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PubMed1997

Discovering Neural Nets with Low Kolmogorov Complexity and High Generalization Capability.

Many neural net learning algorithms aim at finding "simple" nets to explain training data. The expectation is that the "simpler" the networks, the better the generalization on test data (--> Occam's razor). Previous implementations, however, use measures for "simplicity" that lack the power, universality and elegance of those based on Kolmogorov complexity and Solomonoff's algorithmic probability. Likewise, most previous approaches (especially those of the "Bayesian" kind) suffer from the problem of choosing appropriate priors. This paper addresses both issues. It first reviews some basic concepts of algorithmic complexity theory relevant to machine learing, and how the Solomonoff-Levin distribution (or universal prior) deals with the prior problem. The universal prior leads to a probabilistic method for finding "algorithmically simple" problem solutions with high generalization capability. The method is based on Levin complexity (a time-bounded generalization of Kolmogorov complexity) and inspired by Levin's optimal universal search algorithm. For a given problem, solution candidates are computed by efficient "self-sizing" programs that influence their own runtime and storage size. The probabilistic search algorithm finds the "good" programs (the ones quickly computing algorithmically probable solutions fitting the training data). Simulations focus on the task of discovering "algorithmically simple" neural networks with low Kolmogorov complexity and high generalization capability. It is demonstrated that the method, at least with certain toy problems where it is computationally feasible, can lead to generalization results unmatchable by previous neural network algorithms. Much remains to be done, however, to make large scale applications and "incremental learning" feasible. Copyright 1997 Elsevier Science Ltd.

Journal Article↗

PubMedDate not supplied

Predicting protein-ligand binding affinities using novel geometrical descriptors and machine-learning methods.

Inspired by the concept of knowledge-based scoring functions, a new quantitative structure-activity relationship (QSAR) approach is introduced for scoring protein-ligand interactions. This approach considers that the strength of ligand binding is correlated with the nature of specific ligand/binding site atom pairs in a distance-dependent manner. In this technique, atom pair occurrence and distance-dependent atom pair features are used to generate an interaction score. Scoring and pattern recognition results obtained using Kernel PLS (partial least squares) modeling and a genetic algorithm-based feature selection method are discussed.

Algorithms↗

PubMed2007

Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices.

BACKGROUND: Protein-protein interactions are critical for cellular functions. Recently developed computational approaches for predicting protein-protein interactions utilize co-evolutionary information of the interacting partners, e.g., correlations between distance matrices, where each matrix stores the pairwise distances between a protein and its orthologs from a group of reference genomes. RESULTS: We proposed a novel, simple method to account for some of the intra-matrix correlations in improving the prediction accuracy. Specifically, the phylogenetic species tree of the reference genomes is used as a guide tree for hierarchical clustering of the orthologous proteins. The distances between these clusters, derived from the original pairwise distance matrix using the Neighbor Joining algorithm, form intermediate distance matrices, which are then transformed and concatenated into a super phylogenetic vector. A support vector machine is trained and tested on pairs of proteins, represented as super phylogenetic vectors, whose interactions are known. The performance, measured as ROC score in cross validation experiments, shows significant improvement of our method (ROC score 0.8446) over that of using Pearson correlations (0.6587). CONCLUSION: We have shown that the phylogenetic tree can be used as a guide to extract intra-matrix correlations in the distance matrices of orthologous proteins, where these correlations are represented as intermediate distance matrices of the ancestral orthologous proteins. Both the unsupervised and supervised learning paradigms benefit from the explicit inclusion of these intermediate distance matrices, and particularly so in the latter case, which offers a better balance between sensitivity and specificity in the prediction of protein-protein interactions.

Computational Biology↗

PubMed2003

Gene networks inference using dynamic Bayesian networks.

This article deals with the identification of gene regulatory networks from experimental data using a statistical machine learning approach. A stochastic model of gene interactions capable of handling missing variables is proposed. It can be described as a dynamic Bayesian network particularly well suited to tackle the stochastic nature of gene regulation and gene expression measurement. Parameters of the model are learned through a penalized likelihood maximization implemented through an extended version of EM algorithm. Our approach is tested against experimental data relative to the S.O.S. DNA Repair network of the Escherichia coli bacterium. It appears to be able to extract the main regulations between the genes involved in this network. An added missing variable is found to model the main protein of the network. Good prediction abilities on unlearned data are observed. These first results are very promising: they show the power of the learning algorithm and the ability of the model to capture gene interactions.

Algorithms↗

PubMed2002

Using machine learning classifiers to identify glaucomatous change earlier in standard visual fields.

