scholarly journals DREAMTools: a Python package for scoring collaborative challenges

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 1030 ◽  
Author(s):  
Thomas Cokelaer ◽  
Mukesh Bansal ◽  
Christopher Bare ◽  
Erhan Bilal ◽  
Brian M. Bot ◽  
...  
Keyword(s):  
Computational Methods ◽  
Training Data ◽  
Model Parameters ◽  
Automated Scoring ◽  
Statistical Machine Learning ◽  
Science And Engineering ◽  
New Methods ◽  
Wide Range ◽  
Improved Methods ◽  
Python Package

DREAM challenges are community competitions designed to advance computational methods and address fundamental questions in system biology and translational medicine. Each challenge asks participants to develop and apply computational methods to either predict unobserved outcomes or to identify unknown model parameters given a set of training data. Computational methods are evaluated using an automated scoring metric, scores are posted to a public leaderboard, and methods are published to facilitate community discussions on how to build improved methods. By engaging participants from a wide range of science and engineering backgrounds, DREAM challenges can comparatively evaluate a wide range of statistical, machine learning, and biophysical methods. Here, we describe DREAMTools, a Python package for evaluating DREAM challenge scoring metrics. DREAMTools provides a command line interface that enables researchers to test new methods on past challenges, as well as a framework for scoring new challenges. As of September 2015, DREAMTools includes more than 80% of completed DREAM challenges. DREAMTools complements the data, metadata, and software tools available at the DREAM website http://dreamchallenges.org and on the Synapse platform https://www.synapse.org.Availability: DREAMTools is a Python package. Releases and documentation are available at http://pypi.python.org/pypi/dreamtools. The source code is available at http://github.com/dreamtools.

scholarly journals DREAMTools: a Python package for scoring collaborative challenges

F1000Research ◽  
2016 ◽  
Vol 4 ◽  
pp. 1030 ◽  
Author(s):  
Thomas Cokelaer ◽  
Mukesh Bansal ◽  
Christopher Bare ◽  
Erhan Bilal ◽  
Brian M. Bot ◽  
...  
Keyword(s):  
Computational Methods ◽  
Training Data ◽  
Model Parameters ◽  
Automated Scoring ◽  
Statistical Machine Learning ◽  
Science And Engineering ◽  
Link Type ◽  
Wide Range ◽  
Improved Methods ◽  
Python Package

DREAM challenges are community competitions designed to advance computational methods and address fundamental questions in system biology and translational medicine. Each challenge asks participants to develop and apply computational methods to either predict unobserved outcomes or to identify unknown model parameters given a set of training data. Computational methods are evaluated using an automated scoring metric, scores are posted to a public leaderboard, and methods are published to facilitate community discussions on how to build improved methods. By engaging participants from a wide range of science and engineering backgrounds, DREAM challenges can comparatively evaluate a wide range of statistical, machine learning, and biophysical methods. Here, we describe DREAMTools, a Python package for evaluating DREAM challenge scoring metrics. DREAMTools provides a command line interface that enables researchers to test new methods on past challenges, as well as a framework for scoring new challenges. As of March 2016, DREAMTools includes more than 80% of completed DREAM challenges. DREAMTools complements the data, metadata, and software tools available at the DREAM website http://dreamchallenges.org and on the Synapse platform at https://www.synapse.org.Availability: DREAMTools is a Python package. Releases and documentation are available at http://pypi.python.org/pypi/dreamtools. The source code is available at http://github.com/dreamtools/dreamtools.

RESEARCH OF MULTI-TASK LEARNING BASED ON EXTREME LEARNING MACHINE

2013 ◽  
Vol 21 (supp02) ◽  
pp. 75-85 ◽  
Author(s):  
WENTAO MAO ◽  
JIUCHENG XU ◽  
SHENGJIE ZHAO ◽  
MEI TIAN
Keyword(s):  
Domain Knowledge ◽  
Real Life ◽  
Training Data ◽  
Learning Performance ◽  
Mixed Integer ◽  
Model Parameters ◽  
Minimization Method ◽  
Data Set ◽  
Task Learning ◽  
Wide Range

Recently, extreme learning machines (ELMs) have been a promising tool in solving a wide range of regression and classification applications. However, when modeling multiple related tasks in which only limited training data per task are available and the dimension is low, ELMs are generally hard to get impressive performance due to little help from the informative domain knowledge across tasks. To solve this problem, this paper extends ELM to the scenario of multi-task learning (MTL). First, based on the assumption that model parameters of related tasks are close to each other, a new regularization-based MTL algorithm for ELM is proposed to learn related tasks jointly via simple matrix inversion. For improving the learning performance, the algorithm proposed above is further formulated as a mixed integer programming in order to identify the grouping structure in which parameters are closer than others, and finally an alternating minimization method is presented to solve this optimization. Experiments conducted on a toy problem as well as real-life data set demonstrate the effectiveness of the proposed MTL algorithm compared to the classical ELM and the standard MTL algorithm.

