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Results for “Performance benchmarking”

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PubMed2005

Program directors' opinions about surgical competency in otolaryngology residents.

OBJECTIVES: The purpose of this study was to determine whether certain surgical procedures could be used as benchmark skills to monitor resident progress in developing surgical competency. STUDY DESIGN: Survey. METHODS: A two-stage survey was sent to otolaryngology residency program directors in the United States. Respondents were given a list of otolaryngology surgical procedures monitored by the American Board of Otolaryngology (ABO) and were asked to indicate whether they felt residents should be able to do each as a primary surgeon. The appropriate level of training for competency in each procedure and estimated number of procedures to competency was indicated by respondents. RESULTS: Respondents selected 16 common procedures they felt residents at different levels of training should be able to perform independently. There were discrepancies between estimated number of procedures needed for competence and the numbers reported by ABO graduates. CONCLUSIONS: Surgical skill is one aspect of clinical competency, and this indicates agreement among program directors with regard to a set of benchmark skills we can use for concentrated evaluation efforts.

Attitude of Health Personnel↗
PubMed2005

Automatic selection of non-coplanar beam directions for three-dimensional conformal radiotherapy.

An algorithm is described, based on ray-tracing and the beam's-eye-view, that exhaustively searches all permitted beam directions. The evaluation of the search is based on a general cost function that can be adapted to the clinical objectives by means of parameters and weighting factors. The approach takes into account the constraints of the linear accelerator by discarding beam directions that are not permitted. A sensitivity analysis was carried out to determine appropriate parameters for different sized organs, and a prostate case was used to benchmark the approach. The algorithm was also applied to two clinical cases (brain and sinus) to test the benefits of the approach compared with manual angle selection. The time to perform a beam direction search was approximately 2 min for the coplanar and 12 min for the non-coplanar beam space. The angles obtained for the prostate case compared well with reports in the literature. For the brain case, the mean dose to the right and left optic nerves was reduced by 12% and 50%, respectively, whilst the target dose uniformity was improved. For the sinus case, the mean doses to the right and left parotid glands were reduced by 54% and 46%, respectively, to the right and left optic nerves by 37% and 62%, respectively, and to the optic chiasm by 39%, whilst the target dose uniformity was also improved. For the clinical cases the plans based on optimized beam directions were simpler and resulted in better sparing of critical structures compared with plans based on manual angle selection. The approach provides a practical alternative to elaborate and time consuming beam angle optimization schemes and is suitable for routine clinical usage.

Adenocarcinoma↗
PubMed2004

Verbal estimation of peak exertion intensity.

The objectives of this research were to investigate the accuracy and precision with which trained and untrained participants estimate the magnitude of forceful exertion and to evaluate the mathematical relationship between actual and estimated exertion. Three groups of participants estimated, as a percentage of maximum voluntary contraction (%MVC), the magnitude of submaximal exertion for 12 simulated tasks. In addition to the control group, one group was exposed to one physical benchmark (100% MVC) and another to three benchmarks (25%, 75%, and 100% MVC) prior to force estimation. Error (estimated minus actual) significantly decreased (p < .0001) from 14% MVC to 4% MVC with one benchmark and to -3% MVC with three benchmarks, as compared with the control group. Furthermore, the standard deviation decreased significantly (p < .0001 ) from the control group (16.6% MVC) to the one-benchmark group (13.8% MVC) to the three-benchmark group (11.6% MVC), indicating improved precision. Significant interaction effects were observed, but their impact on main effects was negligible. Also, linear, power, and logarithmic regression models described the relationship between perceived and actual exertion equally well (R2 = .64-.81). Applications of this research include improving the accuracy and precision of field-based psychophysical estimates of forceful exertion for epidemiological research and other field-based analyses.

Adult↗
PubMed1998

Performance indicators. All quiet on the front line.

Managers interviewed in hospital trusts, health authorities and regional offices believed performance indicators to be broadly helpful. But our study found evidence that the role of the current performance indicators is distinctly limited. The indicators are primarily used to highlight instances of exceptionally poor performance. Frontline staff, such as junior doctors, are often largely unaware of performance indicators. Performance indicators have led to misrepresentation and manipulation of data.

Attitude of Health Personnel↗
PubMed2002

The pursuit of excellence in medical record reviews.

The ongoing medical record review program at Sioux Valley Hospital USD Medical Center needed reenergizing: the results weren't taken seriously or producing the needed improvements. Using tools from the Joint Commission, an HIM professional and a performance improvement coordinator redesigned the process, making it more efficient and more effective. Here's how they did it.

