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Results for “Performance benchmarking”

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PubMed2004

A benchmark for Affymetrix GeneChip expression measures.

MOTIVATION: The defining feature of oligonucleotide expression arrays is the use of several probes to assay each targeted transcript. This is a bonanza for the statistical geneticist, who can create probeset summaries with specific characteristics. There are now several methods available for summarizing probe level data from the popular Affymetrix GeneChips, but it is difficult to identify the best method for a given inquiry. RESULTS: We have developed a graphical tool to evaluate summaries of Affymetrix probe level data. Plots and summary statistics offer a picture of how an expression measure performs in several important areas. This picture facilitates the comparison of competing expression measures and the selection of methods suitable for a specific investigation. The key is a benchmark data set consisting of a dilution study and a spike-in study. Because the truth is known for these data, we can identify statistical features of the data for which the expected outcome is known in advance. Those features highlighted in our suite of graphs are justified by questions of biological interest and motivated by the presence of appropriate data.

Algorithms↗

PubMed2002

Use of red blood cell transfusions in surgery.

BACKGROUND: Limited blood supplies necessitate the rational use of blood products. The aim of the present study was to provide a basis for audits of red cell usage in surgery by benchmarking common practice. Application of the data to the construction of a maximum surgical blood order schedule may be relevant for centres that perform a serological crossmatch or who collect autologous units. METHODS: Data on surgical procedures identified by Commonwealth Medical Benefits Schedule item numbers, were collected retrospectively from theatre and blood bank records at the Royal Melbourne and Melbourne Private hospitals from May 1997 to April 1998. The percentage of procedures for which red cells were transfused, and the mean, median and range of units transfused for procedures with >/= 30% transfusion likelihood were identified. RESULTS: Over 12 months, 266 surgical procedure codes were itemized >/= 10 times each, contributing 12 300 data entries. Only 38 procedures demonstrated an incidence of transfusion of at least 30%. Most frequently transfused procedures included spinal fusion, total hip replacement, mandible/maxilla resection, prostatectomy and bladder excision. CONCLUSION: The number of common surgical procedures in which there is a 30% or greater likelihood that red cell transfusions will be given is limited. This benchmarking of common red cell usage is a first step in the process of determination of transfusion appropriateness.

Australia↗

PubMed2003

Benchmarking beam alignment for a clinical helical tomotherapy device.

A clinical helical tomotherapy treatment machine has been installed at the University of Wisconsin Comprehensive Cancer Center. Beam alignment has been finalized and accepted by UW staff. Helical tomotherapy will soon be clinically available to other sites. Clinical physicists who expect to work with this machine will need to be familiar with its unique dosimetric characteristics, and those related to the geometrical beam configuration and its verification are described here. A series of alignment tests and the results are presented. Helical tomotherapy utilizes an array of post-patient xenon-filled megavoltage radiation detectors. These detectors have proved capable of performing some alignment verification tests. That is particularly advantageous because those tests can then be automated and easily performed on an ongoing basis.

Benchmarking↗

PubMed2004

Non-empirical calculations of NMR indirect carbon-carbon coupling constants. Part 9--Bicyclobutane-containing polycycloalkanes.

13C--(13)C spin-spin coupling constants characterizing the bicyclobutane moiety of seven well-known bicyclobutane-containing polycycloalkanes were calculated at the SOPPA level. Benchmark calculations on tricyclopentane and octabisvalene revealed an appropriate level of theory and sufficient quality of basis sets used to perform geometry searches and to calculate spin-spin coupling constants. Several experimental uncertainties were resolved and a number of interesting couplings were predicted. The most interesting trend observed in this series of polycycloalkanes is the marked increase (decrease in absolute value) of J(C,C) between bridgehead carbons with increase in the puckering angle of the bicyclobutane moiety. This predicts almost zero coupling between bridgehead carbons of tricyclopentane and explains the positive J(C,C) in tetrahedrane in contrast to the negative bridgehead-bridgehead J(C,C) in bicyclobutane.

Journal Article↗

PubMed2006

A genetic algorithm design for microcalcification detection and classification in digital mammograms.

