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PubMed2005

Self-organizing and self-correcting classifications of biological data.

MOTIVATION: Rapid, automated means of organizing biological data are required if we hope to keep abreast of the flood of data emanating from sequencing, microarray and similar high-throughput analyses. Faced with the need to validate the annotation of thousands of sequences and to generate biologically meaningful classifications based on the sequence data, we turned to statistical methods in order to automate these processes. RESULTS: An algorithm for automated classification based on evolutionary distance data was written in S. The algorithm was tested on a dataset of 1436 small subunit ribosomal RNA sequences and was able to classify the sequences according to an extant scheme, use statistical measurements of group membership to detect sequences that were misclassified within this scheme and produce a new classification. In this study, the use of the algorithm to address problems in prokaryotic taxonomy is discussed. AVAILABILITY: S-Plus is available from Insightful, Inc. An S-Plus implementation of the algorithm and the associated data are available at http://taxoweb.mmg.msu.edu/datasets

Algorithms↗

PubMed2006

Prediction of protein structural class with Rough Sets.

BACKGROUND: A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the decision system, decision rules are generated, which can be used to classify new objects. RESULTS: In this study, self-consistency and jackknife tests on the datasets constructed by G.P. Zhou (Journal of Protein Chemistry, 1998, 17: 729-738) are used to verify the performance of this method, and are compared with some of prior works. The results showed that the rough sets approach is very promising and may play a complementary role to the existing powerful approaches, such as the component-coupled, neural network, SVM, and LogitBoost approaches. CONCLUSION: The results with high success rates indicate that the rough sets approach as proposed in this paper might hold a high potential to become a useful tool in bioinformatics.

Algorithms↗

PubMed1999

Classification algorithms applied to narrative reports.

Narrative text reports represent a significant source of clinical data. However, the information stored in these reports is inaccessible to many automated decision support systems. Data mining techniques can assist in extracting information from narrative data. Multiple classification methods, such as rule generation, decision trees, Bayesian classifiers, and information retrieval were used to classify a set of 200 chest X-ray reports according to 6 clinical conditions indicated. A general-purpose natural language processor was used to convert the narrative text into a coded form that could be used by the classification algorithms. Significant differences in performance were found between algorithms. The best performing algorithm applied to the processor output was significantly better than information retrieval applied to raw text. Predictor variables from the coded processor output were limited to avoid overfitting. Methods that limited by domain knowledge performed significantly better than those that limited by conditional probabilities of the variables in the training set. Algorithms were also shown to be dependent on training set size.

Algorithms↗

PubMed1997

Utility of a software assistant in critical care case review.

A computer program (the Audit Assistant) was developed to help physicians review the care of critically ill emergency department (ED) patients. The program is an example of a new class of decision aids that serves to remind physicians to consider possibilities, not an artificial intelligence program that actually attempts to simulate clinical reasoning. The goal of such programs is to enable physicians to reduce errors--in this case to enable reviewers to notice more of the errors in care in the cases they are reviewing. The objective of this study was to demonstrate on a small set of complex cases that the tested computer program enables the physician to perform a better quality review. The issue of what constitutes improved case review is addressed. In the first part of the study, reviewers reviewed two mock charts without using the Audit Assistant and then immediately reviewed the charts again with the assistance of the program. The reviews were compared. In the second part of the study, a second reviewer also compared the utility of the review of the first reviewer alone and the Audit Assistant output as an aid to review, using an additional mock chart. Six emergency physicians participated; each was a quality assurance director for the ED of one Cleveland area hospital. For the physicians reviewing without the Audit Assistant, 41% of critical actions were listed by three or four reviewers. For those using the Audit Assistant, 83% of critical actions were listed by three or four reviewers. All reviewers preferred the Audit Assistant-suggested list to the critical action list generated by a previous reviewer not using the Audit Assistant (P < .02). Use of the Audit Assistant improved the completeness and the consistency of physician review of mock charts of critically ill ED patients in a small series of cases. The critical actions added for review were important, as demonstrated by the preferential addition of critical actions chosen by other reviewers who were not using the computer program.

