparison, the information content of the analysis using the ST60 segment level alone was only 16% in the categorical model and 27% in the compartmental model. The clinical value of these diagnostic methods (categorical versus compartmental, univariate versus multivariate) was assessed by a probabilistic classification of the patients. The classification provided by the analysis of the ST60 segment changes was barely better than that one provided by the simple history. The probabilistic use of a multivariate and compartmental analysis of the data led to a significantly better and more accurate classification of the patients (83% of correct classification).

Adult↗
PubMed2001

Single-event-related potential analysis by means of fragmentary decomposition.

A recently developed fragmentary decomposition method is employed to analyse single-trial event-related potentials (ERPs), thereby extending the traditional method of averaging. Using a conventional auditory oddball paradigm with 40 target stimuli, single-trial ERPs in 40 normal subjects were analysed for midline scalp (Fz, Cz and Pz) recording sites. The normalization effect, reported in our previous study of eye blink EMGs and proposed to be a characteristic property of a wide class of non-stationary physiological processes, was found to apply to these single-trial ERPs. Fragmentary decomposition of single-trial ERPs may be regarded as re-statement of the normalization effect. This allows both pre-stimulus EEGs and post-stimulus ERPs to be regarded as overlapping generic mass potentials (GMPs), with a characteristic Gaussian amplitude spectrum. On theoretical and empirical grounds we uniquely deduce a model GMP using an introduced d" function, and physically support it by the resting and transient conditions. The model takes into account the shape of the component, which suggests a simple relationship between the peak latency and the time of the component onset. Given that GMPs may be manipulated and sorted out, we present principles of the fragmentary synthesis, i.e. probabilistic ERP reconstructions on the basis of individual and ensemble properties of its identified components. Summarizing the component quantification in the form of the dynamic model provides for the first time the opportunity to quantify all significant components in single-trial ERPs. This method of single-trial analysis opens up new possibilities of exploring the dynamical ERP changes within a recording trial, particularly in late component "cognitive" paradigms.

Adult↗
PubMed2006

The role of the ventromedial prefrontal cortex in abstract state-based inference during decision making in humans.

Many real-life decision-making problems incorporate higher-order structure, involving interdependencies between different stimuli, actions, and subsequent rewards. It is not known whether brain regions implicated in decision making, such as the ventromedial prefrontal cortex (vmPFC), use a stored model of the task structure to guide choice (model-based decision making) or merely learn action or state values without assuming higher-order structure as in standard reinforcement learning. To discriminate between these possibilities, we scanned human subjects with functional magnetic resonance imaging while they performed a simple decision-making task with higher-order structure, probabilistic reversal learning. We found that neural activity in a key decision-making region, the vmPFC, was more consistent with a computational model that exploits higher-order structure than with simple reinforcement learning. These results suggest that brain regions, such as the vmPFC, use an abstract model of task structure to guide behavioral choice, computations that may underlie the human capacity for complex social interactions and abstract strategizing.

Action Potentials↗
PubMed2006

The clinical and cost-effectiveness of oxaliplatin and capecitabine for the adjuvant treatment of colon cancer: systematic review and economic evaluation.

