Difference between revisions of "Team:HUST-China/Software"

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<h1>Software</h1>
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<h3>Best Software Tool Special Prize</h3>
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<p>Regardless of the topic, iGEM projects often create or adapt computational tools to move the project forward. Because they are born out of a direct practical need, these software tools (or new computational methods) can be surprisingly useful for other teams. Without necessarily being big or complex, they can make the crucial difference to a project's success. This award tries to find and honor such "nuggets" of computational work.
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To compete for the <a href="https://2018.igem.org/Judging/Awards">Best Software Tool prize</a>, please describe your work on this page and also fill out the description on the <a href="https://2018.igem.org/Judging/Judging_Form">judging form</a>.
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                          <a href="#" data-toggle="dropdown" class="dropdown-toggle waves-effect waves-dark">Model<b class="caret"></b></a>
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You must also delete the message box on the top of this page to be eligible for this prize.
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Modeling overview">Modeling overview</a></li>
</p>
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Comparison between PSB">Comparison between PSB</a></li>
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Sort of three genes">Sort of three genes</a></li>
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Software">Intelligent device software</a></li>
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Parts Overview">Parts Overview</a></li>
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Composite part">Composite part</a></li>
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Part collection">Part collection</a></li>
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Attributions">Attributions</a></li>
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        <h2 class="pageTitle">Intelligent device software</h2>
  
<div class="column third_size">
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<div class="highlight decoration_A_full">
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    </div>
<h3> Inspiration </h3>
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  </div>
<p>
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  </section>
Here are a few examples from previous teams:
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</p>
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  <section class="content">
<ul>
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  <div class="container"> 
<li><a href="https://2016.igem.org/Team:BostonU_HW">2016 BostonU HW</a></li>
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        <div class="row">
<li><a href="https://2016.igem.org/Team:Valencia_UPV">2016 Valencia UPV</a></li>
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            <div class="col-md-12 content-text">
<li><a href="https://2014.igem.org/Team:Heidelberg/Software">2014 Heidelberg</a></li>
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                <div class="about-logo">
<li><a href="https://2014.igem.org/Team:Aachen/Project/Measurement_Device#Software">2014 Aachen</a></li>
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                  <h3><strong>1. <span class="red-content">Abstract</span></strong></h3>
</ul>
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                  <p>We build a software to capture the situation of our system and learn to decide what to do to interact our system in order to get a better electricity output.</p>
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              </div>
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            </div>
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          </div>
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        <div class="row">
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            <div class="col-md-12 content-text">
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                <div class="about-logo">
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                  <h3><strong>2. <span class="red-content">Introduction</span></strong></h3>
 +
                  <p>Our software consists of two modules, the sensing module and learning module. Sensing module needs to obtain the condition of system based on the data of limited sensors. Learning module needs to learn according to the data from our model of system or the data from experiment, explore in the virtual environment or reality to learn how to make decision and memorize the knowledge. </p>
 +
                  <p>In application, the software will use sensing module to obtain the condition of system and use the knowledge learned by learning module to make decision.</p>
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              </div>
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            </div>
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            <div class="col-md-12">
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                <h3>Algorithms used in sensing module</h3>
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                <p class="red-content">Gradient descent<p>
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                  <p>Gradient descent is a iterative algorithm used find a local minimum of a function using gradient descent. If we want to fit a function h(X) (X is set of independent variable xi), loss function will be j(X). We will calculate the gradient of xi ∈ X : ∇j(X) and x<sub>(n+1)</sub>=x<sub>n</sub>-i*∇j(X).</p>
 +
                <p class="red-content">Mean Shift</p>
 +
                <p>
 +
                  Mean shift is a non-parametric feature-space analysis technique for locating the maxima of a density function, a so-called mode-seeking algorithm (Cheng et al. 1995)<sup>[1]</sup>. This algorithm will set a core whose radius is r, each data x in core will add the move vector:</p>
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            </div>
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                  <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/2/2d/T--HUST-China--2018-model-PSD001.png">
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            </div>
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            <div class="col-md-12">
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                <p>
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                  Each iteration will judge and calculate a new move vector until the coordinate of the core doesn’t move.</p>
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            </div>
 +
            <br>
 +
            <div class="col-md-12">
 +
                <h3>Step of software</h3>
 +
                <p>Firstly, we will feed all variable’s initial value (X_0^all) and use our model to predict all variable’s value in next unit of time. Secondly, we feed the true value of variable that can be sensed (X^s).
 +
Then, we calculate the Euclidean Distance between our prediction and true value(||P_t^s [i]-X_t^s ||) and use it as weight1. Sp is the sum of predictions.</p>
 +
                <p>After that, we use mean shift algorithm based on the weight1 (||P_t^s [i]-X_t^s ||) to find several scores (SC). Next step is to sort possible predictions by weigh2, use gradient descent on top np predictions to get new possible prediction and kill last dp predictions. (np = new_rate *(max_prediction - sp),dp=dead_rate*sp). Finally the software start next iteration.</p>
 +
            </div>
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            <div class="col-md-8 col-md-offset-1">
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                  <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/4/46/T--HUST-China--2018-model-PSD002.png.PNG">
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            </div>
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            <div class="col-md-12">
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                <h3>Learning Module</h3>
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                <p>We use Q-Learning method to learn how to make decision based on environment. Q-learning is a reinforcement learning method used in machine learning. It can learn a policy, which tells us what actions to take under what situations. It can handle problems with stochastic transitions and rewards, without requiring adaptations.</p>
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            </div>
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            <div class="col-md-8 col-md-offset-1">
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                  <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/1/16/T--HUST-China--2018-model-PSD003.png.PNG">
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            </div>
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            <div class="about-logo">
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                <h4><strong>Reference </strong></h4>
 +
                <p>[1] Cheng, Yizong (August 1995). "Mean Shift, Mode Seeking, and Clustering". IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. 17 (8): 790–799. doi:10.1109/34.400568.</p>
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        </div>
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    </div>     
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Revision as of 22:14, 17 October 2018

HillSide Multi purpose HTML5 Template

Intelligent device software

Algorithms used in sensing module

Gradient descent

Gradient descent is a iterative algorithm used find a local minimum of a function using gradient descent. If we want to fit a function h(X) (X is set of independent variable xi), loss function will be j(X). We will calculate the gradient of xi ∈ X : ∇j(X) and x(n+1)=xn-i*∇j(X).

Mean Shift

Mean shift is a non-parametric feature-space analysis technique for locating the maxima of a density function, a so-called mode-seeking algorithm (Cheng et al. 1995)[1]. This algorithm will set a core whose radius is r, each data x in core will add the move vector:

Each iteration will judge and calculate a new move vector until the coordinate of the core doesn’t move.


Step of software

Firstly, we will feed all variable’s initial value (X_0^all) and use our model to predict all variable’s value in next unit of time. Secondly, we feed the true value of variable that can be sensed (X^s). Then, we calculate the Euclidean Distance between our prediction and true value(||P_t^s [i]-X_t^s ||) and use it as weight1. Sp is the sum of predictions.

After that, we use mean shift algorithm based on the weight1 (||P_t^s [i]-X_t^s ||) to find several scores (SC). Next step is to sort possible predictions by weigh2, use gradient descent on top np predictions to get new possible prediction and kill last dp predictions. (np = new_rate *(max_prediction - sp),dp=dead_rate*sp). Finally the software start next iteration.

Learning Module

We use Q-Learning method to learn how to make decision based on environment. Q-learning is a reinforcement learning method used in machine learning. It can learn a policy, which tells us what actions to take under what situations. It can handle problems with stochastic transitions and rewards, without requiring adaptations.