Awards and Prizes↗
PubMedDate not supplied

A balanced scorecard approach for nursing report card development.

In this article we describe the process used to introduce and structure a nursing perspective as part of a balanced scorecard framework within a provincial hospital performance report. Results of a critical literature review and consultative process with key informants are outlined. Nurse-sensitive indicators emerged in the areas of system integration and change, clinical utilization and outcomes, patient satisfaction, and financial performance.

Benchmarking↗
PubMed2006

Award winner engages all sectors to improve quality.

MAPS leaders felt all stakeholders had to be involved to successfully engender safety culture change. Organizations with well-established electronic medical records cite significant benefits to performance improvement. Group focuses on identifying best practices around areas that reports have shown to be challenges.

Awards and Prizes↗
PubMed2006

Accuracy/diversity and ensemble MLP classifier design.

The difficulties of tuning parameters of multilayer perceptrons (MLP) classifiers are well known. In this paper, a measure is described that is capable of predicting the number of classifier training epochs for achieving optimal performance in an ensemble of MLP classifiers. The measure is computed between pairs of patterns on the training data and is based on a spectral representation of a Boolean function. This representation characterizes the mapping from classifier decisions to target label and allows accuracy and diversity to be incorporated within a single measure. Results on many benchmark problems, including the Olivetti Research Laboratory (ORL) face database demonstrate that the measure is well correlated with base-classifier test error, and may be used to predict the optimal number of training epochs. While correlation with ensemble test error is not quite as strong, it is shown in this paper that the measure may be used to predict number of epochs for optimal ensemble performance. Although the technique is only applicable to two-class problems, it is extended here to multiclass through output coding. For the output-coding technique, a random code matrix is shown to give better performance than one-per-class code, even when the base classifier is well-tuned.

Algorithms↗
PubMed2006

Quantifying the functional rehabilitation of injured football players.

OBJECTIVE: To determine whether quantified, auditable records of functional rehabilitation can be generated using subjective assessments of players' performance in fitness tests routinely used in professional football. METHOD: Ten sequential test elements grouped into three phases (fitness, ball and match skills, match pace football) were used to monitor players' functional recovery from injury. Physiotherapists subjectively assessed players' performance in each test element using a six point subjective rating scale. Satisfactory performance in each element of the assessment programme added 10% to the injured player's recovery score. Daily recovery scores for injured players were recorded against the time spent in functional rehabilitation. RESULTS: Rehabilitation data for 118 injuries sustained by 55 players over two seasons were recorded. The average time in functional rehabilitation depended on the time spent in pre-functional rehabilitation and the nature and location of injury. Benchmark functional rehabilitation curves (y = mln(x) + c) were developed for thigh (n = 15) and lower leg (n = 8) muscle strains and knee (n = 7) and ankle (n = 9) ligament sprains (R(2) = 0.95-0.98). CONCLUSIONS: A structured, quantified rehabilitation programme based on routine fitness and skills exercises and a graded subjective assessment of performance provides an auditable record of a player's functional recovery from a range of lower limb injuries and a transparent exit point from rehabilitation. The proposed method provides a permanent record of the functional rehabilitation of players' injuries and evidence based data to support management's return to play decisions.

Adult↗
PubMed2001

DIABCARE Quality Network in Europe--a model for quality management in chronic diseases.

