14243133
Generalization Performance in PARSEC - A Structured Connectionist Parsing Architecture
This paper presents PARSEC--a system for generating connectionist parsing networks from example parses. PARSEC is not based on formal grammar systems and is geared toward spoken language tasks. PARSEC networks exhibit three strengths important for application to speech processing: 1) they learn to parse, and generalize well compared to hand-coded grammars; 2) they tolerate several types of noise; 3) they can learn to use multi-modal input. Presented are the PARSEC architecture and performance analyses along several dimensions that demonstrate PARSEC's features. PARSEC's performance is compared to that of traditional grammar-based parsing systems.
6517871
Deriving quantitative conclusions from microarray expression data
MOTIVATION
The last few years have seen the development of DNA microarray technology that allows simultaneous measurement of the expression levels of thousands of genes. While many methods have been developed to analyze such data, most have been visualization-based. Methods that yield quantitative conclusions have been diverse and complex.


RESULTS
We present two straightforward methods for identifying specific genes whose expression is linked with a phenotype or outcome variable as well as for systematically predicting sample class membership: (1) a conservative, permutation-based approach to identifying differentially expressed genes; (2) an augmentation of K-nearest-neighbor pattern classification. Our analyses replicate the quantitative conclusions of Golub et al. (1999; Science, 286, 531-537) on leukemia data, with better classification results, using far simpler methods. With the breast tumor data of Perou et al. (2000; Nature, 406, 747-752), the methods lend rigorous quantitative support to the conclusions of the original paper. In the case of the lymphoma data in Alizadeh et al. (2000; Nature, 403, 503-511), our analyses only partially support the conclusions of the original authors.


AVAILABILITY
The software and supplementary information are available freely to researchers at academic and non-profit institutions at http://cc.ucsf.edu/jain/public
13887159
JANUS: Speech-to-Speech Translation Using Connectionist and Non-Connectionist Techniques
We present JANUS, a speech-to-speech translation system that utilizes diverse processing strategies, including connectionist learning, traditional AI knowledge representation approaches, dynamic programming, and stochastic techniques. JANUS translates continuously spoken English and German into German, English, and Japanese. JANUS currently achieves 87% translation fidelity from English speech and 97% from German speech. We present the JANUS system along with comparative evaluations of its interchangeable processing components, with special emphasis on the connectionist modules.
13422669
Incremental Parsing by Modular Recurrent Connectionist Networks
We present a novel, modular, recurrent connectionist network architecture which learns to robustly perform incremental parsing of complex sentences. From sequential input, one word at a time, our networks learn to do semantic role assignment, noun phrase attachment, and clause structure recognition for sentences with passive constructions and center embedded clauses. The networks make syntactic and semantic predictions at every point in time, and previous predictions are revised as expectations are affirmed or violated with the arrival of new information. Our networks induce their own "grammar rules" for dynamically transforming an input sequence of words into a syntactic/semantic interpretation. These networks generalize and display tolerance to input which has been corrupted in ways common in spoken language.
16190800
Pathway recognition and augmentation by computational analysis of microarray expression data
MOTIVATION
We present a system, QPACA (Quantitative Pathway Analysis in Cancer) for analysis of biological data in the context of pathways. QPACA supports data visualization and both fine- and coarse-grained specifications, but, more importantly, addresses the problems of pathway recognition and pathway augmentation.


RESULTS
Given a set of genes hypothesized to be part of a pathway or a coordinated process, QPACA is able to reliably distinguish true pathways from non-pathways using microarray expression data. Relying on the observation that only some of the experiments within a dataset are relevant to a specific biochemical pathway, QPACA automates selection of this subset using an optimization procedure. We present data on all human and yeast pathways found in the KEGG pathway database. In 117 out of 191 cases (61%), QPACA was able to correctly identify these positive cases as bona fide pathways with p-values measured using rigorous permutation analysis. Success in recognizing pathways was dependent on pathway size, with the largest quartile of pathways yielding 83% success. In cross-validation tests of pathway membership prediction, QPACA was able to yield enrichments for predicted pathway genes over random genes at rates of 2-fold or better the majority of the time, with rates of 10-fold or better 10-20% of the time.


AVAILABILITY
The software is available for academic research use free of charge by email request.


