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| <a href="https://2017.igem.org/Team:SYSU-Software/Project#description" class="item">Description</a> | | <a href="https://2017.igem.org/Team:SYSU-Software/Project#description" class="item">Description</a> |
| <a href="https://2017.igem.org/Team:SYSU-Software/Project#applied-design" class="item">Applied Design</a> | | <a href="https://2017.igem.org/Team:SYSU-Software/Project#applied-design" class="item">Applied Design</a> |
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| <a href="https://2017.igem.org/Team:SYSU-Software/Project#demonstrate" class="item">Demonstrate</a> | | <a href="https://2017.igem.org/Team:SYSU-Software/Project#demonstrate" class="item">Demonstrate</a> |
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| <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#scut-china-a" class="item">SCUT-CHINA-A</a> | | <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#scut-china-a" class="item">SCUT-CHINA-A</a> |
| <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#nju-china" class="item">NJU-China</a> | | <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#nju-china" class="item">NJU-China</a> |
− | <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#hkust" class="item">HUKST</a> | + | <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#hkust" class="item">Hong_Kong_HKUST</a> |
| <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#sysu-china" class="item">SYSU-CHINA</a> | | <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#sysu-china" class="item">SYSU-CHINA</a> |
| <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#scau-china" class="item">SCAU-CHINA</a> | | <a href="https://2017.igem.org/Team:SYSU-Software/Collaborations#scau-china" class="item">SCAU-CHINA</a> |
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| <a href="https://2017.igem.org/Team:SYSU-Software/Team#instructors" class="item">Instructors</a> | | <a href="https://2017.igem.org/Team:SYSU-Software/Team#instructors" class="item">Instructors</a> |
| <a href="https://2017.igem.org/Team:SYSU-Software/Team#notebook" class="item">Notebook</a> | | <a href="https://2017.igem.org/Team:SYSU-Software/Team#notebook" class="item">Notebook</a> |
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| + | <div class="ui simple dropdown item page-nav"> |
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| + | <a href="https://2017.igem.org/Team:SYSU-Software/Medal#bronze" class="item">Bronze</a> |
| + | <a href="https://2017.igem.org/Team:SYSU-Software/Medal#silver" class="item">Silver</a> |
| + | <a href="https://2017.igem.org/Team:SYSU-Software/Medal#gold" class="item">Gold</a> |
| </div> | | </div> |
| </div> | | </div> |
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| <p>The reason why we use Word2vec is that it can distinguish the semantic meanings of words accurately by Deep Learning technique, which outperforms the traditional semantic analysis methods greatly.</p> | | <p>The reason why we use Word2vec is that it can distinguish the semantic meanings of words accurately by Deep Learning technique, which outperforms the traditional semantic analysis methods greatly.</p> |
| </div> | | </div> |
− | <h4>KD Tree Algorithm</h4> | + | <h4>KD Tree Algorithm</h4></br> |
− | <img class="ui image middle centered" src="https://static.igem.org/mediawiki/2017/1/17/T--SYSU-Software--model_kd.png"> | + | <img class="ui image medium centered" src="https://static.igem.org/mediawiki/2017/1/17/T--SYSU-Software--model_kd.png"></br> |
| <div class="paragraph"> | | <div class="paragraph"> |
| <p>The KD Tree algorithm is rather efficient when searching for the most similar items with averaged time complexity<code>O(log(n))</code>,thus the users can get recommendation instantly after they enter their interested new word to our system.</p> | | <p>The KD Tree algorithm is rather efficient when searching for the most similar items with averaged time complexity<code>O(log(n))</code>,thus the users can get recommendation instantly after they enter their interested new word to our system.</p> |
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| <li>When the user enter a new word , we search the similar key words along the KD Tree that we constructed in step 1) . (Online)</li> | | <li>When the user enter a new word , we search the similar key words along the KD Tree that we constructed in step 1) . (Online)</li> |