The DIABCARE Q-Net project developed a complete and integrated information technology system to monitor diabetes care, according to the gold standards of the St Vincent Declaration Action Program. This is the first Telematic platform for standardized documentation on medical quality and evaluation across Europe, which will serve as a model for other chronic diseases. Quality development starts from the comparison of diabetes services, based on the key data on diabetes care in the basic information sheet. This is a 141 field form, which is to be completed once a year for each patient under the care of the diabetes team. The system performs an analysis of the local data and compares the data with peer teams by means of telecommunication of anonymous data. These data are collected regionally. At the next level these regional data are compared on a national basis across Europe using dedicated communication lines. National data can be compared transnationally by the use of the Internet and the DIABCARE benchmarking servers. These different lines are used according to the necessary security standards. Medical data are transferred via dedicated lines, aggregated data via the Internet. The architecture follows the open-platform concept in order to allow for heterogeneous technical environments. Already at the start of the project, the necessity for expanding the quality approach to telemedicine methodology was identified and included. For each level, specific programs are available to improve the performance of diabetes care delivery: DIABCARE data as client and DIABCARE server as regional and DIABCARE 'international server' as transnational server. Functioning pilots were established across all levels. The clients have been linked to the servers on a routine basis. According to the open architecture design, the various countries decided on different systems at the entry point: full system--Portugal; fax systems--Italy, Bavaria; implementation into doctor's office systems--Norway; paper forms and chip cards--France. This system can improve the local, regional and national diabetes care. Initiatives in several countries proved the feasibility of the system. The most extensive use, from Portugal, will be reported later in this paper. The exploitation of the DIABCARE Q-Net system will be performed with the DIABCARE International European Economic Interest Grouping as a co-ordinator and several commercial companies as contractors to market the products inside the system. The key project participants are: DIABCARE Office EURO, DIABCARE Portugal, DIABCARE France, DIABCARE Bavaria, DIABCARE UK, DIABCARE Netherlands, DIABCARE Norway, DIABCARE Italy, DIABCARE Sweden, DIABCARE Austria, DIABCARE Spain, GSF Research Centre for Health and Environment, FAST Research Institute for Applied Software Technology, Tromsø University Hospital, Stavanger Technical College, Technical University of Ilmenau, World Health Organisation (WHO), Regional Office for Europe.

Benchmarking↗
PubMed2005

Multicoefficient extrapolated density functional theory studies of pi...pi interactions: the benzene dimer.

We report tests of new (2005) and established (1999-2003) multilevel methods against essentially converged benchmark results for nonbonded interactions in benzene dimers. We found that the newly developed multicoefficient extrapolated density functional theory (DFT) methods (which combine DFT with correlated wave function methods) give better performance than multilevel methods such as G3SX, G3SX(MP3), and CBS-QB3 that are based purely on wave function theory (WFT); furthermore, they have a lower computational cost. We conclude that our empirical approach for combining WFT methods with DFT methods is a very efficient and effective way for describing not only covalent interactions (as shown previously) but also nonbonded interactions.

Benzene↗
PubMed2025

The impact of tokenizer selection in genomic language models.

MOTIVATION: Genomic language models have recently emerged as a new method to decode, interpret, and generate genetic sequences. Existing genomic language models have utilized various tokenization methods, including character tokenization, overlapping and nonoverlapping k-mer tokenization, and byte-pair encoding, a method widely used in natural language models. Genomic sequences differ from natural language because of their low character variability, complex and overlapping features, and inconsistent directionality. These features make subword tokenization in genomic language models significantly different from both traditional language models and protein language models. RESULTS: This study explores the impact of tokenization in genomic language models by evaluating their downstream performance on 44 classification fine-tuning tasks. We also perform a direct comparison of byte pair encoding and character tokenization in Mamba, a state-space model. Our results indicate that character tokenization outperforms subword tokenization methods on tasks that rely on nucleotide-level resolution, such as splice site prediction and promoter detection. While byte-pair tokenization had stronger performance on the SARS-CoV-2 variant classification task, we observed limited statistically significant differences between tokenization methods on the remaining downstream tasks. AVAILABILITY AND IMPLEMENTATION: Detailed results of all benchmarking experiments are available in https://github.com/leannmlindsey/DNAtokenization. Training datasets and pretrained models are available at https://huggingface.co/datasets/leannmlindsey. Datasets and processing scripts are available at doi: 10.5281/zenodo.16287401 and doi: 10.5281/zenodo.16287130.

Natural Language Processing↗
PubMed2025

OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis.

MOTIVATION: Structural variants (SVs) influence gene regulation, disease progression, and diagnostics, yet integrating SV calls across platforms remains difficult due to inconsistent annotations, limited merging flexibility, and fragmented workflows. Ambiguous breakend (BND) annotations, which comprise many variant calls, are often discarded or misclassified, hindering variant characterization. Existing tools lack advanced merging operations essential for precise identification of disease-specific or somatic variants across samples or patient groups. Additionally, current SV analysis pipelines require extensive manual intervention and complex parameter tuning, compromising reproducibility and scalability. Addressing these gaps is crucial for improving the accuracy, interpretability, and clinical utility of SV analyses. RESULTS: We developed OctopuSV and TentacleSV to address these long-standing challenges in SV analysis. OctopuSV features a specialized BND correction module that converts ambiguous BND annotations into canonical SV types, recovering important variants that are often overlooked by existing tools. Additionally, it provides advanced set operations (difference, complement, custom-defined) that enable sophisticated variant filtering without programming expertise, critical for identifying tumor-specific SVs or variants unique to specific sample groups. TentacleSV completes our solution by automating the entire SV analysis process from raw sequencing data to high-confidence callsets, ensuring consistency and reproducibility across projects. Benchmarking across short-read and long-read platforms showed superior F1 score, complete SV type consistency compared to existing tools. Our framework enables experimental biologists and clinical researchers to perform sophisticated analyses ranging from cancer subtype-specific SV identification to multi-sample comparative studies without requiring specialized programming skills. AVAILABILITY AND IMPLEMENTATION: All codes are available at https://github.com/ylab-hi/OctopuSV; https://github.com/ylab-hi/TentacleSV.