SUPPLEMENTARY INFORMATION
Data used in the paper may be downloaded from http://www.jainlab.org/downloads.html
5941903
A deterministic motif finding algorithm with application to the human genome
MOTIVATION
We present a novel algorithm, MaMF, for identifying transcription factor (TF) binding site motifs. The method is deterministic and depends on an indexing technique to optimize the search process. On common yeast datasets, MaMF performs competitively with other methods. We also present results on a challenging group of eight sets of human genes known to be responsive to a diverse group of TFs. In every case, MaMF finds the annotated motif among the top scoring putative motifs. We compared MaMF against other motif finders on a larger human group of 21 gene sets and found that MaMF performs better than other algorithms. We analyzed the remaining high scoring motifs and show that many correspond to other TFs that are known to co-occur with the annotated TF motifs. The significant and frequent presence of co-occurring transcription factor binding sites explains in part the difficulty of human motif finding. MaMF is a very fast algorithm, suitable for application to large numbers of interesting gene sets.
16967659
Content-based adaptive compression of educational videos using phase correlation techniques
A serious bottleneck towards multimedia e-learning is the non-availability of required bandwidth to view the lecture videos at good resolution because of large size of lecture videos. Content-based compression of video data can greatly enhance the bandwidth utilization over scarce resource networks. In this paper, an educational video compression technique is presented that dynamically allocates the space according to the content importance of each video segment in the educational videos. We present a phase-correlation-based motion estimation and compensation algorithm that assists in the compression of important moving objects in an efficient manner. Temporal coherence is exploited in a two-phase manner. First, the frames with high similarity are categorized and encoded efficiently. Second, the compression ratio is adapted according to the frame content. Shots that are of high importance are stored at a higher bit rate as compared to the frames of relatively low importance. The importance and priority of the frames is computed automatically by our algorithm. Results over several hours of educational videos and comparison with the state-of-the-art compression algorithms illustrate the high compression performance of our technique.
5467372
Organizing and Searching the World Wide Web of Facts - Step One: The One-Million Fact Extraction Challenge
Due to the inherent difficulty of processing noisy text, the potential of the Web as a decentralized repository of human knowledge remains largely untapped during Web search. The access to billions of binary relations among named entities would enable new search paradigms and alternative methods for presenting the search results. A first concrete step towards building large searchable repositories of factual knowledge is to derive such knowledge automatically at large scale from textual documents. Generalized contextual extraction patterns allow for fast iterative progression towards extracting one million facts of a given type (e.g., Person-BornIn-Year) from 100 million Web documents of arbitrary quality. The extraction starts from as few as 10 seed facts, requires no additional input knowledge or annotated text, and emphasizes scale and coverage by avoiding the use of syntactic parsers, named entity recognizers, gazetteers, and similar text processing tools and resources.
391822
Using Stationary-Dynamic Camera Assemblies for Wide-area Video Surveillance and Selective Attention
In this paper, we present a prototype video surveillance system that uses stationary-dynamic (or master-slave) camera assemblies to achieve wide-area surveillance and selective focus-of-attention. We address two critical issues in deploying such camera assemblies in real-world applications: off-line camera calibration and on-line selective focus-ofattention. Our contributions over existing techniques are twofold: (1) in terms of camera calibration, our technique calibrates all degrees-of-freedom (DOFs) of both stationary and dynamic cameras, using a closed-form solution that is both efficient and accurate, and (2) in terms of selective focus-of-attention, our technique correctly handles dynamic changes in the scene and varying object depths. This is a significant improvement over existing techniques that use an expensive and non-adaptable table-look-up process.
8533646
Dimensionality reduction using genetic algorithms
Pattern recognition generally requires that objects be described in terms of a set of measurable features. The selection and quality of the features representing each pattern affect the success of subsequent classification. Feature extraction is the process of deriving new features from original features to reduce the cost of feature measurement, increase classifier efficiency, and allow higher accuracy. Many feature extraction techniques involve linear transformations of the original pattern vectors to new vectors of lower dimensionality. While this is useful for data visualization and classification efficiency, it does not necessarily reduce the number of features to be measured since each new feature may be a linear combination of all of the features in the original pattern vector. Here, we present a new approach to feature extraction in which feature selection and extraction and classifier training are performed simultaneously using a genetic algorithm. The genetic algorithm optimizes a feature weight vector used to scale the individual features in the original pattern vectors. A masking vector is also employed for simultaneous selection of a feature subset. We employ this technique in combination with the k nearest neighbor classification rule, and compare the results with classical feature selection and extraction techniques, including sequential floating forward feature selection, and linear discriminant analysis. We also present results for the identification of favorable water-binding sites on protein surfaces.
39123560
High Quality Compression of Educational Videos Using Content-Adaptive Framework
With multimedia E-learning becoming popular, better compression algorithms are required that are space efficient but maintain the quality of video data, particularly slide and blackboard text. In this paper, an educational video compression technique is presented that dynamically allocates the space according to the content importance of each video segment in the educational videos. We present a phase correlation based motion estimation and compensation algorithm to encode important moving objects in efficient manner. Temporal coherence is exploited in a two phase manner. First, the frames with high similarity are categorized and encoded efficiently. Secondly, the compression ratio is adapted according to the frame content. The algorithm is compared with the state-of-the-art standards such as H.261, MPEG-4, etc. on large database. The comparison shows that for similar bit rates, the video quality for our algorithm is significantly better than the other methods.