Critical Care↗

PubMed1993

Automatic knowledge base refinement: learning from examples and deep knowledge in rheumatology.

MESICAR is a second generation expert system which contains very general descriptions of rheumatological disorders in the primary medical care field. With the help of a detailed hierarchical description of the human anatomy the system is able to support diagnostic decisions. The paper describes how machine learning techniques are used to automatically construct more specific disease descriptions for common, frequently occurring cases. The system MESICAR-LEARN implements a learning method which integrates analytical and empirical learning techniques. Cases diagnosed by MESICAR form the training examples, and MESICAR's knowledge base is used as domain theory. The learned concepts are integrated into a hierarchy of disease descriptions. They support efficient and fast reasoning on common cases in addition to the general diagnostic support afforded by MESICAR's deep knowledge.

Algorithms↗

PubMedDate not supplied

Virtual local target method for avoiding local minimum in potential field based robot navigation.

A novel robot navigation algorithm with global path generation capability is presented. Local minimum is a most intractable but is an encountered frequently problem in potential field based robot navigation. Through appointing appropriately some virtual local targets on the journey, it can be solved effectively. The key concept employed in this algorithm are the rules that govern when and how to appoint these virtual local targets. When the robot finds itself in danger of local minimum, a virtual local target is appointed to replace the global goal temporarily according to the rules. After the virtual target is reached, the robot continues on its journey by heading towards the global goal. The algorithm prevents the robot from running into local minima anymore. Simulation results showed that it is very effective in complex obstacle environments.

Algorithms↗

PubMed2003

Rough set-based hybrid fuzzy-neural controller design for industrial wastewater treatment.

Recent advances in control engineering suggest that hybrid control strategies, integrating some ideas and paradigms existing in different soft computing techniques, such as fuzzy logic, genetic algorithms, rough set theory, and neural networks, may provide improved control performance in wastewater treatment processes. This paper presents an innovative hybrid control algorithm leading to integrate the distinct aspects of indiscernibility capability of rough set theory and search capability of genetic algorithms with conventional neural-fuzzy controller design. The methodology proposed in this study employs a three-stage analysis that is designed in series for generating a representative state function, searching for a set of multi-objective control strategies, and performing a rough set-based autotuning for the neural-fuzzy logic controller to make it applicable for controlling an industrial wastewater treatment process. Research findings in the case study clearly indicate that the use of rough set theory to aid in the neural-fuzzy logic controller design can produce relatively better plant performance in terms of operating cost, control stability, and response time simultaneously, which is effective at least in the selected industrial wastewater treatment plant. Such a methodology is anticipated to be capable of dealing with many other types of process control problems in waste treatment processes by making only minor modifications.

Artificial Intelligence↗

PubMed2005

Partially connected feedforward neural networks structured by input types.

This paper proposes a new method to model partially connected feedforward neural networks (PCFNNs) from the identified input type (IT) which refers to whether each input is coupled with or uncoupled from other inputs in generating output. The identification is done by analyzing input sensitivity changes as amplifying the magnitude of inputs. The sensitivity changes of the uncoupled inputs are not correlated with the variation on any other input, while those of the coupled inputs are correlated with the variation on any one of the coupled inputs. According to the identified ITs, a PCFNN can be structured. Each uncoupled input does not share the neurons in the hidden layer with other inputs in order to contribute to output in an independent manner, while the coupled inputs share the neurons with one another. After deriving the mathematical input sensitivity analysis for each IT, several experiments, as well as a real example (blood pressure (BP) estimation), are described to demonstrate how well our method works.

Algorithms↗

PubMed2001

Neural networks for improved target differentiation and localization with sonar.

