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PubMed2004

Automatic kernel regression modelling using combined leave-one-out test score and regularised orthogonal least squares.

This paper introduces an automatic robust nonlinear identification algorithm using the leave-one-out test score also known as the PRESS (Predicted REsidual Sums of Squares) statistic and regularised orthogonal least squares. The proposed algorithm aims to achieve maximised model robustness via two effective and complementary approaches, parameter regularisation via ridge regression and model optimal generalisation structure selection. The major contributions are to derive the PRESS error in a regularised orthogonal weight model, develop an efficient recursive computation formula for PRESS errors in the regularised orthogonal least squares forward regression framework and hence construct a model with a good generalisation property. Based on the properties of the PRESS statistic the proposed algorithm can achieve a fully automated model construction procedure without resort to any other validation data set for model evaluation.

Algorithms↗

PubMed2026

PGS-GS: a framework integrating polygenic scores and genomic selection in animal breeding.

Genomic prediction has become a central paradigm in biology, enabling quantitative inference of genetic contributions to complex traits across humans, animals, and plants. Although genomic research in human genetics and animal breeding shares a highly homologous methodological foundation, significant barriers persist in their analytical paradigms and application scenarios. This study aims to promote cross-disciplinary integration by introducing human-derived polygenic scores (PGS) algorithms into animal genomic selection (GS) and proposing a PGS-GS framework with a preliminary weighting-based implementation. We systematically benchmarked the predictive performance and computational efficiency of 20 algorithms, including classical linear models, machine learning, PGS, and PGS-GS using both array and whole-genome sequencing (WGS) data across four major agricultural species: beef cattle, sheep, pigs, and chickens. Our results demonstrate that PGS and PGS-GS algorithms achieve predictive accuracy competitive with genomic best linear unbiased prediction (GBLUP) while offering markedly higher computational efficiency. Moreover, incorporating PGS-derived prior information into weighted linear and non-linear models outperformed conventional weighted GBLUP. The results provide empirical evidence to inform algorithm selection and highlight the potential of integrating human-derived PGS methodologies into animal genomic prediction frameworks.

Animals↗

PubMed2004

Retrieval of images from artistic repositories using a decision fusion framework.

The large volumes of artistic visual data available to museums, art galleries, and online collections motivate the need for effective means to retrieve relevant information from such repositories. This paper proposes a decision making framework for content-based retrieval of art images based on a combination of low-level features. Traditionally, the similarity among two images has been calculated as a weighted distance between two feature vectors. This approach, however, may not be mathematically and computationally appropriate and does not provide enough flexibility in modeling user queries. This paper proposes a framework that generalizes a wide set of previous approaches to similarity calculation including the weighted distance approach. In this framework, image similarities are obtained through a decision making process based on low-level feature distances using fuzzy theory. The analysis and results of this paper indicate that the aggregation technique presented here provides an effective, general, and flexible tool for similarity calculation based on the combination of individual descriptors and features.

Algorithms↗

PubMed2026

TreeFlow: Probabilistic Modelling and Automatic Differentiation for Phylogenetics.

Probabilistic modelling frameworks are powerful tools for statistical modelling and inference. They are not immediately generalizable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object. TreeFlow is a software library for probabilistic modelling and automatic differentiation with phylogenetic trees. It embeds phylogenetic trees in the TensorFlow Probability framework, and implements inference algorithms for phylogenetic models given a fixed tree topology. We demonstrate how TreeFlow can be used to quickly implement and assess new models. We also show that it provides reasonable performance for gradient-based inference algorithms compared to specialized computational libraries for phylogenetics.

Bayesian inference↗

PubMed2026

SpacerScope: binary-vectorized, genome-wide off-target profiling for RNA-guided nucleases without prior candidate-site bias.