PURPOSE: To compare the ability of several machine learning classifiers to predict development of abnormal fields at follow-up in ocular hypertensive (OHT) eyes that had normal visual fields in baseline examination. METHODS: The visual fields of 114 eyes of 114 patients with OHT with four or more visual field tests with standard automated perimetry over three or more years and for whom stereophotographs were available were assessed. The mean (+/-SD) number of visual field tests was 7.89 +/- 3.04. The mean number of years covered (+/-SD) was 5.92 +/- 2.34 (range, 2.81-11.77). Fields were classified as normal or abnormal based on Statpac-like methods (Humphrey Instruments, Dublin, CA) and by several machine learning classifiers. The machine learning classifiers were two types of support vector machine (SVM), a mixture of Gaussian (MoG) classifier, a constrained MoG, and a mixture of generalized Gaussian (MGG). Specificity was set to 96% for all classifiers, using data from 94 normal eyes evaluated longitudinally. Specificity cutoffs required confirmation of abnormality. RESULTS: Thirty-two percent (36/114) of the eyes converted to abnormal fields during follow-up based on the Statpac-like methods. All 36 were identified by at least one machine classifier. In nearly all cases, the machine learning classifiers predicted the confirmed abnormality, on average, 3.92 +/- 0.55 years earlier than traditional Statpac-like methods. CONCLUSIONS: Machine learning classifiers can learn complex patterns and trends in data and adapt to create a decision surface without the constraints imposed by statistical classifiers. This adaptation allowed the machine learning classifiers to identify abnormality in visual field converts much earlier than the traditional methods.

Algorithms↗

PubMed2006

Brain interface research for asynchronous control applications.

The Neil Squire Society has developed asynchronous, direct brain switches for self-paced control applications with mean activation rates of 73% and false positive error rates of 2%. This report summarizes our results to date, lessons learned, and current directions, including research into implanted brain interface designs.

Algorithms↗

PubMed2006

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

Biological Evolution↗

PubMed2004

Evaluating robustness of gait event detection based on machine learning and natural sensors.

A real-time system for deriving timing control for functional electrical stimulation for foot-drop correction, using peripheral nerve activity as a sensor input, was tested for reliability to investigate the potential for clinical use. The system, which was previously reported on, was tested on a hemiplegic subject instrumented with a recording cuff electrode on the Sural nerve, and a stimulation cuff electrode on the Peroneal cuff. Implanted devices enabled recording and stimulation through telelinks. An input domain was derived from the recorded electroneurogram and fed to a detection algorithm based on an adaptive logic network for controlling the stimulation timing. The reliability was tested by letting the subject wear different foot wear and walk on different surfaces than when the training data was recorded. The detection system was also evaluated several months after training. The detection system proved able to successfully detect when walking with different footwear on varying surfaces up to 374 days after training, and thereby showed great potential for being clinically useful.

Action Potentials↗

PubMed2002

On the emergence of rules in neural networks.

A simple associationist neural network learns to factor abstract rules (i.e., grammars) from sequences of arbitrary input symbols by inventing abstract representations that accommodate unseen symbol sets as well as unseen but similar grammars. The neural network is shown to have the ability to transfer grammatical knowledge to both new symbol vocabularies and new grammars. Analysis of the state-space shows that the network learns generalized abstract structures of the input and is not simply memorizing the input strings. These representations are context sensitive, hierarchical, and based on the state variable of the finite-state machines that the neural network has learned. Generalization to new symbol sets or grammars arises from the spatial nature of the internal representations used by the network, allowing new symbol sets to be encoded close to symbol sets that have already been learned in the hidden unit space of the network. The results are counter to the arguments that learning algorithms based on weight adaptation after each exemplar presentation (such as the long term potentiation found in the mammalian nervous system) cannot in principle extract symbolic knowledge from positive examples as prescribed by prevailing human linguistic theory and evolutionary psychology.

Algorithms↗

PubMed2001

A comparison of machine learning methods for the diagnosis of pigmented skin lesions.

We analyze the discriminatory power of k-nearest neighbors, logistic regression, artificial neural networks (ANNs), decision tress, and support vector machines (SVMs) on the task of classifying pigmented skin lesions as common nevi, dysplastic nevi, or melanoma. Three different classification tasks were used as benchmarks: the dichotomous problem of distinguishing common nevi from dysplastic nevi and melanoma, the dichotomous problem of distinguishing melanoma from common and dysplastic nevi, and the trichotomous problem of correctly distinguishing all three classes. Using ROC analysis to measure the discriminatory power of the methods shows that excellent results for specific classification problems in the domain of pigmented skin lesions can be achieved with machine-learning methods. On both dichotomous and trichotomous tasks, logistic regression, ANNs, and SVMs performed on about the same level, with k-nearest neighbors and decision trees performing worse.

