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Results for “generative artificial intelligence”

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PubMed2006

Meticulously detailed eye region model and its application to analysis of facial images.

We propose a system that is capable of detailed analysis of eye region images in terms of the position of the iris, degree of eyelid opening, and the shape, complexity, and texture of the eyelids. The system uses a generative eye region model that parameterizes the fine structure and motion of an eye. The structure parameters represent structural individuality of the eye, including the size and color of the iris, the width, boldness, and complexity of the eyelids, the width of the bulge below the eye, and the width of the illumination reflection on the bulge. The motion parameters represent movement of the eye, including the up-down position of the upper and lower eyelids and the 2D position of the iris. The system first registers the eye model to the input in a particular frame and individualizes it by adjusting the structure parameters. The system then tracks motion of the eye by estimating the motion parameters across the entire image sequence. Combined with image stabilization to compensate for appearance changes due to head motion, the system achieves accurate registration and motion recovery of eyes.

Algorithms↗

PubMed2005

A parallel decision tree-based method for user authentication based on keystroke patterns.

We propose a Monte Carlo approach to attain sufficient training data, a splitting method to improve effectiveness, and a system composed of parallel decision trees (DTs) to authenticate users based on keystroke patterns. For each user, approximately 19 times as much simulated data was generated to complement the 387 vectors of raw data. The training set, including raw and simulated data, is split into four subsets. For each subset, wavelet transforms are performed to obtain a total of eight training subsets for each user. Eight DTs are thus trained using the eight subsets. A parallel DT is constructed for each user, which contains all eight DTs with a criterion for its output that it authenticates the user if at least three DTs do so; otherwise it rejects the user. Training and testing data were collected from 43 users who typed the exact same string of length 37 nine consecutive times to provide data for training purposes. The users typed the same string at various times over a period from November through December 2002 to provide test data. The average false reject rate was 9.62% and the average false accept rate was 0.88%.

Algorithms↗

PubMed2004

prot4EST: translating expressed sequence tags from neglected genomes.

BACKGROUND: The genomes of an increasing number of species are being investigated through generation of expressed sequence tags (ESTs). However, ESTs are prone to sequencing errors and typically define incomplete transcripts, making downstream annotation difficult. Annotation would be greatly improved with robust polypeptide translations. Many current solutions for EST translation require a large number of full-length gene sequences for training purposes, a resource that is not available for the majority of EST projects. RESULTS: As part of our ongoing EST programs investigating these "neglected" genomes, we have developed a polypeptide prediction pipeline, prot4EST. It incorporates freely available software to produce final translations that are more accurate than those derived from any single method. We show that this integrated approach goes a long way to overcoming the deficit in training data. CONCLUSIONS: prot4EST provides a portable EST translation solution and can be usefully applied to >95% of EST projects to improve downstream annotation. It is freely available from http://www.nematodes.org/PartiGene.

Animals↗

PubMed2005

A steerable complex wavelet construction and its application to image denoising.

This work addresses the design of a novel complex steerable wavelet construction, the generation of transform-space feature measurements associated with corner and edge presence and orientation properties, and the application of these measurements directly to image denoising. The decomposition uses pairs of bandpass filters that display symmetry and antisymmetry about a steerable axis of orientation. While the angular characterization of the bandpass filters is similar to those previously described, the radial characteristic is new, as is the manner of constructing the interpolation functions for steering. The complex filters have been engineered into a multirate system, providing a synthesis and analysis subband filtering system with good reconstruction properties. Although the performance of our proposed denoising strategy is currently below that of recently reported state-of-the-art techniques in denoising, it does compare favorably with wavelet coring approaches employing global thresholds and with an "Oracle" shrinkage technique, and presents a very promising avenue for exploring structure-based denoising in the wavelet domain.

Algorithms↗

PubMed2000

Measuring the VC-dimension using optimized experimental design.

