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PubMed1997

Predicting the toxicity of complex mixtures using artificial neural networks.

Industrial and municipal wastewaters constitute major sources of contamination of the aquatic compartment and represent a threat to aquatic life. Artificial neural networks based on three different learning paradigms were studied as a means of predicting acute toxicity to trout (5 days exposure to wastewaters) using input data from two simple microbiotests requiring only 5 or 15 min of incubation. These microbiotests were 1) the chemoluminescent peroxidase (Cl-Per) assay, which can detect radical scavengers and enzyme-inhibiting substances, and 2) the luminescent bacteria toxicity test (Microtox), in which reduction of light emission by bacteria during exposure is taken as a measure of toxicity. The responses obtained with the trout bioassay, the Cl-Per and the Microtox test were analyzed through statistical correlation (Pearson product-moment correlation), unsupervised learning by a self-organizing network, and assisted learning by the backpropagation and the Boltzmann machine (probabilistic) paradigms. No significant correlation (p < 0.05) was found between the responses obtained with either the Cl-Per assay (p = 0.121) or the Microtox (p = 0.061) microbiotest and those resulting from the trout bioassay. The self-organizing network was able to identify by itself a maximum of five classes that were more or less relevant for predicting toxicity to fish: class 1 contained 2 samples that were toxic to fish, class 2 contained 2/3 samples that were toxic, class 3 showed 6/8 samples that were non toxic, class 4 contained 5/6 samples that were non-toxic and class 5 comprised one sample that was toxic. Supervised learning with backpropagation analysis yielded two kinds of networks that hold potential. The first one was able to predict the actual toxic wastewater concentration with an overall performance of 65% when fed fresh data, while the second one, which was designed to differentiate between toxic and non-toxic effluents, exhibited a much better performance (90%). However, the probabilistic network also proved to be a very good predictive model for toxicity to fish, with an overall performance of 90%. Although more data are needed, the network based on the backpropagation paradigm seems to be a better predictor or classifier of trout toxicity when used with the Cl-Per and the Microtox microbiotests.

Algorithms↗
PubMed1996

VLSI neural system architecture for finite ring recursive reduction.

The use of neural-like networks to implement finite ring computations has been presented in a previous paper. This paper develops efficient VLSI neural system architecture for the finite ring recursive reduction (FRRR), including module reduction, MSB carry iteration and feedforward processing. These techniques deal with the basic principles involved in constructing a FRRR, and their implementations are efficiently matched to the VLSI medium. Compared with the other structure models for finite ring computation (e.g. modification of binary arithmetic logic and bit-steered ROM's), the FRRR structure has the lowest area complexity in silicon while maintaining a high throughput rate. Examples of several implementations are used to illustrate the effectiveness of the FRRR architecture.

Algorithms↗
PubMed1997

An ECG classifier designed using modified decision based neural networks.

In this paper, a neural network based generalized software system is presented for automatic analysis of electrocardiograms (ECGs). The proposed system is capable of intuitively diagnosing the disease from the ECG using the knowledge acquired from the training. A modified decision based neural network which converges in a finite amount of time is employed. The training procedure used automatically varies the size of the network. The system is capable of being trained even without an expert's supervision. The physician can correct the network as and when a misclassification occurs, thus making the system less error-prone as time passes. The proposed system has been tested using an ECG data base representing different cardiological conditions such as bundle branch blocks and infarctions. The system is capable of detecting different types of arrhythmias also.

Algorithms↗
PubMed1993

A neural network model for texture discrimination.

A model of texture discrimination in visual cortex was built using a feedforward network with lateral interactions among relatively realistic spiking neural elements. The elements have various membrane currents, equilibrium potentials and time constants, with action potentials and synapses. The model is derived from the modified programs of MacGregor (1987). Gabor-like filters are applied to overlapping regions in the original image; the neural network with lateral excitatory and inhibitory interactions then compares and adjusts the Gabor amplitudes in order to produce the actual texture discrimination. Finally, a combination layer selects and groups various representations in the output of the network to form the final transformed image material. We show that both texture segmentation and detection of texture boundaries can be represented in the firing activity of such a network for a wide variety of synthetic to natural images. Performance details depend most strongly on the global balance of strengths of the excitatory and inhibitory lateral interconnections. The spatial distribution of lateral connective strengths has relatively little effect. Detailed temporal firing activities of single elements in the lateral connected network were examined under various stimulus conditions. Results show (as in area 17 of cortex) that a single element's response to image features local to its receptive field can be altered by changes in the global context.

Cybernetics↗
PubMed1997

Computing machinery and mentality.