This study investigates the processing of sonar signals using neural networks for robust differentiation of commonly encountered features in indoor robot environments. Differentiation of such features is of interest for intelligent systems in a variety of applications. Different representations of amplitude and time-of-flight measurement patterns acquired from a real sonar system are processed. In most cases, best results are obtained with the low-frequency component of the discrete wavelet transform of these patterns. Modular and non-modular neural network structures trained with the back-propagation and generating-shrinking algorithms are used to incorporate learning in the identification of parameter relations for target primitives. Networks trained with the generating-shrinking algorithm demonstrate better generalization and interpolation capability and faster convergence rate. Neural networks can differentiate more targets employing only a single sensor node, with a higher correct differentiation percentage (99%) than achieved with previously reported methods (61-90%) employing multiple sensor nodes. A sensor node is a pair of transducers with fixed separation, that can rotate and scan the target to collect data. Had the number of sensing nodes been reduced in the other methods, their performance would have been even worse. The success of the neural network approach shows that the sonar signals do contain sufficient information to differentiate all target types, but the previously reported methods are unable to resolve this identifying information. This work can find application in areas where recognition of patterns hidden in sonar signals is required. Some examples are system control based on acoustic signal detection and identification, map building, navigation, obstacle avoidance, and target-tracking applications for mobile robots and other intelligent systems.

Algorithms↗

PubMed2006

Characteristics of pixel arrangements in various rhombuses for full-parallax three-dimensional image generation.

In full-parallax three-dimensional (3-D) imaging systems, the pixel cells often have the shape of a rhombus. Proper arrangement of pixels in these rhombic-shaped cells is important to maximize the quality of displayable 3-D images with a given display panel. The possible number of pixel arrangements in a rhombic cell with a definite dimension is found by considering the number of possible crossings between parallel line families forming the pixel cells, when the slopes of the lines are approximated by the ratio between the number of pixels in the vertical and horizontal directions. To make the rhombic cell have a uniquely defined pixel arrangement, its horizontal and vertical dimensions should be equal to the even multiple of the pixel dimension in their corresponding direction.

Algorithms↗

PubMed2026

Safeguarding biomedical AI: a critical scoping review of privacy-enhancing technologies, hybrid approaches, and deployment models.

BACKGROUND: Biomedical artificial intelligence (AI) requires the integration of privacy-enhancing technologies (PETs) to safeguard sensitive clinical, imaging, and genomic data while preserving analytical utility. OBJECTIVES: This review critically and systematically maps applications of PETs across the biomedical AI lifecycle in accordance with PRISMA-ScR guidelines and evaluates their technical trade-offs, deployment feasibility, and residual risks. METHODS: We systematically searched PubMed, IEEE Xplore, ACM Digital Library, and Scopus for studies published between 2015 and 2025. Eligible studies addressed differential privacy, federated learning, secure multiparty computation, homomorphic encryption, or hybrid approaches in biomedical AI. Data were charted on PET type, modality, lifecycle stage, utility metrics, privacy parameters, and deployment considerations. A critical appraisal rubric assessed threat-model adequacy, methodological clarity, reproducibility, privacy-utility transparency, and deployment realism. Additionally, we hand-searched major venues (USENIX Security, NeurIPS, AAAI) and screened Google Scholar for grey literature, applying de-duplication across sources. RESULTS: We identified 87 studies spanning clinical decision support, genomics, and medical imaging. From 25,761 initial records, 3,754 underwent title/abstract screening and 1,968 underwent full-text assessment. PETs demonstrated distinct strengths and limitations: differential privacy provided provable guarantees but reduced performance on imbalanced data; federated learning improved data access but remained vulnerable to gradient leakage; and cryptographic methods ensured confidentiality at high computational cost. Synthetic data generation supported privacy-conscious data sharing and benchmarking but remained sensitive to disclosure risk, fidelity loss, and subgroup representation. Hybrid and emerging approaches, including trusted execution environments, zero-knowledge proofs, and privacy-preserving transformer architectures, mitigated composability gaps yet lacked full end-to-end assurance. Case studies at hospital and biobank scale illustrated practical feasibility and infrastructure demands. CONCLUSIONS: Situating PETs within technical and operational contexts clarifies their capabilities, limitations, and deployment challenges. Residual risks persist, including fairness concerns, inference-time leakage, and overreliance on PETs as compliance proxies. Sustained technical innovation and institutional governance remain essential for the trustworthy integration of PETs in biomedical AI.

biomedical AI↗

PubMed2005

Analysis of mass spectral serum profiles for biomarker selection.