| </ol> | | </ol> |
− | <p>Note that KD Tree Algorithm is based on Euclidean distance measure , while in our case , we need to calculate the cosine distance of the word vectors. To solve this problem ,we normalize all the word vectors of key words before constructing KD Tree and normalize the word vector of new words offered by users before letting it travel along the constructed KD Tree. The reason behind the method is that by Law of Cosines:</p> | + | <p>Note that KD Tree Algorithm is based on Euclidean distance measure , while in our case , we need to calculate the cosine distance of the word vectors. To solve this problem ,we normalize all the word vectors of key words before constructing KD Tree and normalize the word vector of new words offered by users before letting it travel along the constructed KD Tree. The reason behind the method is that by Law of Cosines: |
− | <img src="https://static.igem.org/mediawiki/2017/6/6f/T--SYSU-Software--model_law-of-cos.png" alt="law of cosine" class="centered formula" id="law-of-cos-img"> | + | $$|x_1-x_2|=\sqrt{x_1^2+x_2^2-2|x_1||x_2|\cos(x_1,x_2)}\,,\,\,x_1,x_2\in R^n$$ |
− | <p>while since <code>x<sup>1</sup>,x<sup>2</sup></code> are normalized, we have :</p> | + | </p> |
− | <img src="https://static.igem.org/mediawiki/2017/a/a8/T--SYSU-Software--modeling_law-of-cos2.png" alt="law of cosine" class="centered formula" id="law-of-cos2-img"> | + | |
| + | <p>while since <code>x<sup>1</sup>,x<sup>2</sup></code> are normalized, we have : |
| + | $$|x_1-x_2| = \sqrt{1+1-2\cos(x_1,x_2)}\,,\,\,x_1,x_2\in R^n, |x_1|=|x_2|=1$$ |
| + | </p> |
| + | |
| <p>Now we see that the calculation of cosine distance between normalized vectors can be replaced by the calculation of Euclidean distance since they can determine each other in this normalization context.</p> | | <p>Now we see that the calculation of cosine distance between normalized vectors can be replaced by the calculation of Euclidean distance since they can determine each other in this normalization context.</p> |
| <p>In our Recommendation System , we use the KD Tree implementation in scikit-learn , a simple and efficient open source machine learning module in Python. For more details of KD Tree algorithm, see: <a href=" https://en.wikipedia.org/wiki/K-d_tree" target="_blank">wiki page of K-D Tree</a></p> | | <p>In our Recommendation System , we use the KD Tree implementation in scikit-learn , a simple and efficient open source machine learning module in Python. For more details of KD Tree algorithm, see: <a href=" https://en.wikipedia.org/wiki/K-d_tree" target="_blank">wiki page of K-D Tree</a></p> |
| </div> | | </div> |
| <h4>Random Walk with Restart Algorithm</h4> | | <h4>Random Walk with Restart Algorithm</h4> |
− | <img src="https://static.igem.org/mediawiki/2017/c/c0/T--SYSU-Software--modeling_part-keyword.png" class="centered" alt="" id="keyword-part-img"> | + | <img src="https://static.igem.org/mediawiki/2017/8/89/T--SYSU-Software--model_keywordandpart.png" class="centered" alt="" id="keyword-part-img"> |
| <p>Random Walk with Restart(RWR) is an algorithm adapted from the PageRank algorithm and it focuses on characterizing the affiliation between each item. We treat the relation between key words and genetic parts as an undirected graph where nodes represent key words or parts and edges represent connection between words and parts. Imagine there is a walker travelling on the graph mentioned above and each time he faces two choices: 1) Randomly travelling along an edge connected to the current node. 2) Teleport to node K. After a long time of random travelling , the frequency the walker reaches each node represents the affiliation between each node and node K , which we use to characterize the relation between key words and parts. For more detailed mathematical formulation of PageRank, see: <a href="https://en.wikipedia.org/wiki/PageRank" target="_blank">wiki page of page rank</a></p> | | <p>Random Walk with Restart(RWR) is an algorithm adapted from the PageRank algorithm and it focuses on characterizing the affiliation between each item. We treat the relation between key words and genetic