ppxscal/embedding_network huggingface dataset:
Identifying genes involved in cyclic processes by combining gene expression analysis and prior knowledge
Authors: Wentao Zhao, Erchin Serpedin, Edward R. Dougherty
Venue: EURASIP Journal on Bioinformatics and Systems Biology (2009)

Based on time series gene expressions, cyclic genes can be recognized via spectral analysis and statistical periodicity detection tests. These cyclic genes are usually associated with cyclic biological processes, for example, cell cycle and circadian rhythm. The power of a scheme is practically measured by comparing the detected periodically expressed genes with experimentally verified genes participating in a cyclic process. However, in the above mentioned procedure the valuable prior knowledge only serves as an evaluation benchmark, and it is not fully exploited in the implementation of the algorithm. In addition, partial data sets are also disregarded due to their nonstationarity. This paper proposes a novel algorithm to identify cyclic-process-involved genes by integrating the prior knowledge with the gene expression analysis. The proposed algorithm is applied on data sets corresponding to Saccharomyces cerevisiae and Drosophila melanogaster, respectively. Biological evidences are found to validate the roles of the discovered genes in cell cycle and circadian rhythm. Dendrograms are presented to cluster the identified genes and to reveal expression patterns. It is corroborated that the proposed novel identification scheme provides a valuable technique for unveiling pathways related to cyclic processes.
Automatic generation of heuristics for scheduling
Authors: Robert A. Morris, John L. Bresina, Stuart M. Rodgers
Venue: Proceedings of the Fifteenth international joint conference on Artifical intelligence - Volume 2 (1997)

This paper presents a technique, called GENH, that automatically generates search heuristics for scheduling problems. The impetus for developing this technique is the growing consensus that heuristics encode advice that is, at best, useful in solving most, or typical, problem instances, and, at worst, useful in solving only a narrowly defined set of instances. In either case, heuristic problem solvers, to be broadly applicable, should have a means of automatically adjusting to the idiosyncrasies of each problem instance. GENH generates a search heuristic for a given problem instance by hillclimbing in the space of possible multiattribute heuristics, where the evaluation of a candidate heuristic is based on the quality of the solution found under its guidance. We present empirical results obtained by applying GENH to the real world problem of telescope observation scheduling. These results demonstrate that GENH is a simple and effective way of improving the performance of an heuristic scheduler.
Movie script markup language
Authors: Dieter Van Rijsselbergen, Barbara Van De Keer, Maarten Verwaest, Erik Mannens, Rik Van de Walle
Venue: Proceedings of the 9th ACM symposium on Document engineering (2009)

This paper introduces the Movie Script Markup Language (MSML), a document specification for the structural representation of screenplay narratives for television and feature film drama production. Its definition was motivated by a lack of available structured and open formats that describe dramatic narrative but also support IT-based production methods of audiovisual drama. The MSML specification fully supports contemporary screenplay templates in a structured fashion, and adds provisions for drama manufacturing methods that allow drama crew to define how narrative can be translated to audiovisual material. A timing model based on timed petri nets is included to enable fine-grained event synchronization. Finally, MSML comprises an animation module through which narrative events can drive production elements like 3-D previsualization, content repurposing or studio automation. MSML is currently serialized into XML documents and is formally described by a complement of an XML Schema and ISO Schematron schema. The specification has been developed in close collaboration with actual drama production crew and has been implemented in a number of proof-of-concept demonstrators.
Effects of Plant Species on Nitrous Oxide Emission and Microbial Community Structure Diversity in Constructed Wetlands
Authors: Juan Wu, Jian Zhang, Wenlin Jia, Huijun Xie, Haiming Wu
Venue: Proceedings of the 2009 International Conference on Environmental Science and Information Application Technology - Volume 02 (2009)

Vegetation is the principal component of the constructed wetland (CW) systems. To better understand the effect of plant species, the nitrous oxide (N2O) fluxes and bacterial community structure diversity were compared in different CWs planted with six plants. The results showed that N2O fluxes had obvious differences in vegetation systems. The higher risk of N2O emissions was observed in CWs planted with Typha latifolia and Scirpus validus, while the lowest N2O emission was in Phragmites australis systems. Bacterial communities to understand the bacterial world in the substrate by analyzing data of the denaturing gradient gel electrophoresis (DGGE) band patterns. The result clearly demonstrated that DGGE profiles revealed marked differences in the response of microbial communities under different plants cover.
Confounding definitions: using a continuum to understand interactivity
Authors: Katie Retzinger
Venue: Proceedings of the 27th ACM international conference on Design of communication (2009)