The precision of CRISPR/Cas systems is fundamental to their application in plant and animal biotechnology. However, comprehensive sequence-based off-target candidate discovery remains a computational bottleneck, particularly in large and complex genomes. Here we developed SpacerScope, an off-target candidate discovery framework that enables unbiased, genome-wide discovery by leveraging binary vectorization, bitwise filtering, and right-end-anchored alignment. Benchmarking against human CIRCLE-seq data demonstrated that SpacerScope recovered 100% of validated off-target sites (6142/6142), matching the sensitivity of exhaustive algorithms. Crucially, SpacerScope achieved this maximum candidate recovery while substantially reducing computational overhead. In large-genome evaluations, SpacerScope maintained low peak memory usage of 2.20 GiB and achieved substantial runtime improvements over indel-aware comparator tools, including more than 50-fold speedup relative to Cas-OFFinder 3 (544 s versus 29 185 s). Furthermore, comparative analyses in polyploid species, such as the octoploid strawberry, revealed that SpacerScope identified larger sequence-compatible candidate burdens than standard web-based design platforms. Our results establish SpacerScope as a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes. The source code and program was publicly available at https://github.com/charlesqu666/SpacerScope. Short Abstract CRISPR/Cas sequence-based off-target candidate discovery remains computationally challenging in large, repetitive, and polyploid genomes. Existing tools either miss indel-containing candidate sites or incur prohibitive runtime and memory costs. We developed SpacerScope, a binary-vectorized framework that enables unbiased, genome-wide off-target candidate discovery without pre-selected candidate sites. By integrating bitwise filtering with right-end-anchored alignment, SpacerScope recovered 100% of validated off-target sites in human CIRCLE-seq data while using only 2.20 GiB of memory and achieving more than 10-fold speedup over indel-aware alternatives. Evaluation in plant genomes, including rice and octoploid strawberry, further demonstrated SpacerScope's capacity to identify larger sequence-compatible candidate burdens overlooked by standard tools. SpacerScope thus provides a high-speed framework for sequence-based genome-wide off-target candidate discovery across diverse and highly repetitive genomic landscapes, supporting downstream prioritization.

CRISPR-Cas Systems↗

PubMed1998

The role of the primary visual cortex in higher level vision.

In the classical feed-forward, modular view of visual processing, the primary visual cortex (area V1) is a module that serves to extract local features such as edges and bars. Representation and recognition of objects are thought to be functions of higher extrastriate cortical areas. This paper presents neurophysiological data that show the later part of V1 neurons' responses reflecting higher order perceptual computations related to Ullman's (Cognition 1984; 18:97-159) visual routines and Marr's (Vision NJ: Freeman 1982) full primal sketch, 2 1/2D sketch and 3D model. Based on theoretical reasoning and the experimental evidence, we propose a possible reinterpretation of the functional role of V1. In this framework, because of V1 neurons' precise encoding of orientation and spatial information, higher level perceptual computations and representations that involve high resolution details, fine geometry and spatial precision would necessarily involve V1 and be reflected in the later part of its neurons' activities.

Action Potentials↗

PubMed1990

Structure of donor side components in photosystem II predicted by computer modelling.

Thirty-one and eleven sequences for the photosystem II reaction centre proteins D1 and D2 respectively, were compared to identify conserved single amino acid residues and regions in the sequences. Both proteins are highly conserved. One important difference is that the lumenal parts of the D1 protein are more conserved than the corresponding parts in the D2 protein. The three-dimensional structures around the electron donors tyrosineZ and tyrosineD on the oxidizing side of photosystem II have been predicted by computer modelling using the photosynthetic reaction centre from purple bacteria as a framework. In the model the tyrosines occupy two cavities close to the lumenal surface of the membrane. They are symmetrically arranged around the primary donor P680 and the distances between the centre of the tyrosines and the closest Mg ion in P680 are around 14 A. Both tyrosineZ and tyrosineD are suggested to form a hydrogen bond with histidine 190 from the loop connecting helices C and D in the D1 and D2 proteins, respectively. The Mn cluster in the oxygen evolving complex has been localized by using known and estimated distances from the tyrosine radicals. It is suggested that a binding region for the Mn cluster is constituted by the lumenal ends of helices A and B and the loop connecting them in the D1 protein. This part of the D1 protein contains a large number of strictly conserved carboxylic acid residues and histidines which could participate in the Mn binding. There is little probability that the Mn cluster binds on the lumenal surface of the D2 protein.