OBJECTIVES: To assess the clinical and cost-effectiveness of oxaliplatin in combination with 5-fluorouracil/leucovorin (5-FU/LV), and capecitabine monotherapy (within their licensed indications), as adjuvant therapies in the treatment of patients with Stage III (Dukes' C) colon cancer after complete surgical resection of the primary tumour, as compared with adjuvant chemotherapy with an established fluorouracil-containing regimen. DATA SOURCES: Ten electronic bibliographic databases were searched from inception to January 2005. Searches were supplemented by hand searching relevant articles, sponsor and other submissions of evidence to the National Institute of Health and Clinical Excellence and conference proceedings. REVIEW METHODS: A systematic review and meta-analysis (where appropriate) of clinical efficacy evidence and a cost-effectiveness review and economic modelling were carried out. Marginal costs, life years gained and cost-effectiveness acceptability curves were estimated. Probabilistic sensitivity analysis was used to generate information on the likelihood that each of the interventions was optimal. RESULTS: Three randomised active-controlled trials, of varying methodological quality, were included in the review. The MOSAIC trial and NSABP C-07 study considered the addition of oxaliplatin to adjuvant treatment (albeit administered in different 5-FU/LV regimens) and the X-ACT study compared oral capecitabine with bolus 5-FU/LV alone. A review of the available evidence indicated that in patients with Stage III colon cancer, oxaliplatin in combination with an infusional de Gramont schedule of 5-FU/LV (FOLFOX4) was more effective in preventing and delaying disease recurrence than infusional 5-FU/LV alone (de Gramont regimen). Serious adverse events and treatment discontinuations due to toxicity were more evident with oxaliplatin-based regimens (FOLFOX4 and FLOX regimen) than infusional or bolus 5-FU/LV alone (de Gramont and Roswell Park regimen). Oral capecitabine was at least equivalent in disease-free survival to the bolus Mayo Clinic 5-FU/LV regimen for patients with resected Stage III colon cancer. Although, the safety and tolerability profile of capecitabine was superior to that of the Mayo Clinic 5-FU/LV regimen, it has not been evaluated in comparison with other less toxic 5-FU/LV regimens currently in common use in the UK. Based on the assumptions and survival analysis methods used, the cost-effectiveness analysis using economic modelling estimated that capecitabine was a dominating strategy and resulted in a cost-saving of approximately pound 3320 per patient in comparison with the Mayo Clinic 5-FU/LV regimen, while also providing an additional 0.98 quality-adjusted life-years (QALYs) over a 50-year model time horizon. Oxaliplatin in combination with 5-FU/LV (FOLFOX4 regimen) is estimated to cost an additional pound 2970 per QALY gained when compared with the de Gramont 5-FU/LV regimen and demonstrated superior survival outcomes with marginal costs. The uncertainty analysis suggests that both interventions have a high probability of being cost-effective at a threshold of both pound 20,000 and pound 30,000. An indirect comparison of the FOLFOX4 and Mayo Clinic 5-FU/LV regimens suggests that the use of FOLFOX4 in place of the Mayo Clinic 5-FU/LV regimen would cost an additional pound 5777 per QALY gained. An incremental cost-effectiveness ratio (ICER) is estimated to be approximately pound 13,000 per QALY gained from treatment with FOLFOX4 compared with capecitabine. However, if the Mayo Clinic and the de Gramont 5-FU/LV regimens are assumed to be equivalent in terms of effectiveness, the ICER of FOLFOX4 in comparison with capecitabine may be greater than pound 30,000 per QALY. CONCLUSIONS: The evidence suggests that both capecitabine and FOLFOX4 are clinically effective and cost-effective in comparison with 5-FU/LV regimens (Mayo Clinic and de Gramont schedules). Further research is suggested into the effectiveness, tolerability, patient acceptability and costs of different oxaliplatin/fluoropyrimidine schedules in the adjuvant setting; the effects of treatment duration on efficacy; adverse events; resource data collection strategies and reporting of summary statistics; subgroups benefiting most from adjuvant chemotherapy; and methods for estimating mean survival.

Antimetabolites, Antineoplastic↗
PubMed2006

Supervised pattern recognition procedures for discrimination of whiskeys from gas chromatography/mass spectrometry congener analysis.

The volatile congener analysis of 52 commercialized whiskeys (24 samples of single malt Scotch whiskey, 18 samples of bourbon whiskey, and 10 samples of Irish whiskey) was carried out by gas chromatography/mass spectrometry after liquid-liquid extraction with dichloromethane. Pattern recognition procedures were applied for discrimination of different whiskey categories. Multivariate data analysis includes linear discriminant analysis (LDA), k nearest neighbors (KNN), soft independent modeling of class analogy (SIMCA), procrustes discriminant analysis (PDA), and artificial neural networks techniques involving multilayer perceptrons (MLP) and probabilistic neural networks (PNN). Classification rules were validated by considering the number of false positives (FPs) and false negatives (FNs) of each class associated to the prediction set. Artificial neural networks led to the best results because of their intrinsic nonlinear features. Both techniques, MLP and PNN, gave zero FPs and zero FNs for all of the categories. KNN is a nonparametric method that also provides zero FPs and FNs for every class but only when selecting K = 3 neighbors. PDA produced good results also (zero FPs and FNs always) but only by selecting nine principal components for class modeling. LDA shows a lesser classification performance, because of the building of linear frontiers between classes that does not apply in many real situations. LDA led to one FP for bourbons and one FN for scotches. The worse results were obtained with SIMCA, which gave a higher number of FPs (five for both scotches and bourbons) and FNs (six for scotchs and two for bourbons). The possible cause of these findings is the strong influence of class inhomogeneities on the SIMCA performance. It is remarkable that in any case, all of the methodologies lead to zero FPs and FNs for the Irish whiskeys.