I reconsider the status of computationalism (or, in a weak sense, functionalism): the claim that being a realization of some (as yet unspecified) class of abstract machine is both necessary and sufficient for having genuine, full-blooded, mentality. This doctrine is now quite widely (though by no means universally) seen as discredited. My position is that, though it is undoubtedly an unsatisfactory (perhaps even repugnant) thesis, the arguments against it are still rather weak. In particular, I critically reassess John Searle's infamous Chinese Room Argument and also some relevant aspects of Karl Popper's theory of the Open Universe. I conclude that the status of computationalism must still be regarded as undecided, and that it may still provide a satisfactory framework for research.

Animals↗
PubMed2000

Interhemispheric effects of simulated lesions in a neural model of letter identification.

Experimental studies have produced conflicting results about the extent to which the intact, nonlesioned cerebral hemisphere is responsible for recovery from cognitive deficits following focal brain damage such as a stroke. To obtain a better theoretical understanding of interhemispheric interactions during recovery, we examined the effects of simulated lesions to a bihemispheric neural model of letter identification under various assumptions about hemispheric asymmetries, corpus callosum influence, and lesion size. Among other results, the model demonstrates that the intact hemispheric region's participation in the recovery process is a function of preexisting lateralization and lesion size, indicating that interpretation of experimental work should take these factors into account.

Artificial Intelligence↗
PubMed1993

Computer and the thought process.

Modelling of brain is an eternal problem and was revitalized by arrogant claims of some computer scientists. Several basic results of mathematics, especially in problems of uncertainty, computational complexity and logic prove limits of computation and indications that the brain works otherwise. The complexity of brain is not accessible by current electronic technology. However, brain research and computer science can learn a lot from each other by revealing relevant analogies.

Artificial Intelligence↗
PubMed2005

A general framework for characterizing studies of brain interface technology.

The development of brain interface (BI) technology continues to attract researchers with a wide range of backgrounds and expertise. Though the BI community is committed to accurate and objective evaluation of methods, systems, and technology, the very diversity of the methods and terminology used in the field hinders understanding and impairs technology cross-fertilization and cross-group validation of findings. Underlying this dilemma is a lack of common perspective and language. As seen in our previous works in this area, our approach to remedy this problem is to propose language in the form of taxonomy and functional models. Our intent is to document and validate our best thinking in this area and publish a perspective that will stimulate discussion. We encourage others to do the same with the belief that focused discussion on language issues will accelerate the inherently slow natural evolution of language selection and thus alleviate related problems. In this work, we propose a theoretical framework for describing BI-technology-related studies. The proposed framework is based on the theoretical concepts and terminology from classical science, assistive technology development, human-computer interaction, and previous BI-related works. Using a representative set of studies from the literature, the proposed BI study framework was shown to be complete and appropriate perspective for thoroughly characterizing a BI study. We have also demonstrated that this BI study framework is useful for (1) objectively reviewing existing BI study designs and results, (2) comparing designs and results of multiple BI studies, (3) designing new studies or objectively reporting BI study results, and (4) facilitating intra- and inter-group communication and the education of new researchers. As such, it forms a sound and appropriate basis for community discussion.

Brain↗
PubMed2006

A computational model to link psychophysics and cortical cell activation patterns in human texture processing.

The human visual system uses texture information to automatically, or pre-attentively, segregate parts of the visual scene. We investigate the neural substrate underlying human texture processing using a computational model that consists of a hierarchy of bi-directionally linked model areas. The model builds upon two key hypotheses, namely that (i) texture segregation is based on boundary detection--rather than clustering of homogeneous items--and (ii) texture boundaries are detected mainly on the basis of a large scenic context that is analyzed by higher cortical areas within the ventral visual pathway, such as area V4. Here, we focus on the interpretation of key results from psychophysical studies on human texture segmentation. In psychophysical studies, texture patterns were varied along several feature dimensions to systematically characterize human performance. We use simulations to demonstrate that the activation patterns of our model directly correlate with the psychophysical results. This allows us to identify the putative neural mechanisms and cortical key areas which underlie human behavior. In particular, we investigate (i) the effects of varying texture density on target saliency, and the impact of (ii) element alignment and (iii) orientation noise on the detectability of a pop-out bar. As a result, we demonstrate that the dependency of target saliency on texture density is linked to a putative receptive field organization of orientation-selective neurons in V4. The effect of texture element alignment is related to grouping mechanisms in early visual areas. Finally, the modulation of cell activity by feedback activation from higher model areas, interacting with mechanisms of intra-areal center-surround competition, is shown to result in the specific suppression of noise-related cell activities and to improve the overall model capabilities in texture segmentation. In particular, feedback interaction is crucial to raise the model performance to the level of human observers.

Action Potentials↗
PubMed1993

Segmentation of medical images through competitive learning.