Software↗
PubMed2026

Atlas-level single-cell integration and clustering-free differential expression analysis with GEDI 2.0.

MOTIVATION: GEDI is a generative framework for multi-sample, multi-condition single-cell analysis that performs batch correction, latent representation learning, and clustering-free differential expression within a unified model. However, the original implementation suffered from prohibitive memory use and runtime, preventing its application to modern atlas-scale datasets. RESULTS: We present GEDI 2.0, a complete high-performance reimplementation featuring a standalone C++ computational core with pre-allocated workspaces, strict sparse-matrix preservation, optimized BLAS routines, and multi-threaded block-coordinate descent. Across extensive benchmarks spanning up to 500 000 cells and 10 000 features, GEDI 2.0 achieves 40%-63.6% mean reduction in peak memory, 2.98&#xd7; mean single-threaded speedups, and up to 11.5&#xd7; acceleration with parallel execution, while maintaining full numerical equivalence to the original method. These improvements enable GEDI 2.0 to analyze million-cell datasets, a scale not achievable with the legacy implementation. GEDI 2.0 provides R and Python interfaces and seamless interoperability with common single-cell workflows. AVAILABILITY AND IMPLEMENTATION: Source code, documentation, reproducible codebase, and tutorials are available at https://github.com/csglab/gedi2.

Single-Cell Analysis↗
PubMed2004

Bipartite pattern discovery by entropy minimization-based multiple local alignment.

Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel bipartite algorithm, bipartite pattern discovery (Bipad), which produces a mathematical model based on information maximization or Shannon's entropy minimization principle, for discovery of bipartite sequence patterns. Bipad is a C++ program that applies greedy methods to search the bipartite alignment space and examines the upstream or downstream regions of co-regulated genes, looking for cis-regulatory bipartite patterns. An input sequence file with zero or one site per locus is required, and the left and right motif widths and a range of possible gap lengths must be specified. Bipad can run in either single-block or bipartite pattern search modes, and it is capable of comprehensively searching all four orientations of half-site patterns. Simulation studies showed that the accuracy of this motif discovery algorithm depends on sample size and motif conservation level, but results were independent of background composition. Bipad performed equivalent with or better than other pattern search algorithms in correctly identifying Escherichia coli cyclic AMP receptor protein and Bacillus subtilis sigma factor binding site sequences based on experimentally defined benchmarks. Finally, a new bipartite information weight matrix for vitamin D3 receptor/retinoid X receptor alpha (VDR/RXRalpha) binding sites was derived that comprehensively models the natural variability inherent in these sequence elements.

Algorithms↗
PubMedDate not supplied

The impact of computer-assisted test interpretation on physician decision making: the case of electrocardiograms.

This research investigated the effect of computer-assisted test interpretation (CATI) on physicians' readings of electrocardiograms (ECGs). The authors used an experimental method based on direct observations of 22 cardiologists, each reading 80 ECGs, for a total of 1,760 (of which 1,745 were used in the study). There were 40 sets of clinically-matched pairs of ECGs, one with CATI and one without. Reading time was observed and interpretation accuracy was measured by criterion-referenced aggregate scoring. To control for potential biases, the findings were subjected to multivariate analyses using ordinary least-squares regressions. The impact of CATI on cardiologists' readings of ECGs is demonstrably beneficial: the main empirical conclusion of this study is that, compared with conventional interpretation, the use of computer-assisted interpretation of ECGs cuts physician time by an average of 28% and significantly improves the concordance of the physician's interpretation with the expert benchmark, without increasing the false-positive rate. Moreover, CATI is the most accurate and saves the most time when the ECGs have many unambiguous diagnoses. Given that computers alone cannot perform the task of cardiovascular diagnosis, and that cardiologists' ECG interpretations are greatly enhanced by ubiquitous CATI technology, it appears that the best approach is one that combines person and machine.

Adult↗