In this paper, we propose a genetic algorithm design to automatically classify and detect micocalcification clusters in digital mammograms. The proposed GA technique is characterised by transforming input images into a feature domain, where each pixel is represented by its mean and standard deviation inside a surrounding window of size 9 x 9 pixel. In the feature domain, chromosomes are constructed to populate the initial generation and further features are extracted to enable the proposed GA to search for optimised classification and detection of microcalcification clusters via regions of 128 x 128 pixels. Extensive experiments show that the proposed GA design is able to achieve high performances in microcalcification classification and detection, which are measured by ROC curves, sensitivity against specificity, areas under ROC curves and benchmarked by existing representative techniques.

Algorithms↗

PubMed2005

Online optimization of fuzzy-PID control of a thermal process.

A constrained optimization of a simple fuzzy-PID (PID-proportional integral derivative) system is designed for the online improvement of PID control performance during productive control runs. The cost function design yields a desirable balance between rise time, setpoint overshoot, and settling time to the setpoint. The constraints determined by simulation yield control performance no worse than the existing control performance during online optimization. The optimized fuzzy-PID system is compared to a similarly optimized PID controller and a benchmark model predictive controller.

Journal Article↗

PubMed2003

New local potential useful for genome annotation and 3D modeling.

A new potential energy function representing the conformational preferences of sequentially local regions of a protein backbone is presented. This potential is derived from secondary structure probabilities such as those produced by neural network-based prediction methods. The potential is applied to the problem of remote homolog identification, in combination with a distance-dependent inter-residue potential and position-based scoring matrices. This fold recognition jury is implemented in a Java application called JThread. These methods are benchmarked on several test sets, including one released entirely after development and parameterization of JThread. In benchmark tests to identify known folds structurally similar to (but not identical with) the native structure of a sequence, JThread performs significantly better than PSI-BLAST, with 10% more structures identified correctly as the most likely structural match in a fold library, and 20% more structures correctly narrowed down to a set of five possible candidates. JThread also improves the average sequence alignment accuracy significantly, from 53% to 62% of residues aligned correctly. Reliable fold assignments and alignments are identified, making the method useful for genome annotation. JThread is applied to predicted open reading frames (ORFs) from the genomes of Mycoplasma genitalium and Drosophila melanogaster, identifying 20 new structural annotations in the former and 801 in the latter.

Animals↗

PubMed2003

Process of care and preliminary outcome in limited-stage small-cell lung cancer: results of the 1995-1997 patterns of care study in Japan.

PURPOSE: To evaluate the practice process using the national average (NA); to compare differences in the process of care by age group; and to provide a preliminary outcome data for limited-stage small-cell lung cancer in Japan. METHODS AND MATERIALS: The Patterns of Care Study conducted a nationwide survey of the care process for Stage I-III small-cell lung cancer in Japan. Patients were divided into three age groups: <65 years (younger group, n = 73); between 65 and 74 years (intermediate group, n = 81); and >or=75 years (elderly group, n = 20). RESULTS: The NA for the total dose was 49.0 Gy, and for use of photon energy >or=6 MV, chemotherapy, and prophylactic cranial irradiation was 77.3%, 93.2%, and 1.69%, respectively. Age stratification had no impact on the variables of radiotherapy (RT) such as total dose and field size. Only 37% of patients received chemotherapy and thoracic RT concurrently. The proportion of patients who received chemotherapy and RT concurrently was 44%, 27%, and 25% of the younger, intermediate, and elderly groups, respectively (p = 0.029). Etoposide and cisplatin were less frequently used in the elderly group (>or=75 years old). Overall survival at 3 years for the entire group was 26%. The 3-year survival rate was 30% in the younger group, 28% in the intermediate group, and 9% in the elderly group. Variables found to have a significant impact on survival by multivariate analysis were the use of chemotherapy (p = 0.030), age (p = 0.032), and T stage (p = 0.042). CONCLUSION: Calculated NAs showed that the results of clinical study had favorably penetrated into the practice process in Japan. The results demonstrated that patient age significantly influenced the process of chemotherapy such as the use of etoposide and cisplatin for limited-stage small-cell lung cancer in Japan. More concurrent chemotherapy and thoracic RT and the application of prophylactic cranial irradiation for complete responders need to be investigated in the future.