scholarly journals Doubly Sparsifying Network

2017 ◽  
Author(s):  
Zhangyang Wang ◽  
Shuai Huang ◽  
Jiayu Zhou ◽  
Thomas S. Huang
Keyword(s):  
Response Prediction ◽  
Low Complexity ◽  
Blood Oxygenation ◽  
Training Data ◽  
Superior Performance ◽  
Model Parameters ◽  
Unified Framework ◽  
Model Interpretation ◽  
Wide Range ◽  
Oxygenation Level

We propose the doubly sparsifying network (DSN), by drawing inspirations from the double sparsity model for dictionary learning. DSN emphasizes the joint utilization of both the problem structure and the parameter structure. It simultaneously sparsifies the output features and the learned model parameters, under one unified framework. DSN enjoys intuitive model interpretation, compact model size and low complexity. We compare DSN against a few carefully-designed baselines, to verify its consistently superior performance in a wide range of settings. Encouraged by its robustness to insufficient training data, we explore the applicability of DSN in brain signal processing that has been a challenging interdisciplinary area. DSN is evaluated for two mainstream tasks, electroencephalographic (EEG) signal classification and blood oxygenation level dependent (BOLD) response prediction, both achieving promising results.

Review Lecture: Local weather forecasting

1980 ◽  
Vol 371 (1745) ◽  
pp. 179-211 ◽  
Keyword(s):  
Prediction Models ◽  
Weather Forecasting ◽  
Weather Prediction ◽  
Quarter Century ◽  
New Methods ◽  
Weather Observations ◽  
Wide Range ◽  
Local Weather ◽  
Improved Methods ◽  
Made In

Good progress has been made in forecasting the broad pattern of the weather for periods up to a few days ahead as a result of developments in mathematical weather prediction models. However, our ability to forecast, just a few hours ahead, the detailed weather pattern for specific locations, still leaves a lot to be desired. In this lecture it is suggested that local forecasting, after a quarter century of stagnation, is poised for a decade of slow but steady improvement. Changes will come as a result of new programs which exploit and integrate advances in several areas. These areas include better weather observations, especially from satellites and radar, improved methods of data processing and analysis, and the development of more detailed numerical prediction models. New methods of communications, such as viewdata, will enable the improved local forecasts to be disseminated promptly and in a wide range of specially tailored formats. This will contribute to the development of a more user-oriented meteorological service.

Possession and Repetition

2012 ◽  
Vol 6 (1-3) ◽  
pp. 243-259 ◽  
Author(s):  
Yohan Yoo
Keyword(s):  
First Century ◽  
Daily Lives ◽  
Modern Times ◽  
Sacred Texts ◽  
New Methods ◽  
Wide Range ◽  
Lay Buddhists ◽  
Iconic Status ◽  
And Function ◽  
To Receive

This article demonstrates the need for the iconic status and function of Buddhist scripture to receive more attention by illuminating how lay Korean Buddhists try to appropriate the power of sutras. The oral and aural aspects of scripture, explained by Wilfred Cantwell Smith, provide only a limited understanding of the characteristics of scripture. It should be noted that, before modern times, most lay people, not only in Buddhist cultures but also in Christian and other traditions, neither had the chance to recite scriptures nor to listen to their recitations regularly. Several clear examples demonstrate contemporary Korean Buddhists’ acceptance of the iconic status of sutras and their attempt to appropriate the power and status of those sacred texts. In contemporary Korea, lay Buddhists try to claim the power of scriptures in their daily lives by repeating and possessing them. Twenty-first century lay believers who cannot read or recite in a traditional style have found new methods of repetition, such as internet programs for copying sacred texts and for playing recordings of their recitations. In addition, many Korean Buddhists consider the act of having sutras in one’s possession to be an effective way of accessing the sacred status and power of these texts. Hence, various ways of possessing them have been developed in a wide range of products, from fancy gilded sutras to sneakers embroidered with mantras.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

scholarly journals Antifungal Activity of Propyl Disulfide from Neem (Azadirachta indica) in Vapor and Agar Diffusion Assays against Anthracnose Pathogens (Colletotrichum gloeosporioides and Colletotrichum acutatum) in Mango Fruit

2021 ◽  
Vol 9 (4) ◽  
pp. 839
Author(s):  
Muhammad Rafiullah Khan ◽  
Vanee Chonhenchob ◽  
Chongxing Huang ◽  
Panitee Suwanamornlert
Keyword(s):  
Antifungal Activity ◽  
Mycelial Growth ◽  
Colletotrichum Gloeosporioides ◽  
Colletotrichum Acutatum ◽  
Model Parameters ◽  
Pathogenicity Test ◽  
Agar Diffusion ◽  
Wide Range ◽  
Significant Difference ◽  
Diffusion Assay