MOTIVATION: Mass spectrometric profiles of peptides and proteins obtained by current technologies are characterized by complex spectra, high dimensionality and substantial noise. These characteristics generate challenges in the discovery of proteins and protein-profiles that distinguish disease states, e.g. cancer patients from healthy individuals. We present low-level methods for the processing of mass spectral data and a machine learning method that combines support vector machines, with particle swarm optimization for biomarker selection. RESULTS: The proposed method identified mass points that achieved high prediction accuracy in distinguishing liver cancer patients from healthy individuals in SELDI-QqTOF profiles of serum. AVAILABILITY: MATLAB scripts to implement the methods described in this paper are available from the HWR's lab website http://lombardi.georgetown.edu/labpage

Algorithms↗

PubMed2006

A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.

BACKGROUND: As a variety of functional genomic and proteomic techniques become available, there is an increasing need for functional analysis methodologies that integrate heterogeneous data sources. METHODS: In this paper, we address this issue by proposing a general framework for gene function prediction based on the k-nearest-neighbor (KNN) algorithm. The choice of KNN is motivated by its simplicity, flexibility to incorporate different data types and adaptability to irregular feature spaces. A weakness of traditional KNN methods, especially when handling heterogeneous data, is that performance is subject to the often ad hoc choice of similarity metric. To address this weakness, we apply regression methods to infer a similarity metric as a weighted combination of a set of base similarity measures, which helps to locate the neighbors that are most likely to be in the same class as the target gene. We also suggest a novel voting scheme to generate confidence scores that estimate the accuracy of predictions. The method gracefully extends to multi-way classification problems. RESULTS: We apply this technique to gene function prediction according to three well-known Escherichia coli classification schemes suggested by biologists, using information derived from microarray and genome sequencing data. We demonstrate that our algorithm dramatically outperforms the naive KNN methods and is competitive with support vector machine (SVM) algorithms for integrating heterogenous data. We also show that by combining different data sources, prediction accuracy can improve significantly CONCLUSION: Our extension of KNN with automatic feature weighting, multi-class prediction, and probabilistic inference, enhance prediction accuracy significantly while remaining efficient, intuitive and flexible. This general framework can also be applied to similar classification problems involving heterogeneous datasets.

Algorithms↗

PubMed2005

Nonlinear, near photo-realistic caricatures using a parametric facial appearance model.

A mathematical model previously developed for use in computer vision applications is presented as an empirical model for face space. The term appearance space is used to distinguish this from previous models. Appearance space is a linear vector space that is dimensionally optimal, enables us to model and describe any human facial appearance, and possesses characteristics that are plausible for the representation of psychological face space. Randomly sampling from a multivariate distribution for a location in appearance space produces entirely plausible faces, and manipulation of a small set of defining parameters enables the automatic generation of photo-realistic caricatures. The appearance space model leads us to the new concept of nonlinear caricatures, and we show that the accepted linear method for caricature is only a special case of a more general paradigm. Nonlinear methods are also viable, and we present examples of photographic quality caricatures, using a number of different transformation functions. Results of a simple experiment are presented that suggest that nonlinear transformations can accurately capture key aspects of the caricature effect. Finally, we discuss the relationship between appearance space, caricature, and facial distinctiveness. On the basis of our new theoretical framework, we suggest an experimental approach that can yield new evidence for the plausibility of face space and its ability to explain processes of recognition.

Artificial Intelligence↗

PubMed1997

Lightweight fuzzy processes in clinical computing.

In spite of advances in computing hardware, many hospitals still have a hard time finding extra capacity in their production clinical information system to run artificial intelligence (AI) modules, for example: to support real-time drug-drug or drug-lab interactions; to track infection trends; to monitor compliance with case specific clinical guidelines; or to monitor/ control biomedical devices like an intelligent ventilator. Historically, adding AI functionality was not a major design concern when a typical clinical system is originally specified. AI technology is usually retrofitted 'on top of the old system' or 'run off line' in tandem with the old system to ensure that the routine work load would still get done (with as little impact from the AI side as possible). To compound the burden on system performance, most institutions have witnessed a long and increasing trend for intramural and extramural reporting, (e.g. the collection of data for a quality-control report in microbiology, or a meta-analysis of a suite of coronary artery bypass grafts techniques, etc.) and these place an ever-growing burden on typical the computer system's performance. We discuss a promising approach to adding extra AI processing power to a heavily-used system based on the notion 'lightweight fuzzy processing (LFP)', that is, fuzzy modules designed from the outset to impose a small computational load. A formal model for a useful subclass of fuzzy systems is defined below and is used as a framework for the automated generation of LFPs. By seeking to reduce the arithmetic complexity of the model (a hand-crafted process) and the data complexity of the model (an automated process), we show how LFPs can be generated for three sample datasets of clinical relevance.

