10940267
BioLog: A Browser Based Collaboration and Resource Navigation Assistant for BioMedical Researchers
We often realize that communicating with other colleagues who are studying similar topics helps to identify information relevant to our area of study, which otherwise may not have been found. We wish to accelerate acquisition of collective knowledge in a defined area by identifying specific spheres of inquiry. Such spheres correspond to groups of people who are experts in a field. In this paper we provide a systematic way to gain knowledge from their online search activity, and enable them to organize and share their search findings for further analysis. We have built a prototype system, BioLog, to help biomedical researchers share this implicit knowledge among their peers and store their access patterns into a central system for reuse. BioLog has been deployed it in two labs within TGen as a pilot study. The data has been gathered and analyzed by preliminary text-mining and collaborative filtering methods.
16386059
A Monotonic Measure for Optimal Feature Selection
Feature selection is a problem of choosing a subset of relevant features. In general, only exhaustive search can bring about the optimal subset. With a monotonic measure, exhaustive search can be avoided without sacrificing optimality. Unfortunately, most error- or distancebased measures are not monotonic. A new measure is employed in this work that is monotonic and fast to compute. The search for relevant features according to this measure is guaranteed to be complete but not exhaustive. Experiments are conducted for verification.
5365583
NeuroRule: A Connectionist Approach to Data Mining
Classification, which involves finding rules that partition a given da.ta set into disjoint groups, is one class of data mining problems. Approaches proposed so far for mining classification rules for large databases are mainly decision tree based symbolic learning methods. The connectionist approach based on neura.l networks has been thought not well suited for data mining. One of the major reasons cited is that knowledge generated by neural networks is not explicitly represented in the form of rules suitable for verification or interpretation by humans. This paper examines this issue. With our newly developed algorithms, rules which are similar to, or more concise than those generated by the symbolic methods can be extracted from the neural networks. The data mining process using neural networks with the emphasis on rule extraction is described. ExperimenM results and comparison with previously published works are presented.
46794790
Analysis of Hidden Representations by Greedy Clustering
The hidden layer of backpropagation neural networks (NNs) holds the key to the networks' success in solving pattern classification problems. The units in the hidden layer encapsulate the network's internal representations of the outside world described by the input data. this paper, the hidden representations of trained networks are investigated by means simple greedy clustering algorithm. This clustering algorithm is applied to networks have been trained to solve well-known problems: the monks problems, the 5-bit problem and the contiguity problem. The results from applying the algorithm to problems with known concepts provide us with a better understanding of NN learning. These also explain why NNs achieve higher predictive accuracy than that of decision-tree methods. The results of this study can be readily applied to rule extraction from Production rules are extracted for the parity and the monks problems, as well as benchmark data set: Pima Indian diabetes diagnosis. The extracted rules from the Indi...
8367210
Sensor Sequence Modeling for Driving
Intelligent systems in automobiles need to be aware of the driving and driver context. Available sensor data stream has to be modeled and monitored in order to do so. Currently there exist no building blocks for hierarchical modeling of driving. By semi-supervised segmentation such building blocks can be discovered. We call them drivemes in analogy to phonemes. More parsimonious modeling of driving becomes now possible.
14543078
Resource description framework: metadata and its applications
Universality, the property of the Web that makes it the largest data and information source in the world, is also the property behind the lack of a uniform organization scheme that would allow easy access to data and information. A semantic web, wherein different applications and Web sites can exchange information and hence exploit Web data and information to their full potential, requires the information about Web resources to be represented in a detailed and structured manner. Resource Description Framework (RDF), an effort in this direction supported by the World Wide Web Consortium, provides a means for the description of metadata which is a necessity for the next generation of interoperable Web applications. The success of RDF and the semantic web will depend on (1) the development of applications that prove the applicability of the concept, (2) the availability of application interfaces which enable the development of such applications, and (3) databases and inference systems that exploit RDF to identify and locate most relevant Web resources. In addition, many practical issues, such as security, ease of use, and compatibility, will be crucial in the success of RDF. This survey aims at providing a glimpse at the past, present, and future of this upcoming technology and highlights why we believe that the next generation of the Web will be more organized, informative, searchable, accessible, and, most importantly, useful. It is expected that knowledge discovery and data mining can benefit from RDF and the Semantic Web.