Microorganisms causing anthracnose diseases have a medium to a high level of resistance to the existing fungicides. This study aimed to investigate neem plant extract (propyl disulfide, PD) as an alternative to the current fungicides against mango’s anthracnose. Microorganisms were isolated from decayed mango and identified as Colletotrichum gloeosporioides and Colletotrichum acutatum. Next, a pathogenicity test was conducted and after fulfilling Koch’s postulates, fungi were reisolated from these symptomatic fruits and we thus obtained pure cultures. Then, different concentrations of PD were used against these fungi in vapor and agar diffusion assays. Ethanol and distilled water were served as control treatments. PD significantly (p ≤ 0.05) inhibited more of the mycelial growth of these fungi than both controls. The antifungal activity of PD increased with increasing concentrations. The vapor diffusion assay was more effective in inhibiting the mycelial growth of these fungi than the agar diffusion assay. A good fit (R2, 0.950) of the experimental data in the Gompertz growth model and a significant difference in the model parameters, i.e., lag phase (λ), stationary phase (A) and mycelial growth rate, further showed the antifungal efficacy of PD. Therefore, PD could be the best antimicrobial compound against a wide range of microorganisms.

scholarly journals A flexible framework for anomaly Detection via dimensionality reduction

2021 ◽  
Author(s):  
Alireza Vafaei Sadr ◽  
Bruce A. Bassett ◽  
M. Kunz
Keyword(s):  
Anomaly Detection ◽  
Dimensionality Reduction ◽  
Dimensional Space ◽  
High Dimensions ◽  
Detection Algorithms ◽  
Latent Space ◽  
Wide Range ◽  
Flexible Framework ◽  
Online Anomaly Detection ◽  
Python Package

AbstractAnomaly detection is challenging, especially for large datasets in high dimensions. Here, we explore a general anomaly detection framework based on dimensionality reduction and unsupervised clustering. DRAMA is released as a general python package that implements the general framework with a wide range of built-in options. This approach identifies the primary prototypes in the data with anomalies detected by their large distances from the prototypes, either in the latent space or in the original, high-dimensional space. DRAMA is tested on a wide variety of simulated and real datasets, in up to 3000 dimensions, and is found to be robust and highly competitive with commonly used anomaly detection algorithms, especially in high dimensions. The flexibility of the DRAMA framework allows for significant optimization once some examples of anomalies are available, making it ideal for online anomaly detection, active learning, and highly unbalanced datasets. Besides, DRAMA naturally provides clustering of outliers for subsequent analysis.

scholarly journals A Reinforcement Learning Framework for Spiking Networks with Dynamic Synapses

2011 ◽  
Vol 2011 ◽  
pp. 1-12 ◽  
Author(s):  
Karim El-Laithy ◽  
Martin Bogdan
Keyword(s):  
Reinforcement Learning ◽  
Spike Timing ◽  
Neural Representation ◽  
Model Parameters ◽  
Learning Framework ◽  
Reference Target ◽  
Wide Range ◽  
Spiking Network ◽  
Dynamic Synapses ◽  
Exclusive Or

An integration of both the Hebbian-based and reinforcement learning (RL) rules is presented for dynamic synapses. The proposed framework permits the Hebbian rule to update the hidden synaptic model parameters regulating the synaptic response rather than the synaptic weights. This is performed using both the value and the sign of the temporal difference in the reward signal after each trial. Applying this framework, a spiking network with spike-timing-dependent synapses is tested to learn the exclusive-OR computation on a temporally coded basis. Reward values are calculated with the distance between the output spike train of the network and a reference target one. Results show that the network is able to capture the required dynamics and that the proposed framework can reveal indeed an integrated version of Hebbian and RL. The proposed framework is tractable and less computationally expensive. The framework is applicable to a wide class of synaptic models and is not restricted to the used neural representation. This generality, along with the reported results, supports adopting the introduced approach to benefit from the biologically plausible synaptic models in a wide range of intuitive signal processing.

scholarly journals Unsupervised content-preserving transformation for optical microscopy

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Xinyang Li ◽  
Guoxun Zhang ◽  
Hui Qiao ◽  
Feng Bao ◽  
Yue Deng ◽  
...  
Keyword(s):  
Deep Learning ◽  
Optical Microscopy ◽  
Training Data ◽  
Fluorescence Labeling ◽  
Imaging Data ◽  
Image Transformation ◽  
General Applicability ◽  
Data Annotation ◽  
Biomedical Image ◽  
Wide Range

AbstractThe development of deep learning and open access to a substantial collection of imaging data together provide a potential solution for computational image transformation, which is gradually changing the landscape of optical imaging and biomedical research. However, current implementations of deep learning usually operate in a supervised manner, and their reliance on laborious and error-prone data annotation procedures remains a barrier to more general applicability. Here, we propose an unsupervised image transformation to facilitate the utilization of deep learning for optical microscopy, even in some cases in which supervised models cannot be applied. Through the introduction of a saliency constraint, the unsupervised model, named Unsupervised content-preserving Transformation for Optical Microscopy (UTOM), can learn the mapping between two image domains without requiring paired training data while avoiding distortions of the image content. UTOM shows promising performance in a wide range of biomedical image transformation tasks, including in silico histological staining, fluorescence image restoration, and virtual fluorescence labeling. Quantitative evaluations reveal that UTOM achieves stable and high-fidelity image transformations across different imaging conditions and modalities. We anticipate that our framework will encourage a paradigm shift in training neural networks and enable more applications of artificial intelligence in biomedical imaging.

Sign in / Sign up

Export Citation Format

Share Document