Age Factors↗

PubMed2026

Transfer Learning across Material Properties Using Center-Environment Features: From Energetics to Mechanical Properties in Multicomponent Mo Alloys.

Transfer learning (TL) provides a viable approach to mitigate data scarcity in materials informatics. While conventional TL focuses on predicting identical properties across different systems, this work demonstrates a cross-property extension of TL from energy to mechanical properties via end-to-end model weight pre-training and fine-tuning: knowledge learned from predicting substitution energies is transferred to predict distinctly different mechanical properties, substantially improving computational efficiency given the typically higher cost of acquiring target-domain data. To accelerate computational alloy design, machine learning models using center-environment (CE) features were first developed to predict substitution energies of alloying elements in molybdenum (Mo)-based alloys. The Random Forest models achieved the optimal performance and transferability-R2 = 0.97, 〈MAE〉 = 0.11 eV, and 〈RMSE〉 = 0.16 eV-against the density functional theory (DFT) benchmark. The model dependency of feature selection and importance analysis was discussed. The transferability of the energy models was validated on unknown systems with new elements. Subsequently, the energy models were fine-tuned using limited mechanical property data to construct energy-to-property (E2P) TL models capable of predicting elastic properties, including bulk modulus, Young's modulus, shear modulus, and elastic constants, achieving an improved accuracy over the non-transferred ML by ∼10-30%, with its transferability verified by additional DFT calculations. This cross-property E2P transfer learning framework opens a new avenue for accelerating computational materials discovery and may be extended to other multiproperty predictions governed by similar physical principles.

center-environment feature↗

PubMedDate not supplied

FLUFF-BALL, a template-based grid-independent superposition and QSAR technique: validation using a benchmark steroid data set.

The Flexible Ligand Unified Force Field (FLUFF) is a molecular mechanistic superposition algorithm utilizing a template structure, on top of which the ligand(s) are superimposed. FLUFF enables a flexible semiautomatic superimposition in which the ligand and the template are allowed to seek the best common conformation, which can then be used to predict the biological activity by Boundless Adaptive Localized Ligand (BALL). In BALL, the similarity of the electrostatic and van der Waals volumes of the template and ligand is evaluated using the template-based coordinate system which makes the FLUFF-BALL invariant as to the rotations and translations of the global coordinate system. When tested using the CBG (corticosteroid binding globulin) affinities of 31 benchmark steroids, the FLUFF-BALL technique produced results comparable to standard 3D-QSAR methods. Supplementary test calculations were performed with five additional data sets. Due to its high level of automation and high throughput, the FLUFF-BALL is highly suitable for use in drug design and in scanning of large molecular libraries.

Algorithms↗

PubMed2005

Ab initio study on the spectroscopy of CuCl2. II. Benchmark calculations on the X2Pi g-C2Deltag and X2Pi g-D2Deltag transitions.

The X (2)Pi(g)-C (2)Delta(g) and X (2)Pi(g)-D (2)Delta(g) transitions on CuCl(2) have been studied using the most sophisticated nondynamic and dynamic electronic correlation treatments. We report here ab initio benchmark calculations using especially developed basis sets to study, at the complete active space self-consistent field plus second-order Møller-Plesset algorithm (CASSCF+CASPT2) and CASSCF+ACPF levels, the transition energies as well as the corresponding equilibrium geometries (ACPF-averaged coupled pair functional). The spin-orbit (SO) effects of both atoms were included in a second step through the effective Hamiltonian formalism, using the calibrated SO effective potentials developed by the Stuttgart group. Without SO at the CASSCF+ACPF level, the vertical excitation energy for the (2)Delta(g) state is 6711 cm(-1) and the symmetric stretching equilibrium Cu-Cl distance is 4.04 a.u. The inclusion of the SO effects leads to a pure (2)Delta(g) Omega=5/2C state and a Omega=3/2 (0.7% (2)Pi(g),99.3% (2)Delta(g))D state. The calculated transition energies for the C and D states are 6340 and 8020 cm(-1), in good agreement with the spin-orbit splitting recent values from gas-phase and rare-gas matrix isolation laser induced fluorescence experiments. The present benchmark results show, as was recently done for the X (2)Pi(g)-(2)Sigma(g) transition, the rather poor performance of all the density functional theory-based descriptions for the (2)Delta(g) state, which largely overestimate its T(e), systematically placing it around 19 000 cm(-1). The CASSCF+CASPT2 method also overestimates, by around 50%, the X (2)Pi(g)-(2)Delta(g) transition energy, showing that only large variational calculations can produce reliable spectroscopic results for this kind of complex systems where delicate electronic correlation effects have to be carefully dealt with.