Amino Acid Sequence↗

PubMed1998

Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses.

Quaternary structure polymorphism found in quasiequivalent virus capsids provides a static framework for studying the dynamics of protein interactions. The same protein subunits are found in different structural environments within these particles, and in some cases, the molecular switching required for the polymorphic quaternary interactions is obvious from high-resolution crystallographic studies. Employing atomic resolution structures, molecular mechanics, and continuum electrostatic methods, we have computed association energies for unique subunit interfaces of three icosahedral viruses, black beetle virus, southern bean virus, and human rhinovirus 14. To quantify the chemical determinants of quasiequivalence, the energetic contributions of individual residues forming quasiequivalent interfaces were calculated and compared. The potential significance of the differences in stabilities at quasiequivalent interfaces was then explored with the combinatorial assembly approach. The analysis shows that the unique association energies computed for each virus serve as a sensitive basis set that may determine distinct intermediates and pathways of virus capsid assembly. The pathways for the quasiequivalent viruses displayed isoenergetic oligomers at specific points, suggesting that these may determine the quaternary structure polymorphism required for the assembly of a quasiequivalent particle.

Animals↗

PubMed1999

Treatment planning for brachytherapy: an integer programming model, two computational approaches and experiments with permanent prostate implant planning.

An integer linear programming model is proposed as a framework for optimizing seed placement and dose distribution in brachytherapy treatment planning. The basic model involves using 0/1 indicator variables to describe the placement or non-placement of seeds in a prespecified three-dimensional grid of potential locations. The dose delivered to each point in a discretized representation of the diseased organ and neighbouring healthy tissue can then be modelled as a linear combination of the indicator variables. A system of linear constraints is imposed to attempt to keep the dose level at each point to within specified target bounds. Since it is physically impossible to satisfy all constraints simultaneously, each constraint uses a variable to either record when the target dose level is achieved, or to record the deviation from the desired level. These additional variables are embedded into an objective function to be optimized. Variations on this model are discussed and two computational approaches--a branch-and-bound algorithm and a genetic algorithm--for finding 'optimal' seed placements are described. Results of computational experiments on a collection of prostate cancer cases are reported. The results indicate that both optimization algorithms are capable of producing good solutions within 5 to 15 min, and that small variations in model parameters can have a measurable effect on the dose distribution of the resulting plans.

Algorithms↗

PubMed1987

Pulsed-field electrophoresis: application of a computer model to the separation of large DNA molecules.

The biased reptation theory has been applied to the pulsed-field electrophoresis of DNA in agarose gels. A computer simulation of the theoretical model that calculates the mobility of large DNA molecules as a function of agarose pore size, DNA chain properties, and electric field conditions has been used to generate mobility curves for DNA molecules in the size range of the larger yeast chromosomes. Pulsed-field electrophoresis experiments resulting in the establishment of an electrophoretic karyotype for yeast, where the mobility of the DNA fragments is a monotonic function of molecular size for the entire size range that is resolved (200-2200 kilobase pairs), has been compared to the theoretical mobility curves generated by the computer model. The various physical mechanisms and experimental conditions responsible for band inversion and improved electrophoretic separation are identified and discussed in the framework of the model.

Chromosomes↗

PubMed2000

Supramolecular steric effects as the means of making reactive carbon radicals persistent. Quantitative characterization of the external surface of MFI zeolites through a persistent radical probe and a langmuir adsorption isotherm