In image analysis applications, segmentation of gray-level images into meaningful regions is an important low-level processing step. Various approaches to segmentation investigated in the literature, in general, use either local information of gray-level values of pixels (region growing based methods, for example) or the global information (histogram thresholding based methods, for example). Application of these approaches for segmenting medical images often does not provide satisfactory results. Medical images are usually characterized by low local contrast and noisy or faded features causing unacceptable performance of local information based segmentation methods. In addition, because of a large amount of structural information found in medical images, global information based segmentation methods yield inadequate results in region extraction. We present a novel approach to image segmentation that combines local contrast as well as global gray-level distribution information. The presented method adaptively learns useful features and regions through the use of a normalized contrast function as a measure of local information and a competitive learning based method to update region segmentation incorporating global information about the gray-level distribution of the image. In this paper, we present the framework of such a self organizing feature map, and show the results on simulated as well as real medical images.

Algorithms↗
PubMed1996

Hybrid evolutionary programming for heavily constrained problems.

A hybrid of evolutionary programming (EP) and a deterministic optimization procedure is applied to a series of non-linear and quadratic optimization problems. The hybrid scheme is compared with other existing schemes such as EP alone, two-phase (TP) optimization, and EP with a non-stationary penalty function (NS-EP). The results indicate that the hybrid method can outperform the other methods when addressing heavily constrained optimization problems in terms of computational efficiency and solution accuracy.

Biological Evolution↗
PubMedDate not supplied

Automatic detection of intracranial contours in MR images.

Segmentation of the intracranial cavity in medical images is valuable in several research areas such as the quantitative analysis of normal and abnormal brain tissues, the registration of different imaging modalities (MRI, PET, CT) based on surface models of the brain, and the rendering of volume data. Because the manual delineation of the brain contour in the images can be demanding and error prone, an automatic procedure to perform this task is desirable. We have developed and tested a robust method that permits the automatic detection of the intracranial contour in transverse MR images. The method is described and its performance evaluated.

Algorithms↗
PubMed2005

Applying instance-based techniques to prediction of final outcome in acute stroke.

OBJECTIVE: Acute cerebral stroke is a frequent cause of death and the major cause of adult neurological disability in the western world. Thrombolysis is the only established treatment of ischemic stroke; however, its use carries a substantial risk of symptomatic intracerebral hemorrhage. A clinical tool to guide the use of thrombolysis would be very valuable. One of the major goals of such a tool would be the identification of potentially salvageable tissue. This requires an accurate prediction of the extent of infarction if untreated. In this study, we investigate the applicability of highly flexible instance-based (IB) methods for such predictions. METHODS AND MATERIALS: Based on information obtained from magnetic resonance imaging of 14 patients with acute stroke, we explored three different implementations of the IB method: k-NN, Gaussian weighted, and constant radius search classification. Receiver operating characteristics analysis, in particular area under the curve (AUC), was used as performance measure. RESULTS: We found no significant difference (P = 0.48) in performance for the optimal k-NN (k = 164, AUC = 0.814 +/- 0.001) and Gaussian weight (sigma = 0.17, AUC = 0.813 +/- 0.001) implementations, while they were both significantly better (P < 1 x 10(-6) for both) than the constant radius implementation (R = 0.28, AUC = 0.809 +/- 0.001). Qualitative analyses of the distribution of instances in the feature space indicated that non-infarcted instances tends to cluster together while infarcted instances are more dispersed, and that there may not exist a stringent boundary separating infarcted from non-infarcted instances. CONCLUSIONS: This study shows that IB methods can be used, and may be advantageous, for predicting final infarct in patients with acute stroke, but further work must be done to make them clinically applicable.

Adult↗
PubMed2006

Using ontologies linked with geometric models to reason about penetrating injuries.

OBJECTIVE: Medical assessment of penetrating injuries is a difficult and knowledge-intensive task, and rapid determination of the extent of internal injuries is vital for triage and for determining the appropriate treatment. Physical examination and computed tomographic (CT) imaging data must be combined with detailed anatomic, physiologic, and biomechanical knowledge to assess the injured subject. We are developing a methodology to automate reasoning about penetrating injuries using canonical knowledge combined with specific subject image data. METHODS AND MATERIAL: In our approach, we build a three-dimensional geometric model of a subject from segmented images. We link regions in this model to entities in two knowledge sources: (1) a comprehensive ontology of anatomy containing organ identities, adjacencies, and other information useful for anatomic reasoning and (2) an ontology of regional perfusion containing formal definitions of arterial anatomy and corresponding regions of perfusion. We created computer reasoning services ("problem solvers") that use the ontologies to evaluate the geometric model of the subject and deduce the consequences of penetrating injuries. RESULTS: We developed and tested our methods using data from the Visible Human. Our problem solvers can determine the organs that are injured given particular trajectories of projectiles, whether vital structures--such as a coronary artery--are injured, and they can predict the propagation of injury ensuing after vital structures are injured. CONCLUSION: We have demonstrated the capability of using ontologies with medical images to support computer reasoning about injury based on those images. Our methodology demonstrates an approach to creating intelligent computer applications that reason with image data, and it may have value in helping practitioners in the assessment of penetrating injury.