Journal Article↗

PubMed2025

Accurate prediction of toxicity peptide and its function using multi-view tensor learning and latent semantic learning framework.

MOTIVATION: Therapeutic peptide is an important ingredient in the treatment of various diseases and drug discovery. The toxicity of peptides is one of the major challenges in peptide drug therapy. With the abundance of therapeutic peptides generated in the post-genomics era, it is a challenge to promptly identify toxicity peptides using computational methods. Although several efforts have been made, few algorithms are designed to identify whether a query peptide exhibits toxicity. Considering the varied levels of biological activities, the toxicity peptides should be further classified into multi-functional peptides. RESULTS: This study introduces a two-level predictor, ToxPre-2L, developed using the multi-view tensor learning and latent semantic learning framework. The proposed method utilized multi-label learning with feature induced labels to avoid the redundancy of information from each view. Then the multi-view tensor learning was employed to establish the latent semantic information among different views, while low-rank constraint learning was leveraged to exploit the correlation information among multi-labels. Finally, we constructed an updated toxicity peptide benchmark dataset to assess the effectiveness of the proposed method. Experimental results demonstrated that ToxPre-2L achieves a better performance than alternative computational methods in the prediction of toxicity peptides and their multi-functional types. AVAILABILITY AND IMPLEMENTATION: The source code and data of ToxPre-2L can be accessed at http://bliulab.net/ToxPre-2L.

Peptides↗

PubMed2026

Local ancestry inference identifies robust evidence of selection in Neolithic Europe.

During the European Neolithic, migrating Anatolian farmers admixed with local hunter-gatherers, coinciding with major shifts in diet, environment, and lifestyle that imposed strong selective pressures. Local ancestry inference is widely used to detect selection following admixture, but most methods were developed and validated on present-day populations. Their performance in ancient DNA - where reference panels are smaller, data are sparser, and admixture is more ancient - remains unresolved. We benchmark eight local ancestry inference methods on 176 imputed Neolithic genomes. While individual-level ancestry estimates are highly correlated across methods, inferred tract lengths and admixture time estimates vary by an order of magnitude. Overall, we recommend Gnomix or RFMix for general use. We also investigated our ability to detect natural selection using LAI. Integrating results across methods and replicating across methods and in two independent datasets (n=378 and 1,121) we identify a robust ancestry deviation at FADS1/2, consistent with adaptation on metabolism. We also identify IRAK4 (innate immunity) as a candidate locus, but with less consistent signal across methods. Finally, we replicate previous reports of excess hunter-gatherer ancestry at the HLA, but these results are inconsistent across methods and suggest that they may be affected by bias in local ancestry inference. Our findings demonstrate that while local ancestry inference recovers biologically meaningful signals in ancient genomes, results can be sensitive to the methods used for inference, particularly in complex regions like the HLA. Method choice critically influences inferred ancestry patterns and selection signals, underscoring the importance of multi-method validation.

Journal Article↗

PubMed2002

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.

Computer Simulation↗

PubMed2002

Improving Pap test turnaround time using external benchmark data and engineering process improvement tools.