The photochemistry of tetraphenylacetone (1) adsorbed on the external surface of a MFI zeolite (the sodium form of LZ-105) has been investigated in combination with computational chemistry, surface area measurements, EPR analysis, and classical adsorption isotherms. All of the methods are consistent with a supramolecular structural model in which 1 is first adsorbed strongly through intercalation of a single benzene ring into a hole on the LZ-105 external surface (site I) followed by a weaker binding to the external framework between the holes (site II) until a monolayer of 1 is formed. From both computational and surface area measurements, it is estimated that the site I holes on the external surface will be filled at ca. 0.3-0.5 wt %/wt loading of 1/LZ-105, which corresponds to 6.5 x 10(18) (ca. 10(-)(5) mol) of holes or molecules of 1 adsorbed in holes per gram of zeolite. The supramolecular composition of ca. 0.3-0.5% of 1 on LZ-105 characterizes a "break point" for the photochemistry and the EPR measurements, since it represents the value for saturation of the site I holes with 1. These conclusions are supported quantitatively by experimental isotherms of the adsorption of 1 on LZ-105. Photolysis of 1 intercalated in the site I holes causes fragmentation into two isomeric supramolecular diphenylmethyl (DPM) radicals, one (DMP)(in) which is adsorbed into the internal surface and becomes strongly persistent (half-life of many weeks) and the other (DMP)(ex) which diffuses on the external surface and rapidly dimerizes (less than a few minutes) to produce the radical-radical combination product tetraphenylethane (2). Photolysis of 1 adsorbed on the solid external surface produces two supramolecularly equivalent DPM radicals (DMP)(ex) that diffuse on the external surface and rapidly dimerize to produce 2, and do not produce persistent DPM radicals.

Journal Article↗

PubMed2005

Stochastic inverse consistency in medical image registration.

An essential goal in medical image registration is, the forward and reverse mapping matrices should be inverse to each other, i.e., inverse consistency. Conventional approaches enforce consistency in deterministic fashions, through incorporation of sub-objective cost function to impose source-destination symmetric property during the registration process. Assuming that the initial forward and reverse matching matrices have been computed and used as the inputs to our system, this paper presents a stochastic framework which yields perfect inverse consistency with the simultaneous considerations of the errors underneath the registration matrices and the imperfectness of the consistent constraint. An iterative generalized total least square (GTLS) strategy has been developed such that the inverse consistency is optimally imposed.

Algorithms↗

PubMed2026

Failure modes and effects analysis for clinical implementation of online adaptive radiotherapy: A systematic review.

BACKGROUND: The accuracy of radiotherapy is limited by anatomical variations occurring over time scales ranging from sub-seconds to days. Online Adaptive Radiotherapy (OART) addresses this by enabling daily plan adaptation based on real-time imaging. While OART offers improved dose conformity, its dynamic, time-constrained workflow introduces novel failure modes that challenge traditional quality assurance protocols. PURPOSE: This study aims to synthesize the existing literature on Failure Modes and Effects Analysis (FMEA) for OART to systematically catalog risks and identify mitigation strategies. METHODS: A systematic literature search was conducted to identify studies applying FMEA to OART workflows. Eleven studies were included, covering MR-guided (ViewRay MRIdian, Elekta Unity), CBCT-guided (Varian Ethos), and MR-enhanced C-arm linac systems. To address heterogeneity in risk scoring methodologies (e.g., TG-100 10-point scales vs. 5-point rankings), extracted failure modes were harmonized into a standardized three-tier risk classification system (Class I: Low, Class II: Intermediate, Class III: High). RESULTS: A total of 300 unique failure modes were identified, with 49.6 percent classified as high-risk (Class III). Analysis revealed that the majority of high-risk failures were concentrated in the online treatment delivery phase, specifically within human-computer interactions and anatomical contouring steps. CONCLUSIONS: This study supports the development of tailored, robust QA frameworks that prioritize human factors and process consistency to guide safe implementation in diverse clinical settings.

Humans↗

PubMed2005

Power and robustness of linkage tests for quantitative traits in general pedigrees.