The term interactivity is used in many disciplines, including communication, professional/technical writing, new media, computer science, and marketing to describe a specific feature of different types of texts. However, little consensus has been achieved as to what interactivity actually is or can be. Using and categorizing definitions of interactivity from the fields of new media, computer science, communication, and advertising in order to begin to conceptualize interactivity, this paper will argue that rather than coming up with a single definition of interactivity that can be used in multiple disciplines, interactivity should be conceptualized along a continuum. By conceptualizing the term interactivity along a continuum, practitioners and instructors can be better able to use the term interactivity more productively, which can help practitioners and instructors who create or who teach others how to create interactive documents have a more generally agreed upon meaning that will further the ability to produce texts appropriate for an audience, purpose, and context.
Global optimization for first order Markov Random Fields with submodular priors
Authors: Jérôme Darbon
Venue: Discrete Applied Mathematics (2009)

This paper copes with the global optimization of Markovian energies. Energies are defined on an arbitrary graph and pairwise interactions are considered. The label set is assumed to be linearly ordered and of finite cardinality, while each interaction term (prior) shall be a submodular function. We propose an algorithm that computes a global optimizer under these assumptions. The approach consists of mapping the original problem into a combinatorial one that is shown to be globally solvable using a maximum-flow/s-t minimum-cut algorithm. This restatement relies on considering the level sets of the labels (seen as binary variables) instead of the label values themselves. The submodularity assumption of the priors is shown to be a necessary and sufficient condition for the applicability of the proposed approach. Finally, some numerical results are presented.
niSiDe: Interactive Tool for Understanding Distributed Software
Authors: Dan C. Cosma
Venue: Proceedings of the 2008 10th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (2008)

Understanding object-oriented distributed applications is currently an important concern as this type of systems is widely represented in the industry. While analyzing such systems can be done using the available tools built for understanding general, object-oriented, systems, they may fail to capture the most important aspect of this type of systems: their distribution-related functionality.This paper presents niSiDe, the tool developed to support our approach in understanding distributed software, which automates all involved tasks while allowing for user interaction, and provides the visualizations necessary to capture the essential aspects of the system's distributed nature. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Automatic Detecting Documents Containing Personal Health Information
Authors: Yunli Wang, Hongyu Liu, Liqiang Geng, Matthew S. Keays, Yonghua You
Venue: Proceedings of the 12th Conference on Artificial Intelligence in Medicine: Artificial Intelligence in Medicine (2009)

With the increasing usage of computers and Internet, personal health information (PHI) is distributed across multiple institutes and often scattered on multiple devices and stored in diverse formats. Non-traditional medical records such as emails and e-documents containing PHI are in a high risk of privacy leakage. We are facing the challenges of locating and managing PHI in the distributed environment. The goal of this study is to classify electronic documents into PHI and non-PHI. A supervised machine learning method was used for this text categorization task. Three classifiers: SVM, decision tree and Naive Bayesian were used and tested on three data sets. Lexical, semantic and syntactic features and their combinations were compared in terms of their effectiveness of classifying PHI documents. The results show that combining semantic and/or syntactic with lexical features is more effective than lexical features alone for PHI classification. The supervised machine learning method is effective in classifying documents into PHI and non-PHI.
Audio-Based Emotion Recognition in Judicial Domain: A Multilayer Support Vector Machines Approach
Authors: E. Fersini, E. Messina, G. Arosio, F. Archetti
Venue: Proceedings of the 6th International Conference on Machine Learning and Data Mining in Pattern Recognition (2009)

Thanks to the recent progresses in judicial proceedings management, especially related to the introduction of audio/video recording systems, semantic retrieval is a key challenge. In this context emotion recognition engine, through the analysis of vocal signature of actors involved in judicial proceedings, could provide useful annotations for semantic retrieval of multimedia clips. With respect to the generation of semantic emotional tag in judicial domain, two main contributions are given: (1) the construction of an Italian emotional database for Italian proceedings annotation; (2) the investigation of a hierarchical classification system, based on risk minimization method, able to recognize emotional states from vocal signatures. In order to estimate the degree of affection we compared the proposed classification method with SVM, K-Nearest Neighbors and Naive Bayes, highlighting in terms of classification accuracy, the improvements given by a hierarchical learning approach.
Designing a Safer Interactive Healthcare System - The Impact of Authentic User Participation
Authors: Kathryn L. Went, Peter Gregor, Ian W. Ricketts
Venue: Proceedings of the 12th IFIP TC 13 International Conference on Human-Computer Interaction: Part II (2009)