parts as an undirected graph where nodes represent key words or parts and edges represent connection between words and parts. Imagine there is a walker travelling on the graph mentioned above and each time he faces two choices: 1) Randomly travelling along an edge connected to the current node. 2) Teleport to node K. After a long time of random travelling , the frequency the walker reaches each node represents the affiliation between each node and node K , which we use to characterize the relation between key words and parts. For more detailed mathematical formulation of PageRank, see: <a href="https://en.wikipedia.org/wiki/PageRank" target="_blank">wiki page of page rank</a></p> |
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| <p><code>for</code> keyword <code>i</code> in <code>1 to N</code></p> | | <p><code>for</code> keyword <code>i</code> in <code>1 to N</code></p> |
| <h6>Define and initialize <code>v</code></h6> | | <h6>Define and initialize <code>v</code></h6> |
− | <p>Let <code>e<sub>i</sub></code> be the column vector that has 1 in the row for node <code>i</code> and 0’s elsewhere, i.e.</p> | + | <p>Let <code>e<sub>i</sub></code> be the column vector that has 1 in the row for node <code>i</code> and 0’s elsewhere, i.e. |
− | <img src="https://static.igem.org/mediawiki/2017/5/58/T--SYSU-Software--modeling_eij.png" alt="eij" id="eij-img" class="centered formula"> | + | $$e_{ij}=\delta_{ij}= |
| + | \begin{cases} |
| + | 1, & \text{if $i=j$} \\ |
| + | 0, & \text{if $i\neq j$} |
| + | \end{cases}$$ |
| + | </p> |
| + | |
| <p>And <code>e<sub>i</sub></code> is the column vector such that each item reflects the probability the walker stays at each node of the graph and the initial <code>v</code> is set to be <code>e<sub>i</sub></code>.</p> | | <p>And <code>e<sub>i</sub></code> is the column vector such that each item reflects the probability the walker stays at each node of the graph and the initial <code>v</code> is set to be <code>e<sub>i</sub></code>.</p> |
| <h6>Update <code>v</code> by</h6> | | <h6>Update <code>v</code> by</h6> |
− | <img src="https://static.igem.org/mediawiki/2017/2/2e/T--SYSU-Software--modeling_bmv.png" alt="bmv+(1-b)ei" id="bmv-img" class="centered formula"> | + | <p>$$v'=\beta M v+(1-\beta)e_N$$</p> |
− | <p>update code{v} until the terminal condition is satisfied, i.e.</p> | + | <p>update code{v} until the terminal condition is satisfied, i.e. |
− | <img src="https://static.igem.org/mediawiki/2017/e/e6/T--SYSU-Software--modeling_term-cond.png" alt="terminal condition" id="time-cond-img" class="centered formula"> | + | $$|v^{(t)}-v^{(t-1)}|<\epsilon,\,\,\text{for sometime $t$}$$ |
| + | </p> |
| + | |
| <h6>Modify <code>v</code></h6> | | <h6>Modify <code>v</code></h6> |
| <p>Since the first n components of <code>v</code> are the affiliation between key word <code>i</code> and the other key words which we are not interested , therefore we only keep the last m components of <code>v</code>, which reflects the affiliation between key word <code>i</code> and all the parts.</p> | | <p>Since the first n components of <code>v</code> are the affiliation between key word <code>i</code> and the other key words which we are not interested , therefore we only keep the last m components of <code>v</code>, which reflects the affiliation between key word <code>i</code> and all the parts.</p> |
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| <h5>Train word vector model</h5> | | <h5>Train word vector model</h5> |
| <div class="paragraph"> | | <div class="paragraph"> |
− | <p>We feed our word vector model with Wikimedia corpus . After the training process is done, we have a model that can convert words into numerical vectors, i.e.</p> | + | <p>We feed our word vector model with Wikimedia corpus . After the training process is done, we have a model that can convert words into numerical vectors, i.e. |
− | <img src="https://static.igem.org/mediawiki/2017/c/c0/T--SYSU-Software--modeling_f-gamma-r.png" id="f-gamma-r-img" alt="" class="centered formula"> | + | $$f:\Gamma\rightarrow R^n$$ |
| + | </p> |
| <p>where Γ denoted the corpus space</p> | | <p>where Γ denoted the corpus space</p> |
| </div> | | </div> |
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| <p>let <code>T</code> denotes the set of word vectors</p> | | <p>let <code>T</code> denotes the set of word vectors</p> |