There are numerous statistical methods for quantitative trait linkage analysis in human studies. An ideal such method would have high power to detect genetic loci contributing to the trait, would be robust to non-normality in the phenotype distribution, would be appropriate for general pedigrees, would allow the incorporation of environmental covariates, and would be appropriate in the presence of selective sampling. We recently described a general framework for quantitative trait linkage analysis, based on generalized estimating equations, for which many current methods are special cases. This procedure is appropriate for general pedigrees and easily accommodates environmental covariates. In this report, we use computer simulations to investigate the power and robustness of a variety of linkage test statistics built upon our general framework. We also propose two novel test statistics that take account of higher moments of the phenotype distribution, in order to accommodate non-normality. These new linkage tests are shown to have high power and to be robust to non-normality. While we have not yet examined the performance of our procedures in the context of selective sampling via computer simulations, the proposed tests satisfy all of the other qualities of an ideal quantitative trait linkage analysis method.

Algorithms↗

PubMedDate not supplied

Sampling framework for accurate curvature estimation in discrete surfaces.

Accurate curvature estimation in discrete surfaces is an important problem with numerous applications. Curvature is an indicator of ridges and can be used in applications such as shape analysis and recognition, object segmentation, adaptive smoothing, anisotropic fairing of irregular meshes, and anisotropic texture mapping. In this paper, a new framework is proposed for accurate curvature estimation in discrete surfaces. The proposed framework is based on a local directional curve sampling of the surface where the sampling frequency can be controlled. This local model has a large number of degrees of freedoms compared with known techniques and, so, can better represent the local geometry. The proposed framework is quantitatively evaluated and compared with common techniques for surface curvature estimation. In order to perform an unbiased evaluation in which smoothing effects are factored out, we use a set of randomly generated Bezier surface patches for which the curvature values can be analytically computed. It is demonstrated that, through the establishment of sampling conditions, the error in estimations obtained by the proposed framework is smaller and that the proposed framework is less sensitive to low sampling density, sampling irregularities, and sampling noise.

Algorithms↗

PubMed1999

Justification of automated decision-making: medical explanations as medical arguments.

People use arguments to justify their claims. Computer systems use explanations to justify their conclusions. We are developing WOZ, an explanation framework that justifies the conclusions of a clinical decision-support system. WOZ's central component is the explanation strategy that decides what information justifies a claim. The strategy uses Toulmin's argument structure to define pieces of information and to orchestrate their presentation. WOZ uses explicit models that abstract the core aspects of the framework such as the explanation strategy. In this paper, we present the use of arguments, the modeling of explanations, and the explanation process used in WOZ. WOZ exploits the wealth of naturally occurring arguments, and thus can generate convincing medical explanations.

Artificial Intelligence↗

PubMed1990

SCAN. Schedules for Clinical Assessment in Neuropsychiatry.

After more than 12 years of development, the ninth edition of the Present State Examination (PSE-9) was published, together with associated instruments and computer algorithm, in 1974. The system has now been expanded, in the framework of the World Health Organization/Alcohol, Drug Abuse, and Mental Health Administration Joint Project on Standardization of Diagnosis and Classification, and is being tested with the aim of developing a comprehensive procedure for clinical examination that is also capable of generating many of the categories of the International Classification of Diseases, 10th edition, and the Diagnostic and Statistical Manual of Mental Disorders, revised third edition. The new system is known as SCAN (Schedules for Clinical Assessment in Neuropsychiatry). It includes the 10th edition of the PSE as one of its core schedules, preliminary tests of which have suggested that reliability is similar to that of PSE-9. SCAN is being field tested in 20 centers in 11 countries. A final version is expected to be available in January 1990.

Algorithms↗

PubMed1991

A database model for medical consultation.

The database model presented in this article is suitable for applications in which queries may require noncrisp references to certain attributes. The data item (attribute) values may be crisp or fuzzy. For instance, such adjectives as "high" or "normal" may be attribute values for the attribute "blood pressure." A disease or a condition can be described by a number of symptoms which may be crisp alphanumeric values or fuzzy terms such as "high" or "normal." A query into this database can retrieve diseases which have "similar" symptoms. The similarity or "indistinguishability" is a measure defined by the database user on the relations that describe a family of diseases. This database system in conjunction with a rule base can provide the framework for a medical consultation system.

Computer Simulation↗