Information technology has been widely promoted in the healthcare sector to improve current practice and patient safety. However, end users are seldom involved extensively in the design and development of healthcare systems, with lip service often paid to the idea of true user involvement. In this case study the impact of sustained authentic user participation was explored using an interdisciplinary team, consisting of experts both in interaction and healthcare design and consultant anaesthetists, nurses, and pharmacists, to create an electronic prescribing and administration system. This paper details the interface that was created and provides examples of the way in which the design evolved in response to the sustained authentic user participation methods. The working prototype both reduced the opportunity for user error and was preferred by its users to the existing manual system.
Research on Particle Swarm Optimization for Grain Logistics Vehicle Routing Problem
Authors: Tong Zhen, Hongyi Ge, Yi Che, Yuying Jiang
Venue: Proceedings of the 2009 IITA International Conference on Services Science, Management and Engineering (2009)

Grain logistics vehicle routing problem is a kind of combination NP-hard problem. According to the large batch and multi-point to multi-point transportation of grain logistics, this paper considers vehicle routing problem with time windows and its intelligent algorithm. An algorithm of PSO for VRPTW is proposed in this work, experiments are made to compare the algorithm with GA on solving this problem. The experimental results indicate that algorithm of PSO will be an effective and feasible approach for grain logistics VRPTM, and reduce distribution cost.
Generalized point based value iteration for interactive POMDPs
Authors: Prashant Doshi, Dennis Perez
Venue: Proceedings of the 23rd national conference on Artificial intelligence - Volume 1 (2008)

We develop a point based method for solving finitely nested interactive POMDPs approximately. Analogously to point based value iteration (PBVI) in POMDPs, we maintain a set of belief points and form value functions composed of those value vectors that are optimal at these points. However, as we focus on muItiagent settings, the beliefs are nested and computation of the value vectors relies on predicted actions of others. Consequently, we develop a novel interactive gen eralization of PBVI applicable to muItiagent settings.
Evaluating Non-In-Place Update Techniques for Flash-Based Transaction Processing Systems
Authors: Yongkun Wang, Kazuo Goda, Masaru Kitsuregawa
Venue: Proceedings of the 20th International Conference on Database and Expert Systems Applications (2009)

Recently, flash memory is emerging as the storage device. With price sliding fast, the cost per capacity is approaching to that of SATA disk drives. So far flash memory has been widely deployed in consumer electronics even partly in mobile computing environments. For enterprise systems, the deployment has been studied by many researchers and developers. In terms of the access performance characteristics, flash memory is quite different from disk drives. Without the mechanical components, flash memory has very high random read performance, whereas it has a limited random write performance because of the erase-before-write design. The random write performance of flash memory is comparable with or even worse than that of disk drives. Due to such a performance asymmetry, naive deployment to enterprise systems may not exploit the potential performance of flash memory at full blast. This paper studies the effectiveness of using non-in-place-update (NIPU) techniques through the IO path of flash-based transaction processing systems. Our deliberate experiments using both open-source DBMS and commercial DBMS validated the potential benefits; x3.0 to x6.6 performance improvement was confirmed by incorporating non-in-place-update techniques into file system without any modification of applications or storage devices.
Multi-Modal Registration of Embryonic Images for In Vitro Fertilization
Authors: Chia-Ling Tsai, Su-Ching Liang, William Warger II, Charles DiMarzio
Venue: Proceedings of the 2009 Ninth IEEE International Conference on Bioinformatics and Bioengineering (2009)

This paper presents a robust and fully automated registration algorithm for alignment of embryonic images taken by Optical Quadrate Microscopy (OQM) and Differential Interference Contrast (DIC) Microscopy. Registration of such images allows recognition of distinguishing features of viable embryos, such as growth rate, to reduce multiple births from In Vitro Fertilization. OQM is an optical interferometer whereas the DIC images gradient of the phase.Due to the very different nature of the image formation, the interior of the embryo appears substantially different if not totally uncorrelated between different modalities. We present an algorithm which extracts and aligns the silhouettes of the embryo—the most invariant features between different modalities. The algorithm is tested with 28 image pairs taken from different embryos at various development stages.The success rate is 85.7% if only affine transformation is adopted, and 96% if similarity transformation is allowed for embryos without sufficient outline complexity.
Formal and conceptual modeling of spatio-temporal granularities
Authors: Alberto Belussi, Carlo Combi, Gabriele Pozzani
Venue: Proceedings of the 2009 International Database Engineering & Applications Symposium (2009)

In the database research field the management of temporal and spatial information is crucial. Many information may be temporally and spatially qualified, i.e., data may be associated to temporal and spatial locations. In the management of qualified data, the notion of "granularity" plays an important role; it allows one to reason about temporal and spatial data expressed with different units of measure. By merging together notions of temporal and spatial granularity, in this work we present a formal framework for the representation and management of spatio-temporal granularities. This framework includes relationships and operations between granularities. Moreover, we propose a conceptual design allowing us to represent temporal, spatial, and spatio-temporal granularities in a relational database.
An Analysis of Sum-Based Incommensurable Belief Base Merging
Authors: Salem Benferhat, Sylvain Lagrue, Julien Rossit
Venue: Proceedings of the 3rd International Conference on Scalable Uncertainty Management (2009)