Diagnosis, Computer-Assisted↗
PubMed2005

Machine learning in bioinformatics: a brief survey and recommendations for practitioners.

Machine learning is used in a large number of bioinformatics applications and studies. The application of machine learning techniques in other areas such as pattern recognition has resulted in accumulated experience as to correct and principled approaches for their use. The aim of this paper is to give an account of issues affecting the application of machine learning tools, focusing primarily on general aspects of feature and model parameter selection, rather than any single specific algorithm. These aspects are discussed in the context of published bioinformatics studies in leading journals over the last 5 years. We assess to what degree the experience gained by the pattern recognition research community pervades these bioinformatics studies. We finally discuss various critical issues relating to bioinformatic data sets and make a number of recommendations on the proper use of machine learning techniques for bioinformatics research based upon previously published research on machine learning.

Algorithms↗
PubMed2025

Three-dimensional U-Net with transfer learning improves automated whole brain delineation from MRI brain scans of rats, mice, and monkeys.

BACKGROUND: Automated whole-brain delineation (WBD) techniques often struggle to generalize across pre-clinical studies due to variations in animal models, magnetic resonance imaging (MRI) scanners, and tissue contrasts. We developed a 3D U-Net neural network for WBD pre-trained on organophosphate intoxication (OPI) rat brain MRI scans. We used transfer learning (TL) to adapt this OPI-pretrained network to other animal models: rat model of Alzheimer's disease (AD), mouse model of tetramethylenedisulfotetramine (TETS) intoxication, and titi monkey model of social bonding. METHODS: We assessed an OPI-pretrained 3D U-Net across animal models under three conditions: (1) direct application to each dataset; (2) utilizing TL; and (3) training disease-specific U-Net models. For each condition, training dataset size (TDS) was optimized, and output WBDs were compared to manual segmentations for accuracy. RESULTS: The OPI-pretrained 3D U-Net (TDS&#xa0;=&#xa0;100) achieved the best accuracy [median[min-max]] for the test OPI dataset with a Dice coefficient (DC)&#xa0;=&#xa0;[0.987 [0.977-0.992]] and Hausdorff distance (HD)&#xa0;=&#xa0;[0.86 [0.55-1.27]]mm. TL improved generalization across all models [AD (TDS&#xa0;=&#xa0;40): DC&#xa0;=&#xa0;0.987 [0.977-0.992] and HD&#xa0;=&#xa0;0.72 [0.54-1.00]mm; TETS (TDS&#xa0;=&#xa0;10): DC&#xa0;=&#xa0;0.992 [0.984-0.993] and HD&#xa0;=&#xa0;0.40 [0.31-0.50]mm; Monkey (TDS&#xa0;=&#xa0;8): DC&#xa0;=&#xa0;0.977 [0.968-0.979] and HD&#xa0;=&#xa0;3.03 [2.19-3.91]mm], showing performance comparable to disease-specific networks. CONCLUSIONS: The OPI-pretrained 3D U-Net with TL achieved accuracy comparable to disease-specific networks with reduced training data (TDS &#x2264; 40 scans) across all models. Future work will focus on developing a multi-region delineation pipeline for pre-clinical MRI brain data, utilizing the proposed WBD as an initial step.

Animals↗
PubMed2005

Tumor feature visualization with unsupervised learning.

Dynamic contrast enhanced magnetic resonance imaging (DCE MRI) is applied for diagnosis and therapy control of breast cancer. The malignancy of a lesion is expressed in the average signal kinetics of selected regions of interest (ROI) representing the lesion. The technique is reported to characterize malignant tumors with high sensitivity and highly variable specificity. Computer-based diagnosis (CAD) systems have been proposed to analyze and classify signal time curve data, extracted from hand selected ROI in the DCE MRI data. In this paper, we apply the self-organizing map (SOM) to a set of time curve feature vectors of single voxels from seven benign lesions and seven malignant tumors. Applying the SOM we are able to project the time curve values of each voxel on a two-dimensional map. The results show, that the SOM is able to visualize the hidden two-dimensional structure of the six-dimensional signal space. Using the trained SOM, we are able to identify voxels with benign or malignant signal characteristics and to visualize lesion cross-sections with pseudo-colors. A comparison with the established three time points method shows that the SOM has clear potential for deriving visualization parameters in DCE MRI analysis.

Breast Neoplasms↗