Biopsy, Needle↗

PubMed2005

Combining multiple clusterings using evidence accumulation.

We explore the idea of evidence accumulation (EAC) for combining the results of multiple clusterings. First, a clustering ensemble--a set of object partitions, is produced. Given a data set (n objects or patterns in d dimensions), different ways of producing data partitions are: 1) applying different clustering algorithms and 2) applying the same clustering algorithm with different values of parameters or initializations. Further, combinations of different data representations (feature spaces) and clustering algorithms can also provide a multitude of significantly different data partitionings. We propose a simple framework for extracting a consistent clustering, given the various partitions in a clustering ensemble. According to the EAC concept, each partition is viewed as an independent evidence of data organization, individual data partitions being combined, based on a voting mechanism, to generate a new n x n, similarity matrix between the n patterns. The final data partition of the n patterns is obtained by applying a hierarchical agglomerative clustering algorithm on this matrix. We have developed a theoretical framework for the analysis of the proposed clustering combination strategy and its evaluation, based on the concept of mutual information between data partitions. Stability of the results is evaluated using bootstrapping techniques. A detailed discussion of an evidence accumulation-based clustering algorithm, using a split and merge strategy based on the K-means clustering algorithm, is presented. Experimental results of the proposed method on several synthetic and real data sets are compared with other combination strategies, and with individual clustering results produced by well-known clustering algorithms.

Algorithms↗

PubMed1992

Self-organizing neural network that discovers surfaces in random-dot stereograms.

The standard form of back-propagation learning is implausible as a model of perceptual learning because it requires an external teacher to specify the desired output of the network. We show how the external teacher can be replaced by internally derived teaching signals. These signals are generated by using the assumption that different parts of the perceptual input have common causes in the external world. Small modules that look at separate but related parts of the perceptual input discover these common causes by striving to produce outputs that agree with each other. The modules may look at different modalities (such as vision and touch), or the same modality at different times (for example, the consecutive two-dimensional views of a rotating three-dimensional object), or even spatially adjacent parts of the same image. Our simulations show that when our learning procedure is applied to adjacent patches of two-dimensional images, it allows a neural network that has no prior knowledge of the third dimension to discovery depth in random dot stereograms of curved surfaces.

Artificial Intelligence↗

PubMedDate not supplied

Filmless digital radiology--feasibility and 20 month experience in clinical routine.

We present the clinical experiences of PACS based on 20 months routine operation of the first filmless radiology department worldwide. PACS planning and implementation strategies for potential vendors are discussed. The actual implementation status of this major teaching hospital with currently 560 acute-care beds comprises three computed radiography systems, five digital fluoroscopic units, eight ultrasound machines, five mobile units, three angio suites and two CT's interconnected with a PACS, a RIS, which is coupled with three voice-recognition systems for report generation during nights, and a HIS. Primary diagnosis is performed on 16 workstations with two to six high-resolution, high-contrast monitors. Twenty-six peripheral viewing stations provide image display on the wards and in outpatient clinics. During the first 20 months 586.047 images have been acquired, resulting in 1.3 Tbyte of data stored on optical disks. Currently the daily data production is 5-6 Gbyte, the network traffic 15-18 Gbyte. Benefits of PACS primarily are reliable access to image information, speeding up report cycle time, which contributes to the reduction of the average patient length of stay (LOS). The LOS in our hospital is the shortest (6.4 days) of all Austrian hospitals. So it may be stated that PACS improves the quality of health care.

Artificial Intelligence↗