VC-dimension is the measure of model complexity (capacity) used in VC-theory. The knowledge of the VC-dimension of an estimator is necessary for rigorous complexity control using analytic VC generalization bounds. Unfortunately, it is not possible to obtain the analytic estimates of the VC-dimension in most cases. Hence, a recent proposal is to measure the VC-dimension of an estimator experimentally by fitting the theoretical formula to a set of experimental measurements of the frequency of errors on artificially generated data sets of varying sizes (Vapnik, Levin, & Le Cun, 1994). However, it may be difficult to obtain an accurate estimate of the VC-dimension due to the variability of random samples in the experimental procedure proposed by Vapnik et al. (1994). We address this problem by proposing an improved design procedure for specifying the measurement points (i.e., the sample size and the number of repeated experiments at a given sample size). Our approach leads to a nonuniform design structure as opposed to the uniform design structure used in the original article (Vapnik et al., 1994). Our simulation results show that the proposed optimized design structure leads to a more accurate estimation of the VC-dimension using the experimental procedure. The results also show that a more accurate estimation of VC-dimension leads to improved complexity control using analytic VC-generalization bounds and, hence, better prediction accuracy.

Algorithms↗

PubMed1997

Simulation of soft-tissue tumor excisions: a multimodal interactive approach.

Total 3-D reconstruction of the tumor size, shape, and relations with surrounding structures using CT, MRI, sonography, and angiography images can make simulated radical resection of soft-tissue sarcomas possible, thus sparing normal tissues. With our approach, starting from three MR images for a given patient, a new single image representation of all three parameters is generated by using two different techniques on a workstation in a standard UNIX and X-11 environment. The first one is a transformation linking together the MR parameters and the RGB (red, green, blue) color components. The second one is an unsupervised segmentation method based on a number of neural and fuzzy models. We can dinamically render and update a stereo display using field sequential presentation of left and right eye views on the monitor, with Cristal Eyes LCD shutter eyewear (StereoGraphics Inc., San Rafael, CA) to view it. As 3D locating tool, a 3D locating control system based on low-frequency magnetic fields (Polhemus Fastrak) has been chosen. Simulations of soft-tissues excisions may be performed in this interactive environment with augmented-reality modalities. All this, in our experience, has greatly facilitated the simulation of soft-tissue sarcoma excisions.

Artificial Intelligence↗

PubMedDate not supplied

A new method for representing the human anatomy.

In current practice, anatomical atlases are based on a collection of planar images presented in a book or, recently, stored on digital media. We present a new method for generating interactive true three-dimensional (3D) anatomical atlases based on a volume model derived from MRI and CT. The model has a two layer structure. The lower level is a volume model with a set of semantic attributes connected to each voxel. The semantic attributes are assigned by an anatomist using a volume editor. The upper level is a set of relations between these attributes. Interactive visualization tools such as multiple surface display, transparent rendering, and cutting are provided. It is shown that the combination of this data structure with advanced volume visualization tools provides the "look and feel" of real dissection. First tests show that the atlas system cannot only be used successfully for anatomy teaching, but also as a reference for radiologists or surgeons. As a replacement of classical atlases, however, the spatial resolution has still to be improved.

Anatomy↗

PubMed2004

Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser.

MOTIVATION: Text-mining research in the biomedical domain has been motivated by the rapid growth of new research findings. Improving the accessibility of findings has potential to speed hypothesis generation. RESULTS: We present the Arizona Relation Parser that differs from other parsers in its use of a broad coverage syntax-semantic hybrid grammar. While syntax grammars have generally been tested over more documents, semantic grammars have outperformed them in precision and recall. We combined access to syntax and semantic information from a single grammar. The parser was trained using 40 PubMed abstracts and then tested using 100 unseen abstracts, half for precision and half for recall. Expert evaluation showed that the parser extracted biologically relevant relations with 89% precision. Recall of expert identified relations with semantic filtering was 35 and 61% before semantic filtering. Such results approach the higher-performing semantic parsers. However, the AZ parser was tested over a greater variety of writing styles and semantic content. AVAILABILITY: Relations extracted from over 600 000 PubMed abstracts are available for retrieval and visualization at http://econport.arizona.edu:8080/NetVis/index.html.