Algorithms↗

PubMed2025

Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment.

BACKGROUND: Growing evidence supports the importance of characterizing the organizational patterns of various cellular constituents in the tumor microenvironment in precision oncology. Most existing data on immune cell infiltrates in tumors, which are based on immune cell counts or nearest neighbor-type analyses, have failed to fully capture the cellular organization and heterogeneity. METHODS: We introduce a computational algorithm, termed Tumor-Immune Partitioning and Clustering (TIPC), that jointly measures immune cell partitioning between tumor epithelial and stromal areas and immune cell clustering versus dispersion. As proof-of-principle, we applied TIPC to a prospective cohort incident tumor biobank containing 931 colorectal carcinoma cases. TIPC identified tumor subtypes with unique spatial patterns between tumor cells and T lymphocytes linked to certain molecular pathologic and prognostic features. T lymphocyte identification and phenotyping were achieved using multiplexed (multispectral) immunofluorescence. In a separate hepatocellular carcinoma cohort, we replaced the stromal component with specific immune cell types-CXCR3+CD68+ or CD8+-to profile their spatial relationships with CXCL9+CD68+ cells. RESULTS: Six unsupervised TIPC subtypes based on T lymphocyte distribution patterns were identified, comprising two cold and four hot subtypes. Three of the four hot subtypes were associated with significantly longer colorectal cancer (CRC)-specific survival compared to a reference cold subtype. Our analysis showed that variations in T-cell densities among the TIPC subtypes did not strictly correlate with prognostic benefits, underscoring the prognostic significance of immune cell spatial patterns. Additionally, TIPC revealed two spatially distinct and cell density-specific subtypes among microsatellite instability-high colorectal cancers, indicating its potential to upgrade tumor subtyping. TIPC was also applied to additional immune cell types, eosinophils and neutrophils, identified using morphology and supervised machine learning; here two tumor subtypes with similarly low densities, namely 'cold, tumor-rich' and 'cold, stroma-rich', exhibited differential prognostic associations. Lastly, we validated our methods and results using The Cancer Genome Atlas colon and rectal adenocarcinoma data (n = 570). Moreover, applying TIPC to hepatocellular carcinoma cases (n = 27) highlighted critical cell interactions like CXCL9-CXCR3 and CXCL9-CD8. CONCLUSIONS: Unsupervised discoveries of microgeometric tissue organizational patterns and novel tumor subtypes using the TIPC algorithm can deepen our understanding of the tumor immune microenvironment and likely inform precision cancer immunotherapy.

Humans↗

PubMed2004

ESPD: a pattern detection model underlying gene expression profiles.

MOTIVATION: DNA arrays permit rapid, large-scale screening for patterns of gene expression and simultaneously yield the expression levels of thousands of genes for samples. The number of samples is usually limited, and such datasets are very sparse in high-dimensional gene space. Furthermore, most of the genes collected may not necessarily be of interest and uncertainty about which genes are relevant makes it difficult to construct an informative gene space. Unsupervised empirical sample pattern discovery and informative genes identification of such sparse high-dimensional datasets present interesting but challenging problems. RESULTS: A new model called empirical sample pattern detection (ESPD) is proposed to delineate pattern quality with informative genes. By integrating statistical metrics, data mining and machine learning techniques, this model dynamically measures and manipulates the relationship between samples and genes while conducting an iterative detection of informative space and the empirical pattern. The performance of the proposed method with various array datasets is illustrated.

Algorithms↗

PubMed2005

On the use of qualitative reasoning to simulate and identify metabolic pathways.

MOTIVATION: Perhaps the greatest challenge of modern biology is to develop accurate in silico models of cells. To do this we require computational formalisms for both simulation (how according to the model the state of the cell evolves over time) and identification (learning a model cell from observation of states). We propose the use of qualitative reasoning (QR) as a unified formalism for both tasks. The two most commonly used alternative methods of modelling biochemical pathways are ordinary differential equations (ODEs), and logical/graph-based (LG) models. RESULTS: The QR formalism we use is an abstraction of ODEs. It enables the behaviour of many ODEs, with different functional forms and parameters, to be captured in a single QR model. QR has the advantage over LG models of explicitly including dynamics. To simulate biochemical pathways we have developed 'enzyme' and 'metabolite' QR building blocks that fit together to form models. These models are finite, directly executable, easy to interpret and robust. To identify QR models we have developed heuristic chemoinformatics graph analysis and machine learning procedures. The graph analysis procedure is a series of constraints and heuristics that limit the number of ways metabolites can combine to form pathways. The machine learning procedure is generate-and-test inductive logic programming. We illustrate the use of QR for modelling and simulation using the example of glycolysis. AVAILABILITY: All data and programs used are available on request.

