Synapse at CAp 2017 NER challenge: Fasttext CRF

We present our system for the CAp 2017 NER challenge which is about named entity recognition on French tweets. Our system leverages unsupervised learning on a larger dataset of French tweets to learn features feeding a CRF model. It was ranked first without using any gazetteer or structured external data, with an F-measure of 58.89\%. To the best of our knowledge, it is the first system to use fasttext embeddings (which include subword representations) and an embedding-based sentence representation for NER

Evidence for meiosis and initial cells.

<p><b>A:</b> 18s rRNA phylogeny of diatoms including pennates (pink rectangle), centrics (blue rectangle). Highlighted in red are the four strains induced into sexual reproduction in this study. Species for which some evidence already exists for sexual reproduction are starred [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181098#pone.0181098.ref009" target="_blank">9</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181098#pone.0181098.ref013" target="_blank">13</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181098#pone.0181098.ref016" target="_blank">16</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181098#pone.0181098.ref028" target="_blank">28</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181098#pone.0181098.ref033" target="_blank">33</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181098#pone.0181098.ref038" target="_blank">38</a>]. <b>B-D:</b> Changes in DNA and chlorophyll fluorescence in exponential (EXP), stationary (STA) and late stationary (L-STA) growth phases of <i>T</i>. <i>pseudonana</i> induced by ammonium; 30,000 events recorded, representative of two biological replicates. <b>E:</b> Coulter Counter distributions of cell diameter for <i>T</i>. <i>pseudonana</i> cultures in exponential phase of growth and maintained in NaNO₃ (red) and after six successive 25% transfers to medium with ammonium (blue). Each new culture was allowed to remain in stationary phase for three days before the next 25% transfer was made. Single replicates of cultures with cell densities of 2.4 x 10⁶ ml^-1 (NaNO₃) and 2.3 x 10⁶ ml^-1 (ammonium). Dashed lines are the mode for each peak.</p

Effects of growth parameters on induction of sexual reproduction in <i>T</i>. <i>pseudonana</i> CCMP1335, <i>T</i>. <i>weissflogii</i> and <i>C</i>. <i>cryptica</i>.

<p>Oogonia and auxospores always appeared in stationary phase. The percentage of the total population (at least 300 cells counted per replicate) differentiated into oogonia or auxospores when grown in nitrate or ammonium is shown for the day they were at their maximum number; data are mean values ± s.d., biological replicates n = 3.</p

Transcriptomic evidence for sexual reproduction in <i>T</i>. <i>pseudonana</i>.

<p><b>A:</b> Heat map of 89 genes having annotated functions that were differentially expressed during differentiation and sexual reproduction in <i>T</i>. <i>pseudonana</i> CCMP1335. Color indicates normalized expression value (FPKM) for each nitrogen treatment (control = 100 μM NO₃^-; 100NH4 = 100 μM NH₄⁺; 800NH4 = 800 μM NH₄⁺) and growth phase (EXP, STA, L-STA). <b>B:</b> FPKM values of select genes across growth phases for each nitrogen treatment.</p

The life cycle of a centric diatom.

<p>The average cell size of a population of asexually dividing diatoms decreases as a result of differential thecae inheritance. At a critically small size, cells can initiate sexual reproduction and differentiate into male and female cells. Meiosis in the male spermatogonangium produces multinucleate spermatogonia that divide into individual haploid spermatocytes. Meiosis in the female oogonia produces a single functional haploid nucleus that is fertilized by a flagellated spermatocyte through an opening in the oogonia thecae. Fertilized oogonia expand into a large auxospore where new, large thecae are formed for the new initial cell.</p