| <p><code>for</code> keyword <code>i</code> in <code>1 to N</code>:</p> | | <p><code>for</code> keyword <code>i</code> in <code>1 to N</code>:</p> |
− | <p><code>T</code>.append(<img id="normalize-i" class="inlined-formula" src="https://static.igem.org/mediawiki/2017/6/64/T--SYSU-Software--modeling_normalize-i.png" alt="f(i)/|f(i)|">)</p> | + | <p><code>T</code>.append \( \frac{f(i)}{|f(i)|_2} \)</p> |
| </div> | | </div> |
| <h5>Build KD Tree</h5> | | <h5>Build KD Tree</h5> |
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| | | |
| <h4>Collaborative Filtering</h4> | | <h4>Collaborative Filtering</h4> |
| + | <img src="https://static.igem.org/mediawiki/2017/6/66/T--SYSU-Software--model_workflow.jpg" alt="" id="workflow-img" class="ui image middle"> |
| <div class="paragraph"> | | <div class="paragraph"> |
| <p>This is the final step to construct our Recommendation System , overall we use collaborative filtering strategy to make prediction.</p> | | <p>This is the final step to construct our Recommendation System , overall we use collaborative filtering strategy to make prediction.</p> |
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| </div> | | </div> |
| <h5>Transform users input</h5> | | <h5>Transform users input</h5> |
− | <p>We get users input word <code>k</code>, we then convert it into normalized word vector <code>v</code>, i.e.</p> | + | <p>We get users input word <code>k</code>, we then convert it into normalized word vector <code>v</code>, i.e. $$v=\frac{f(k)}{|f(k)|}$$</p> |
− | <img src="https://static.igem.org/mediawiki/2017/0/00/T--SYSU-Software--modeling_normalize-k.png" alt="" id="normalize-k-img" class="centered formula"> | + | |
| <h5>Search K most similar keywords(KNN)</h5> | | <h5>Search K most similar keywords(KNN)</h5> |
| <p>Let <code>v</code> travel along the KD Tree in a way like binary search , we can end up with <code>K</code>(in our case , <code>K</code> is set to be 5) most similar key words(KNN) to the current word <code>k</code>.</p> | | <p>Let <code>v</code> travel along the KD Tree in a way like binary search , we can end up with <code>K</code>(in our case , <code>K</code> is set to be 5) most similar key words(KNN) to the current word <code>k</code>.</p> |
| <h5>Make Recommendation</h5> | | <h5>Make Recommendation</h5> |
| <div class="paragraph"> | | <div class="paragraph"> |
− | <p>We have calculated the affiliation between key words and parts which shall be used to guide our final recommendation. Let <code>p<sub>i</sub></code> denotes the connection between the <code>i</code>th part and the current word <code>k</code> , we calculate <code>p<sub>i</sub></code> by formula</p> | + | <p>We have calculated the affiliation between key words and parts which shall be used to guide our final recommendation. Let <code>p<sub>i</sub></code> denotes the connection between the <code>i</code>the part and the current word <code>k</code> , we calculate <code>p<sub>i</sub></code> by formula $$p_i=\sum^K_{n=1}\frac{\text{Affiliation}(w_n,p_i)}{\text{distance}(w_n,k)+\text{bias}}$$ |
− | <img src="https://static.igem.org/mediawiki/2017/0/00/T--SYSU-Software--modeling_affiliation.png" alt="" id="affi-img" class="centered formula"> | + | </p> |
− | <p>where <img src="https://static.igem.org/mediawiki/2017/f/f1/T--SYSU-Software--modeling_wn.png" alt="" class="inlined-formula"> denotes the <code>k</code> most similar key words</p> | + | |
| + | <p>where \( \{w_n|n=1,2,...,K\}\) denotes the <code>k</code> most similar key words</p> |
| <p><code>Affiliation(w<sub>n</sub>, p<sub>i</sub>)</code>denotes the connection between <code>w<sub>i</sub></code> and the <code>i</code>th part and <code>distance(w<sub>i</sub>, k)</code> denotes the the Euclidean distance between the normalized word vectors of <code>w<sub>n</sub></code> and word <code>k</code>.</p> | | <p><code>Affiliation(w<sub>n</sub>, p<sub>i</sub>)</code>denotes the connection between <code>w<sub>i</sub></code> and the <code>i</code>th part and <code>distance(w<sub>i</sub>, k)</code> denotes the the Euclidean distance between the normalized word vectors of <code>w<sub>n</sub></code> and word <code>k</code>.</p> |