Alcoholic Beverages↗
PubMed2000

Linkage analysis in the presence of errors IV: joint pseudomarker analysis of linkage and/or linkage disequilibrium on a mixture of pedigrees and singletons when the mode of inheritance cannot be accurately specified.

There is a lot of confusion in the literature about the "differences" between "model-based" and "model-free" methods and about which approach is better suited for detection of the genes predisposing to complex multifactorial phenotypes. By starting from first principles, we demonstrate that the differences between the two approaches have more to do with study design than statistical analysis. When simple data structures are repeatedly ascertained, no assumptions about the genotype-phenotype relationship need to be made for the analysis to be powerful, since simple data structures admit only a small number of df. When more complicated and/or heterogeneous data structures are ascertained, however, the number of df in the underlying probability model is too large to have a powerful, truly "model-free" test. So-called "model-free" methods typically simplify the underlying probability model by implicitly assuming that, in some sense, all meioses connecting two affected individuals are informative for linkage with identical probability and that the affected individuals in a pedigree share as many disease-predisposing alleles as possible. By contrast, "model-based" methods add structure to the underlying parameter space by making assumptions about the genotype-phenotype relationship, making it possible to probabilistically assign disease-locus genotypes to all individuals in the data set on the basis of the observed phenotypes. In this study, we demonstrate the equivalence of these two approaches in a variety of situations and exploit this equivalence to develop more powerful and efficient likelihood-based analogues of "model-free" tests of linkage and/or linkage disequilibrium. Through the use of a "pseudomarker" locus to structure the space of observations, sib-pairs, triads, and singletons can be analyzed jointly, which will lead to tests that are more well-behaved, efficient, and powerful than traditional "model-free" tests such as the affected sib-pair, transmission/disequilibrium, haplotype relative risk, and case-control tests. Also described is an extension of this approach to large pedigrees, which, in practice, is equivalent to affected relative-pair analysis. The proposed methods are equally applicable to two-point and multipoint analysis (using complex-valued recombination fractions).

Case-Control Studies↗
PubMed1996

Predictive diagnostics for logistic models.

Novel methodology is implemented to assess the predictive power of covariate information associated with sequential binary events. Logistic models are first fitted on the basis of a subset of the observations and then evaluated sequentially on the rest. The probabilistic forecasts are compared to the outcomes via a scoring function, but as most validation samples are small, the usual reference distribution for the test statistics is inadequate. However, bootstrap-based distributions can easily be constructed. The first example pertains to the evaluation of screening tests for major depression. It illustrates that goodness-of-fit and predictive assessments lead to the selection of very different models. The second example deals with the prediction of a major event in the natural history of HIV-induced disease. It shows that this type of analysis can reveal features missed by other approaches.

Calibration↗
PubMed2006

Ventral-striatal/nucleus-accumbens sensitivity to prediction errors during classification learning.

A prominent theory in neuroscience suggests reward learning is driven by the discrepancy between a subject's expectation of an outcome and the actual outcome itself. Furthermore, it is postulated that midbrain dopamine neurons relay this mismatch to target regions including the ventral striatum. Using functional MRI (fMRI), we tested striatal responses to prediction errors for probabilistic classification learning with purely cognitive feedback. We used a version of the Rescorla-Wagner model to generate prediction errors for each subject and then entered these in a parametric analysis of fMRI activity. Activation in ventral striatum/nucleus-accumbens (Nacc) increased parametrically with prediction error for negative feedback. This result extends recent neuroimaging findings in reward learning by showing that learning with cognitive feedback also depends on the same circuitry and dopaminergic signaling mechanisms.

Basal Ganglia↗