12471299
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity
MOTIVATION
Small molecules play a fundamental role in organic chemistry and biology. They can be used to probe biological systems and to discover new drugs and other useful compounds. As increasing numbers of large datasets of small molecules become available, it is necessary to develop computational methods that can deal with molecules of variable size and structure and predict their physical, chemical and biological properties.


RESULTS
Here we develop several new classes of kernels for small molecules using their 1D, 2D and 3D representations. In 1D, we consider string kernels based on SMILES strings. In 2D, we introduce several similarity kernels based on conventional or generalized fingerprints. Generalized fingerprints are derived by counting in different ways subpaths contained in the graph of bonds, using depth-first searches. In 3D, we consider similarity measures between histograms of pairwise distances between atom classes. These kernels can be computed efficiently and are applied to problems of classification and prediction of mutagenicity, toxicity and anti-cancer activity on three publicly available datasets. The results derived using cross-validation methods are state-of-the-art. Tradeoffs between various kernels are briefly discussed.


AVAILABILITY
Datasets available from http://www.igb.uci.edu/servers/servers.html
1954824
ChemDB: a public database of small molecules and related chemoinformatics resources
MOTIVATION
The development of chemoinformatics has been hampered by the lack of large, publicly available, comprehensive repositories of molecules, in particular of small molecules. Small molecules play a fundamental role in organic chemistry and biology. They can be used as combinatorial building blocks for chemical synthesis, as molecular probes in chemical genomics and systems biology, and for the screening and discovery of new drugs and other useful compounds.


RESULTS
We describe ChemDB, a public database of small molecules available on the Web. ChemDB is built using the digital catalogs of over a hundred vendors and other public sources and is annotated with information derived from these sources as well as from computational methods, such as predicted solubility and three-dimensional structure. It supports multiple molecular formats and is periodically updated, automatically whenever possible. The current version of the database contains approximately 4.1 million commercially available compounds and 8.2 million counting isomers. The database includes a user-friendly graphical interface, chemical reactions capabilities, as well as unique search capabilities.


AVAILABILITY
Database and datasets are available on http://cdb.ics.uci.edu.
36321582
Enacting object-oriented methods by a process environment
Abstract This paper describes modeling and enactment of two object-oriented methods, namely the OMT method and the Booch method, using the concurrent software process language (CSPL). CSPL is a process-centered environment using Ada95-like syntax to model a method as a process program which is then compiled to C-shell executing in UNIX. A method can thus be enacted (executed) using this approach. Experiences of the approach are depicted. It is demonstrated that CSPL is feasible and appropriate for modeling and enacting methods, including object-oriented methods. Additionally, partial CSPL program modeling the Booch method is included in the Appendix.
987186
Implementing Minimized Multivariate PKC on Low-Resource Embedded Systems
Multivariate (or $\mathcal{MQ}$) public-key cryptosystems (PKC) are alternatives to traditional PKCs based on large algebraic structures (e.g., RSA and ECC); they usually execute much faster than traditional PKCs on the same hardware. However, one major challenge in implementing multivariates in embedded systems is that the key size can be prohibitively large for applications with stringent resource constraints such as low-cost smart cards, sensor networks (e.g., Berkeley motes), and radio-frequency identification (RFID). In this paper, we investigate strategies for shortening the key of a multivariate PKC. We apply these strategies to the Tame Transformation Signatures (TTS) as an example and quantify the improvement in key size and running speed, both theoretically and via implementation. We also investigate ways to save die space and energy consumption in hardware, reporting on our ASIC implementation of TTS on a TSMC 0.25μm process. Even without any key shortening, the current consumption of TTS is only 21 μA for computing a signature, using 22,000 gate equivalents and 16,000 100-kHz cycles (160 ms). With circulant-matrix key shortening, the numbers go down to 17,000 gates and 4,400 cycles (44 ms). We therefore conclude: besides representing a future-proofing investment against the emerging quantum computers, multivariates can be immediately useful in niches.
2913360
Dynamic verification of temporal constraints on-the-fly for workflow systems
Temporal verification is an important method to check the temporal correctness of workflow management systems (WfMSs). However, the current temporal verification is relatively independent of the workflow system environments. It does not pay sufficient attention to the interrelationship between the temporal verification at different stages, the mutual dependency between some temporal constraints, and the run-time checkpoint selection strategy, which hence hinders the incorporation and consistency between the temporal verification and the workflow system environments. In this paper, we effectively integrate the temporal verification at different stages and explore the dependency between some temporal constraints. In addition, we present a new effective runtime checkpoint selection strategy which dynamically selects appropriate checkpoints based on the activity completion duration. Furthermore, based on these analyses, we develop some new methods for more efficient temporal verification. These analyses and new methods help to eliminate the gap between the temporal verification and the workflow system environments.
37840776
Design and implementation of a network application architecture for thin clients
This paper explores the issues and the techniques of enabling multimedia applications for the thin client computing. Our study on the network applications over thin clients is devoted to the universal plug-in architecture which supports multimedia applications over thin clients. With the proposed architecture, the universal plug-in technique is devised to shift jobs from thin clients to a supporting server, thus reducing the computing overhead required by the thin clients. In addition, this plug-in architecture is implemented and empirically evaluated It is shown by our experiments that the proposed architecture not only significantly enhances the multimedia capability of thin clients but also reduces the memory consumed by the clients for various applications, showing the very advantage of the universal plug-in architecture for thin clients of limited resources.
14053079
Face Samples Re-lighting for Detection Based on the Harmonic Images
Different environment illumination has a great impact on face detection. In this paper, we present a solution by the face relighting based on the harmonic images. The basic idea is that there exist nine harmonic images which can be derived from a 3D model of a face, and by which we can estimate the illumination coefficient of any face samples. To detect faces under the certain lighting conditions, we relight those original face samples to get more new face samples under the various possible lighting conditions by an illumination ratio image and then add them to the training set. By train a classifier based on Support Vector Machine (SVM), the experimental results turn out that the relighting subspace is effective during the detection under the diverse lighting conditions. We also use the relighting database to train an AdaBoost-based face detector and test it on the MIT+CMU frontal face test set. The experimental results show that the data collection can be efficiently speeded up by the proposed methods.