Artificial Intelligence↗

PubMed2006

3-D/2-D registration by integrating 2-D information in 3-D.

In image-guided therapy, high-quality preoperative images serve for planning and simulation, and intraoperatively as "background", onto which models of surgical instruments or radiation beams are projected. The link between a preoperative image and intraoperative physical space of the patient is established by image-to-patient registration. In this paper, we present a novel 3-D/2-D registration method. First, a 3-D image is reconstructed from a few 2-D X-ray images and next, the preoperative 3-D image is brought into the best possible spatial correspondence with the reconstructed image by optimizing a similarity measure (SM). Because the quality of the reconstructed image is generally low, we introduce a novel SM, which is able to cope with low image quality as well as with different imaging modalities. The novel 3-D/2-D registration method has been evaluated and compared to the gradient-based method (GBM) using standardized evaluation methodology and publicly available 3-D computed tomography (CT), 3-D rotational X-ray (3DRX), and magnetic resonance (MR) and 2-D X-ray images of two spine phantoms, for which gold standard registrations were known. For each of the 3DRX, CT, or MR images and each set of X-ray images, 1600 registrations were performed from starting positions, defined as the mean target registration error (mTRE), randomly generated and uniformly distributed in the interval of 0-20 mm around the gold standard. The capture range was defined as the distance from gold standard for which the final TRE was less than 2 mm in at least 95% of all cases. In terms of success rate, as the function of initial misalignment and capture range the proposed method outperformed the GBM. TREs of the novel method and the GBM were approximately the same. For the registration of 3DRX and CT images to X-ray images as few as 2-3 X-ray views were sufficient to obtain approximately 0.4 mm TREs, 7-9 mm capture range, and 80%-90% of successful registrations. To obtain similar results for MR to X-ray registrations, an image, reconstructed from at least 11 X-ray images was required. Reconstructions from more than 11 images had no effect on the registration results.

Algorithms↗

PubMed1998

Computational studies of lateralization of phoneme sequence generation.

The mechanisms underlying cerebral lateralization of language are poorly understood. Asymmetries in the size of hemispheric regions and other factors have been suggested as possible underlying causal factors, and the corpus callosum (interhemispheric connections) has also been postulated to play a role. To examine these issues, we created a neural model consisting of paired cerebral hemispheric regions interacting via the corpus callosum. The model was trained to generate the correct sequence of phonemes for 50 monosyllabic words (simulated reading aloud) under a variety of assumptions about hemispheric asymmetries and callosal effects. After training, the ability of the full model and each hemisphere acting alone to perform this task was measured. Lateralization occurred readily toward the side having larger size, higher excitability, or higher-learning-rate parameter. Lateralization appeared most readily and intensely with strongly inhibitory callosal connections, supporting past arguments that the effective functionality of the corpus callosum is inhibitory. Many of the results are interpretable as the outcome of a "race to learn" between the model's two hemispheric regions, leading to the concept that asymmetric hemispheric plasticity is a critical common causative factor in lateralization. To our knowledge, this is the first computational model to demonstrate spontaneous lateralization of function, and it suggests that such models can be useful for understanding the mechanisms of cerebral lateralization.

Algorithms↗

PubMed2004

Extending self-organizing particle systems to problem solving.