23466581
Object watermarks for digital images and video
Abstract The growth of new image technologies has created a need for techniques that can be used for copyright protection of digital images and video. One approach for copyright protection is to introduce an invisible signal, known as a digital watermark, into an image or video sequence. With the development of MPEG-4, frame-based approach has been migrating to object-based approach. Therefore, object-based watermarking schemes are needed. In this article, we propose a novel blind object watermarking scheme for images and video using shape adaptive-discrete wavelet transform (SA-DWT). To make the watermark robust and perceptual invisible, we embed it in the weighting mean of the wavelet blocks using the quantisation visual model based on the human visual system. Watermark detection is accomplished without the original, unwatermarked object by using statistical detection technique. Experimental results demonstrate that the proposed watermarking scheme is perceptual invisible and robust against many attacks such as lossy image/video compression (e.g. JPEG, JPEG2000 and MPEG-4), scaling, adding noise, filtering, D/A and A/D conversion, etc.
9642703
Discovering typical structures of documents: a road map approach
The structure of a document refers to the role and hierarchy of subdocument references. Many online documents are similarly structured, though not identically structured. We study the problem of discovering “typical” structures of a collection of such documents, where the user specifies the minimum frequency of a typical structure. We will consider structural features of subdocument references such as labeling, nesting, ordering, cyclicity, and wild-card references, like those found on the Web and digital libraries. Typical structures can be used to serve the following purposes. (a) The “table-ofcontent” for gaining the general information of a source. (b) A road map for browsing and querying a source. (c) A basis for clustering documents. (d) Partial schemas for building structured layers to provide standard database access methods. (e) User/customer’s interests and browsing patterns. We present a solution to the discovery problem.
11306780
Mean-entropy discretized features are effective for classifying high-dimensional biomedical data
This paper studies an empirical feature selection heuristics for classifying high-dimensional bio-medical data. A feature's discriminating power can be measured by its entropy value. Based on this idea, we do not consider those features that are ignored by the entropy idea. Such a selection can usually reduce the dimensionality of the data by 90-95%. Then we rank the remaining features, and select features whose entropy is smaller than the average of all the remaining features' entropies. This round of selection can usually further reduce two thirds of the features. So, we can achieve a reduction from tens of thousands of features to only hundreds of important features. Furthermore, we also observe that learning algorithms, including our new tree-committee classifier, generally improve their accuracy after the feature selection. This heuristics appears to be more systematic than the prevailing use of specific numbers of top-ranked features for classification.
10722883
Use of extreme patient samples for outcome prediction from gene expression data
MOTIVATION
Patient outcome prediction using microarray technologies is an important application in bioinformatics. Based on patients' genotypic microarray data, predictions are made to estimate patients' survival time and their risk of tumor metastasis or recurrence. So, accurate prediction can potentially help to provide better treatment for patients.


RESULTS
We present a new computational method for patient outcome prediction. In the training phase of this method, we make use of two types of extreme patient samples: short-term survivors who got an unfavorable outcome within a short period and long-term survivors who were maintaining a favorable outcome after a long follow-up time. These extreme training samples yield a clear platform for us to identify relevant genes whose expression is closely related to the outcome. The selected extreme samples and the relevant genes are then integrated by a support vector machine to build a prediction model, by which each validation sample is assigned a risk score that falls into one of the special pre-defined risk groups. We apply this method to several public datasets. In most cases, patients in high and low risk groups stratified by our method have clearly distinguishable outcome status as seen in their Kaplan-Meier curves. We also show that the idea of selecting only extreme patient samples for training is effective for improving the prediction accuracy when different gene selection methods are used.
23957657
Terminology model discovery using natural language processing and visualization techniques
Medical terminologies are important for unambiguous encoding and exchange of clinical information. The traditional manual method of developing terminology models is time-consuming and limited in the number of phrases that a human developer can examine. In this paper, we present an automated method for developing medical terminology models based on natural language processing (NLP) and information visualization techniques. Surgical pathology reports were selected as the testing corpus for developing a pathology procedure terminology model. The use of a general NLP processor for the medical domain, MedLEE, provides an automated method for acquiring semantic structures from a free text corpus and sheds light on a new high-throughput method of medical terminology model development. The use of an information visualization technique supports the summarization and visualization of the large quantity of semantic structures generated from medical documents. We believe that a general method based on NLP and information visualization will facilitate the modeling of medical terminologies.