103,673 research outputs found
Automation on the generation of genome scale metabolic models
Background: Nowadays, the reconstruction of genome scale metabolic models is
a non-automatized and interactive process based on decision taking. This
lengthy process usually requires a full year of one person's work in order to
satisfactory collect, analyze and validate the list of all metabolic reactions
present in a specific organism. In order to write this list, one manually has
to go through a huge amount of genomic, metabolomic and physiological
information. Currently, there is no optimal algorithm that allows one to
automatically go through all this information and generate the models taking
into account probabilistic criteria of unicity and completeness that a
biologist would consider. Results: This work presents the automation of a
methodology for the reconstruction of genome scale metabolic models for any
organism. The methodology that follows is the automatized version of the steps
implemented manually for the reconstruction of the genome scale metabolic model
of a photosynthetic organism, {\it Synechocystis sp. PCC6803}. The steps for
the reconstruction are implemented in a computational platform (COPABI) that
generates the models from the probabilistic algorithms that have been
developed. Conclusions: For validation of the developed algorithm robustness,
the metabolic models of several organisms generated by the platform have been
studied together with published models that have been manually curated. Network
properties of the models like connectivity and average shortest mean path of
the different models have been compared and analyzed.Comment: 24 pages, 2 figures, 2 table
Bayesian inference for queueing networks and modeling of internet services
Modern Internet services, such as those at Google, Yahoo!, and Amazon, handle
billions of requests per day on clusters of thousands of computers. Because
these services operate under strict performance requirements, a statistical
understanding of their performance is of great practical interest. Such
services are modeled by networks of queues, where each queue models one of the
computers in the system. A key challenge is that the data are incomplete,
because recording detailed information about every request to a heavily used
system can require unacceptable overhead. In this paper we develop a Bayesian
perspective on queueing models in which the arrival and departure times that
are not observed are treated as latent variables. Underlying this viewpoint is
the observation that a queueing model defines a deterministic transformation
between the data and a set of independent variables called the service times.
With this viewpoint in hand, we sample from the posterior distribution over
missing data and model parameters using Markov chain Monte Carlo. We evaluate
our framework on data from a benchmark Web application. We also present a
simple technique for selection among nested queueing models. We are unaware of
any previous work that considers inference in networks of queues in the
presence of missing data.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS392 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Learning Fast and Slow: PROPEDEUTICA for Real-time Malware Detection
In this paper, we introduce and evaluate PROPEDEUTICA, a novel methodology
and framework for efficient and effective real-time malware detection,
leveraging the best of conventional machine learning (ML) and deep learning
(DL) algorithms. In PROPEDEUTICA, all software processes in the system start
execution subjected to a conventional ML detector for fast classification. If a
piece of software receives a borderline classification, it is subjected to
further analysis via more performance expensive and more accurate DL methods,
via our newly proposed DL algorithm DEEPMALWARE. Further, we introduce delays
to the execution of software subjected to deep learning analysis as a way to
"buy time" for DL analysis and to rate-limit the impact of possible malware in
the system. We evaluated PROPEDEUTICA with a set of 9,115 malware samples and
877 commonly used benign software samples from various categories for the
Windows OS. Our results show that the false positive rate for conventional ML
methods can reach 20%, and for modern DL methods it is usually below 6%.
However, the classification time for DL can be 100X longer than conventional ML
methods. PROPEDEUTICA improved the detection F1-score from 77.54% (conventional
ML method) to 90.25%, and reduced the detection time by 54.86%. Further, the
percentage of software subjected to DL analysis was approximately 40% on
average. Further, the application of delays in software subjected to ML reduced
the detection time by approximately 10%. Finally, we found and discussed a
discrepancy between the detection accuracy offline (analysis after all traces
are collected) and on-the-fly (analysis in tandem with trace collection). Our
insights show that conventional ML and modern DL-based malware detectors in
isolation cannot meet the needs of efficient and effective malware detection:
high accuracy, low false positive rate, and short classification time.Comment: 17 pages, 7 figure
High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)
Computing plays an essential role in all aspects of high energy physics. As
computational technology evolves rapidly in new directions, and data throughput
and volume continue to follow a steep trend-line, it is important for the HEP
community to develop an effective response to a series of expected challenges.
In order to help shape the desired response, the HEP Forum for Computational
Excellence (HEP-FCE) initiated a roadmap planning activity with two key
overlapping drivers -- 1) software effectiveness, and 2) infrastructure and
expertise advancement. The HEP-FCE formed three working groups, 1) Applications
Software, 2) Software Libraries and Tools, and 3) Systems (including systems
software), to provide an overview of the current status of HEP computing and to
present findings and opportunities for the desired HEP computational roadmap.
The final versions of the reports are combined in this document, and are
presented along with introductory material.Comment: 72 page
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