Self-organizing particle systems consist of numerous autonomous, purely reflexive agents ("particles") whose collective movements through space are determined primarily by local influences they exert upon one another. Inspired by biological phenomena (bird flocking, fish schooling, etc.), particle systems have been used not only for biological modeling, but also increasingly for applications requiring the simulation of collective movements such as computer-generated animation. In this research, we take some first steps in extending particle systems so that they not only move collectively, but also solve simple problems. This is done by giving the individual particles (agents) a rudimentary intelligence in the form of a very limited memory and a top-down, goal-directed control mechanism that, triggered by appropriate conditions, switches them between different behavioral states and thus different movement dynamics. Such enhanced particle systems are shown to be able to function effectively in performing simulated search-and-collect tasks. Further, computational experiments show that collectively moving agent teams are more effective than similar but independently moving ones in carrying out such tasks, and that agent teams of either type that split off members of the collective to protect previously acquired resources are most effective. This work shows that the reflexive agents of contemporary particle systems can readily be extended to support goal-directed problem solving while retaining their collective movement behaviors. These results may prove useful not only for future modeling of animal behavior, but also in computer animation, coordinated movement control in robotic teams, particle swarm optimization, and computer games.

Animals↗

PubMed2000

Accurate prediction of protein functional class from sequence in the Mycobacterium tuberculosis and Escherichia coli genomes using data mining.

The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60-80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, convergent evolution and horizontal gene transfer. We identify rules that predict protein functional class even in the absence of detectable sequence or structural homology. These rules give insight into the evolutionary history of M. tuberculosis and E. coli.

Amino Acid Sequence↗

PubMed1993

Knowledge based lipid management system for general practitioners.

The aim of this system is to provide computer generated interpretative reports with management advice for General Practitioners (GPs). The lipid domain was chosen because of its importance in preventive medicine. Request forms to elicit extra clinical information were designed and distributed to a group of randomly selected GPs. Interpretation of laboratory and clinical data categorizes patients according to risk of coronary heart disease. The management system is rule based and provides advice on lifestyle modifications, diet and drug intervention. Previous clinical and laboratory results are taken into account in determining a management strategy. To date 435 request forms have been processed: 309 (71%) from first visits and 126 (29%) from follow-up visits. Normal lipid profiles were found in 19% of cases. There was 93% agreement between management advice given by the system and the expert. The system has now been modified and further evaluation is under way.

Artificial Intelligence↗

PubMed2004

The cell graphs of cancer.

We report a novel, proof-of-concept, computational method that models a type of brain cancer (glioma) only by using the topological properties of its cells in the tissue image. From low-magnification (80x) tissue images of 384 x 384 pixels, we construct the graphs of the cells based on the locations of the cells within the images. We generate such cell graphs of 1000-3000 cells (nodes) with 2000-10,000 links, each of which is calculated as a decaying exponential function of the Euclidean distance between every pair of cells in accordance with the Waxman model. At the cellular level, we compute the graph metrics of the cell graphs, including the degree, clustering coefficient, eccentricity and closeness for each cell. Working with a total of 285 tissue samples surgically removed from 12 different patients, we demonstrate that the self-organizing clusters of cancerous cells exhibit distinctive graph metrics that distinguish them from the healthy cells and the unhealthy inflamed cells at the cellular level with an accuracy of at least 85%. At the tissue level, we accomplish correct tissue classifications of cancerous, healthy and non-neoplastic inflamed tissue samples with an accuracy of 100% by requiring correct classification for the majority of the cells within the tissue sample.

Algorithms↗

PubMed2006

A probabilistic model for binaural sound localization.

This paper proposes a biologically inspired and technically implemented sound localization system to robustly estimate the position of a sound source in the frontal azimuthal half-plane. For localization, binaural cues are extracted using cochleagrams generated by a cochlear model that serve as input to the system. The basic idea of the model is to separately measure interaural time differences and interaural level differences for a number of frequencies and process these measurements as a whole. This leads to two-dimensional frequency versus time-delay representations of binaural cues, so-called activity maps. A probabilistic evaluation is presented to estimate the position of a sound source over time based on these activity maps. Learned reference maps for different azimuthal positions are integrated into the computation to gain time-dependent discrete conditional probabilities. At every timestep these probabilities are combined over frequencies and binaural cues to estimate the sound source position. In addition, they are propagated over time to improve position estimation. This leads to a system that is able to localize audible signals, for example human speech signals, even in reverberating environments.