Different methods have been proposed for merging multiple and potentially conflicting informations. Sum-based operators offer a natural method for merging commensurable prioritized belief bases. Their popularity is due to the fact that they satisfy the majority property and they adopt a non cautious attitude in deriving plausible conclusions.This paper analyses the sum-based merging operator when sources to merge are incommensurable, namely they do not share the same meaning of uncertainty scales. We first show that the obtained merging operator can be equivalently characterized either in terms of an infinite set of compatible scales, or by a well-known Pareto ordering on a set of models. We then study different families of compatible scales useful for merging process. This paper also provides a postulates-based analysis of our merging operators.
A frequent pattern based framework for event detection in sensor network stream data
Authors: Li Wan, Jianxin Liao, Xiaomin Zhu
Venue: Proceedings of the Third International Workshop on Knowledge Discovery from Sensor Data (2009)

In this paper, we presented a frequent pattern based framework for event detection in stream data, it consists of frequent pattern discovery, frequent pattern selection and modeling three phases: In the first phase, a MNOE (Mining Non-Overlapping Episode) algorithm is proposed to find the non-overlapping frequent pattern in time series. In the frequent pattern selection phase, we proposed an EGMAMC (Episode Generated Memory Aggregation Markov Chain) model to help us selecting episodes which can describe stream data significantly. Then we defined feature flows to represent the instances of discovered frequent patterns and categorized the distribution of frequent pattern instances into three categories according to the spectrum of their feature flows. At last, we proposed a clustering algorithm EDPA (Event Detection by Pattern Aggregation) to aggregate strongly correlated frequent patterns together. We argue that strongly correlated frequent patterns form events and frequent patterns in different categories can be aggregated to form different kinds of events. Experiments on real-world sensor network datasets demonstrate that the proposed MNOE algorithm is more efficient than the existing non-overlapping episode mining algorithm and EDPA performs better when the input frequent patterns are maximal, significant and non-overlapping.
You Are Here
Authors: Luc Courchesne
Venue: Proceedings of the 8th International Conference on Entertainment Computing (2009)

The continuing expansion of the visible domain, increasingly including and giving force (and reality) to the creations of our imagination and to formerly inaccessible places and dimensions of our unfolding universe, has produced a radical shift of the shared concepts of time and space. Suddenly, the statement « you are here » has a very different meaning. Thanks to the proliferation and increased mastery of interactive, immersive and socially engaging media, we have passed beyond the simple curiosity for technologies to find ourselves, as MacLuhan professed, dressed and immersed in them. Immersed indeed we are, collectively engaged in a « reality jam » with the physical, the artificial, the augmented, and the virtual. In the process, we have turned from spectators to users, visitors and now inhabitants of our own crafts. Questions such as « Who am I? », « Who are you? », « Where are we? », « How are we supposed to behave? », are now being asked with new relevance and urgency. Survival skills such as conversation, posture, attitude, or simply what to wear, are being reformulated on the fly by the natives and immigrants of this new territory that does not always perfectly accommodates the biological features we inherited from evolution.The Author. Luc Courchesne took part in the emergence of new media arts in the nineteen eighties when, as a videographer inspired by a generation of experimental filmmakers such as Michael Snow and Hollis Frampton, he was introduced to computers and interactive video technologies. Initially, his work focused on portraiture which he attempted to renovate with his use of interactive technologies to simulate conversion. He later moved toward landscape art which he made interactive and immersive with the Panoscope 360°, a system and method he invented to, in his words, « transform the spectator of the artwork into a visitor ». He created to date over 30 installation works that were exhibited in close to 100 venues the world over including the ICA in Boston in 1983, the Museum of Modern Art in New York in 1994, The ZKM/Karlsruhe since 1997, Paris's La Villette in 1999, Helsinki's Kiasma in 1997 and 2003, The Museum of New South Wales, in 1996 and 2001, the Montreal Museum of Fine Arts in 2007 and the National Art Museum of China in 2008. He was awarded the Grand Prize of The ICC Biennale in Tokyo (1997) and an award of distinction at Prix Ars Electronica in Linz (1999).Courchesne, who graduated from the Nova Scotia College of Art and Design (1974) and from the Massachusetts Institute of Technology (1984), is now director of the School of industrial design at University of Montreal, a board member of the Conseil des arts et des lettres du Québec and a founding member of the Society for Arts and Technology. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player