− | <p>After the computation of <img src="https://static.igem.org/mediawiki/2017/0/00/T--SYSU-Software--modeling_pi.png" alt="" class="inlined-formula">, we use heap sort algorithm to get <code>R</code> highest <code>p<sub>i</sub></code> and recommend to the users the corresponding parts.Besides, we use exactly the same strategy to make recommendation of related projects to the users. For simplicity, we ignore the details here.</p> | + | <p>After the computation of \(\{p_i|i=1,2,...,m\}\), we use heap sort algorithm to get <code>R</code> highest <code>p<sub>i</sub></code> and recommend to the users the corresponding parts.Besides, we use exactly the same strategy to make recommendation of related projects to the users. For simplicity, we ignore the details here.</p> |
| </div> | | </div> |
| </section> | | </section> |
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| <h3>Model</h3> | | <h3>Model</h3> |
| <div class="paragraph"> | | <div class="paragraph"> |
− | <p>The interaction among the substances in genetic circuits can be characterized by a <code>n * n</code> relation matrix <code>R</code>, where <code>n</code> is number of substances. The entry in row <code>i</code> and column <code>j</code> has 3 possible values for 3 possible relations, i.e. </p> | + | <p>The interaction among the substances in genetic circuits can be characterized by a <code>n * n</code> relation matrix <code>R</code>, where <code>n</code> is number of substances. The entry in row <code>i</code> and column <code>j</code> has 3 possible values for 3 possible relations, i.e. $$ |
− | <img src="https://static.igem.org/mediawiki/2017/6/6c/T--SYSU-Software--model_rij.png" id="rij-img" alt="" class="centered formula"> | + | R_{i,j}= |
| + | \begin{cases} |
| + | 1 & \text{if $i$ promotes $j$} \\ |
| + | -1 & \text{if $i$ inhibits $j$} \\ |
| + | 0 & \text{No effect} |
| + | \end{cases} |
| + | $$</p> |
| + | |
| <p>Therefore , the <code>j</code>th column records all the impacts the system exerts to the <code>j</code>th substances.</p> | | <p>Therefore , the <code>j</code>th column records all the impacts the system exerts to the <code>j</code>th substances.</p> |
− | <p>Let <code>x<sub>j</sub>(t)</code> denotes the concentration of substance <code>j</code> at time <code>t</code> , then we use the following ODE to characterize <code>x<sub>j</sub>(t)</code> for <img src="https://static.igem.org/mediawiki/2017/5/51/T--SYSU-Software--modeling_j-1-to-n.png" alt="" class="inlined-formula"></p> | + | <p>Let <code>x<sub>j</sub>(t)</code> denotes the concentration of substance <code>j</code> at time <code>t</code> , then we use the following ODE to characterize <code>x<sub>j</sub>(t)</code> for \(j\in\{1,2,...n\}\) |
− | <img src="https://static.igem.org/mediawiki/2017/d/d2/T--SYSU-Software--modeling_longest.png" id="longest-img" alt="" class="centered formula"> | + | $$ \frac{\mathbb{d}x_j(t)}{\mathbb{d}t} = \prod_{i=1}^n\{ \frac{R_{ij}(R_{ij}+1)}{2}f(x_i(t))+\frac{(R_{ij}+1)(R_{ij}-1)}{-1}+\frac{R_{ij}(R_{ij}-1)}{2}g(x_i(t))\}- \beta \times x_j(t) |
− | <p>where β represents the degradation rate and:</p> | + | $$ |
− | <img src="https://static.igem.org/mediawiki/2017/8/86/T--SYSU-Software--modeling_fx-gx.png" id="fx-gx-img" alt="" class="centered formula"> | + | </p> |
− | <p></p> | + | |
| + | <p>where β represents the degradation rate and: |
| + | $$ f(x)=1+\frac{1}{1+\mathbb{e}^{-x}}; f(x)=1-\frac{1}{1+\mathbb{e}^{-x}} $$ |
| + | </p> |
| + | |
| <h3>Imlementation</h3> | | <h3>Imlementation</h3> |
− | <p>We use Scipy, an efficient open source numerical module in Python, to give the numerical solutions to the ODE system. Specifically, we use the odeint function in Scipy. For more information about odeint function, see <a href=" https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.odeint.html" target="_blank">documentation of scipy</a></p> | + | <p>We use Scipy, an efficient open source numerical module in Python, to give the numerical solutions to the ODE system. Specifically, we use the odeint function in Scipy. For more information about odeint function, see <a href=" https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.odeint.html" target="_blank">documentation of scipy</a>.</p> |
| </div> | | </div> |
| </section> | | </section> |
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