Algorithms↗

PubMed1993

Prediction of primate splice junction gene sequences with a cooperative knowledge acquisition system.

We propose a cooperative conceptual modelling environment in which two agents interact: the machine and the human expert. The former is able to extract knowledge from data using a symbolic-numeric machine learning system, and the latter is able to control the learning process by accepting and validating the machine results, or by criticizing those results or the explanation that the system produces on them. The improvement of the conceptual modelling relies on the cooperation between the two agents. Results obtained with our method on prediction of primate splice junctions sites in genetic sequences are far better than those reported in the literature with other symbolic machine learning systems, and are as better as those obtained with some artificial neural networks methods reported at present. But in opposite to neural networks which lack of argumentation, our system provides the user a plausible explanation of its prediction.

Algorithms↗

PubMed2005

Automated expert multiexponential biomodeling interactively over the Internet.

DIMSUM, an acronym for DIMension of a SUM of exponentials, is a highly automated expert system for fitting multiexponential models of increasing dimension to time series data. Up to now, a researcher has needed an individual copy of DIMSUM on his or her own computer as well as support to learn how to use it. W3DIMSUM, a new implementation of DIMSUM, is web-based, new territory for interactive biomodeling, allowing interactive multiexponential model building and model discrimination over the Internet. The algorithms used are numerically intensive, so we have implemented a distributed system, with numerical processing done on our server. Only the user interface is run on the client machine, but users can load and save data and results on their machines, facilitated by our use of Java WebStart.

Algorithms↗

PubMed2005

Application of machine learning and visualization of heterogeneous datasets to uncover relationships between translation and developmental stage expression of C. elegans mRNAs.

The relationships between genes in neighboring clusters in a self-organizing map (SOM) and properties attributed to them are sometimes difficult to discern, especially when heterogeneous datasets are used. We report a novel approach to identify correlations between heterogeneous datasets. One dataset, derived from microarray analysis of polysomal distribution, contained changes in the translational efficiency of Caenorhabditis elegans mRNAs resulting from loss of specific eIF4E isoform. The other dataset contained expression patterns of mRNAs across all developmental stages. Two algorithms were applied to these datasets: a classical scatter plot and an SOM. The outputs were linked using a two-dimensional color scale. This revealed that an mRNA's eIF4E-dependent translational efficiency is strongly dependent on its expression during development. This correlation was not detectable with a traditional one-dimensional color scale.

Algorithms↗

PubMed1993

Reconstructing muscle activation during normal walking: a comparison of symbolic and connectionist machine learning techniques.

One symbolic (rule-based inductive learning) and one connectionist (neural network) machine learning technique were used to reconstruct muscle activation patterns from kinematic data measured during normal human walking at several speeds. The activation patterns (or desired outputs) consisted of surface electromyographic (EMG) signals from the semitendinosus and vastus medialis muscles. The inputs consisted of flexion and extension angles measured at the hip and knee of the ipsilateral leg, their first and second derivatives, and bilateral foot contact information. The training set consisted of data from six trials, at two different speeds. The testing set consisted of data from two additional trials (one at each speed), which were not in the training set. It was possible to reconstruct the muscular activation at both speeds using both techniques. Timing of the reconstructed signals was accurate. The integrated value of the activation bursts was less accurate. The neural network gave a continuous output, whereas the rule-based inductive learning rule tree gave a quantised activation level. The advantage of rule-based inductive learning was that the rules used were both explicit and comprehensible, whilst the rules used by the neural network were implicit within its structure and not easily comprehended. The neural network was able to reconstruct the activation patterns of both muscles from one network, whereas two separate rule sets were needed for the rule-based technique. It is concluded that machine learning techniques, in comparison to explicit inverse muscular skeletal models, show good promise in modelling nearly cyclic movements such as locomotion at varying walking speeds.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

PubMed2002

The bionic man: restoring mobility.

Bionics engineers are making increasingly bold and successful use of their tools to restore mobility to persons with missing or nonfunctional limbs. These tools include the latest materials, minielectronics and megacomputers, advanced robotic mechanisms, and algorithms. With crucial help from their pioneering users, they are learning how and where the residual sensorimotor system can be tapped in order to transmit its intents to replacement or reactivated body parts.

Animals↗