Turnaround time for Papanicolaou (Pap) tests became an important service quality issue at our institution. We studied Pap test turnaround time using engineering process improvement tools and benchmarked turnaround time against data published as a College of American Pathologists Q-Probes study. An IDEF3 process map revealed the complexity of the Pap test process and the opportunities for process improvement. We used these data and the action-research method to initiate changes in cytopathology laboratory operations with the goal of reducing turnaround time. Before intervention, mean Pap test turnaround time was highly variable; during a 6-month period, monthly means ranged from 2.5 to 10.8 days. A cycle time study conducted over a 2-week period validated these data. After system improvements were implemented, the monthly mean turnaround time decreased and became more consistent, with 11 of 12 months having a mean turnaround time of 3 days or less (range, 1.5-3.9 days). Our study illustrates the value of publishing Q-Probes data for use as external benchmarks and the benefits of using tools from other disciplines to improve laboratory processes.

Benchmarking↗

PubMed2003

Surgical site infections in patients undergoing major operations in a university hospital: using standardized infection ratio as a benchmarking tool.

BACKGROUND: Because patterns of infection acquired in patients undergoing operation are ever changing, it is an essential part of nosocomial infection surveillance programs to periodically document the epidemiologic features of infection in these patients. This study was conducted with the primary intention of describing the incidence and risk factors of the surgical site infection (SSI). METHODS: We performed a prospective study in patients undergoing certain major operations at a 750-bed university hospital in Thailand. The National Nosocomial Infection Surveillance (NNIS) system method and criteria were used for identifying and diagnosing infection. The infection rates were benchmarked with the NNIS report by means of indirect standardization and reported in terms of standardized infection ratio. Risk factors for SSI were evaluated using the multiple logistic regression model. RESULTS: From September 1998 to March 2000, the study included 4193 patients with 4437 major operations. The study identified 192 SSIs, 76 urinary catheter-related urinary tract infections, 26 central line-related bloodstream infections, and 39 instances of ventilator-associated pneumonia (VAP), yielding an infection rate of 4.3 SSIs/100 operations, 11.0 catheter-related urinary tract infections/1000 urinary catheter-days, 6.1 central line-related bloodstream infections/1000 central line-days, and 11.0 VAPs/1000 ventilator-days. When compared with data from NNIS, the standardized infection ratio of SSI, catheter-related urinary tract infection, central line-related bloodstream infection, and VAP were 2.3, 2.1, 1.1, and 0.8, respectively. The factors that significantly associated with SSI were duration of operation in minutes, American Society of Anesthesiologists (ASA) class, and degree of wound contamination. CONCLUSION: All of the infection rates identified, except VAP, were higher than the average NNIS rates. The risk factors for SSI were prolonged duration of operation, poor physical status according to ASA classification, and higher degree of wound contamination.

Adolescent↗

PubMed2006

Partitioning protein structures into domains: why is it so difficult?

This analysis takes an in-depth look into the difficulties encountered by automatic methods for domain decomposition from three-dimensional structure. The analysis involves a multi-faceted set of criteria including the integrity of secondary structure elements, the tendency toward fragmentation of domains, domain boundary consistency and topology. The strength of the analysis comes from the use of a new comprehensive benchmark dataset, which is based on consensus among experts (CATH, SCOP and AUTHORS of the 3D structures) and covers 30 distinct architectures and 211 distinct topologies as defined by CATH. Furthermore, over 66% of the structures are multi-domain proteins; each domain combination occurring once per dataset. The performance of four automatic domain assignment methods, DomainParser, NCBI, PDP and PUU, is carefully analyzed using this broad spectrum of topology combinations and knowledge of rules and assumptions built into each algorithm. We conclude that it is practically impossible for an automatic method to achieve the level of performance of human experts. However, we propose specific improvements to automatic methods as well as broadening the concept of a structural domain. Such work is prerequisite for establishing improved approaches to domain recognition. (The benchmark dataset is available from http://pdomains.sdsc.edu).

Computational Biology↗

PubMed2006

Application of the quality index methodology for dosimetric verification of build-up effect beyond air-tissue interface in treatment planning system algorithms.

We have designed a simple benchmark test for the user of a treatment planning system to check the calculation algorithm's ability to model the build up effect beyond an air/tissue interface. The expected result is expressed as an inhomogeneity correction factor CF derived from measurements and from Monte Carlo calculations for a full range of photon beam qualities. The linear regression lines obtained from plotting CF as a function of beam quality index form the basis for a quantitative check of the algorithm performance.

Air↗