Artificial Intelligence↗

PubMed2006

Automating the assignment of diagnosis codes to patient encounters using example-based and machine learning techniques.

OBJECTIVE: Human classification of diagnoses is a labor intensive process that consumes significant resources. Most medical practices use specially trained medical coders to categorize diagnoses for billing and research purposes. METHODS: We have developed an automated coding system designed to assign codes to clinical diagnoses. The system uses the notion of certainty to recommend subsequent processing. Codes with the highest certainty are generated by matching the diagnostic text to frequent examples in a database of 22 million manually coded entries. These code assignments are not subject to subsequent manual review. Codes at a lower certainty level are assigned by matching to previously infrequently coded examples. The least certain codes are generated by a naïve Bayes classifier. The latter two types of codes are subsequently manually reviewed. MEASUREMENTS: Standard information retrieval accuracy measurements of precision, recall and f-measure were used. Micro- and macro-averaged results were computed. RESULTS At least 48% of all EMR problem list entries at the Mayo Clinic can be automatically classified with macro-averaged 98.0% precision, 98.3% recall and an f-score of 98.2%. An additional 34% of the entries are classified with macro-averaged 90.1% precision, 95.6% recall and 93.1% f-score. The remaining 18% of the entries are classified with macro-averaged 58.5%. CONCLUSION: Over two thirds of all diagnoses are coded automatically with high accuracy. The system has been successfully implemented at the Mayo Clinic, which resulted in a reduction of staff engaged in manual coding from thirty-four coders to seven verifiers.

Abstracting and Indexing↗

PubMed2005

Effective representation using ICA for face recognition robust to local distortion and partial occlusion.

The performance of face recognition methods using subspace projection is directly related to the characteristics of their basis images, especially in the cases of local distortion or partial occlusion. In order for a subspace projection method to be robust to local distortion and partial occlusion, the basis images generated by the method should exhibit a part-based local representation. We propose an effective part-based local representation method named locally salient ICA (LS-ICA) method for face recognition that is robust to local distortion and partial occlusion. The LS-ICA method only employs locally salient information from important facial parts in order to maximize the benefit of applying the idea of "recognition by parts." It creates part-based local basis images by imposing additional localization constraint in the process of computing ICA architecture I basis images. We have contrasted the LS-ICA method with other part-based representations such as LNMF (Localized Nonnegative Matrix Factorization) and LFA (Local Feature Analysis). Experimental results show that the LS-ICA method performs better than PCA, ICA architecture I, ICA architecture II, LFA, and LNMF methods, especially in the cases of partial occlusions and local distortions.

Algorithms↗

PubMed2004

Understanding protein dispensability through machine-learning analysis of high-throughput data.

MOTIVATION: Protein dispensability is fundamental to the understanding of gene function and evolution. Recent advances in generating high-throughput data such as genomic sequence data, protein-protein interaction data, gene-expression data and growth-rate data of mutants allow us to investigate protein dispensability systematically at the genome scale. RESULTS: In our studies, protein dispensability is represented as a fitness score that is measured by the growth rate of gene-deletion mutants. By the analyses of high-throughput data in yeast Saccharomyces cerevisiae, we found that a protein's dispensability had significant correlations with its evolutionary rate and duplication rate, as well as its connectivity in protein-protein interaction network and gene-expression correlation network. Neural network and support vector machine were applied to predict protein dispensability through high-throughput data. Our studies shed some lights on global characteristics of protein dispensability and evolution. AVAILABILITY: The original datasets for protein dispensability analysis and prediction, together with related scripts, are available at http://digbio.missouri.edu/~ychen/ProDispen/ CONTACT: xudong@missouri.edu.

Artificial Intelligence↗