What is the Machine Learning?

Applications of machine learning tools to problems of physical interest are often criticized for producing sensitivity at the expense of transparency. To address this concern, we explore a data planing procedure for identifying combinations of variables -- aided by physical intuition -- that can discriminate signal from background. Weights are introduced to smooth away the features in a given variable(s). New networks are then trained on this modified data. Observed decreases in sensitivity diagnose the variable's discriminating power. Planing also allows the investigation of the linear versus non-linear nature of the boundaries between signal and background. We demonstrate the efficacy of this approach using a toy example, followed by an application to an idealized heavy resonance scenario at the Large Hadron Collider. By unpacking the information being utilized by these algorithms, this method puts in context what it means for a machine to learn.Comment: 6 pages, 3 figures. Version published in PRD, discussion adde

Additional file 5: Figure S3. of Glyceollins trigger anti-proliferative effects through estradiol-dependent and independent pathways in breast cancer cells

GO enrichment analysis of different treatment-related expression patterns. Eight expression patterns are matched with a selection of GO terms from the ontology “phenotypes,” “biological process,” “cellular component” and “pathways.” The numbers of genes associated with each GO term are indicated in the first column. Enrichment is indicated by bolded rectangles, where the first number indicates the number of genes found in our analysis and the second the number expected with a random list of genes. Overrepresented genes in a specific GO term are shown in red, and underrepresented genes are shown in blue. (TIFF 2724 kb

Hsf2 deletion in blastocyst is characterized by a higher Hsp70 induction.

<p>(A) Relative quantity of total Hsf2 and Hsf2α transcripts was assessed in blastocyst and testis using RT-real time PCR. Results are expressed as relative expression of Hsf2α compared to total Hsf2 and correspond to the mean of two independent experiments. (B) Hsp70 induction after 4 h of MG132 treatment was assessed by RT-real time PCR in WT and <i>Hsf2^−/−</i> blastocysts. Results are expressed as fold induction of Hsp70 expression after MG132 treatment, normalized to DMSO for each sample, and correspond to the mean of two independent experiments.</p

Transcriptional activity of HSF1 and HSF2 isoforms.

<p>(A) <i>Hsf1.2^−/−</i> iMEFs were co-transfected with increasing quantity of pCR3.1-HSF1α (left), or pCR3.1-HSF1β (right), in addition to pHSE_x2-TATA-Luc used as a reporter gene. DNA quantities were adjusted with empty pCR3.1. Transfection efficiency was assessed using the pTK-Rluc reporter gene. Cells were treated with MG132 at 2.5 µM (white) or with DMSO (black) as control, for 8 h. Results correspond to the ratio between firefly luciferase (FLucif) and renilla luciferase (RLucif) activities. The data are from a representative experiment including three independent replicates (mean +/− SD). (B) Representative Western-blot showing the expression of HSF1 isoforms after transfection. <i>Hsf1.2^−/−</i> iMEFs were co-transfected with increasing quantity of pCR3.1-HSF1α (left) or pCR3.1-HSF1β (right) and pEGFP as control for transfection efficiency. Cells were treated with MG132 at 2.5 µM and immunoblots for HSF1 and GFP were performed. (C) <i>Hsf1.2^−/−</i> iMEFs were co-transfected with 12.5 ng of pCR3.1-HSF1α (full line), or pCR3.1-HSF1β (dotted line), with two reporter genes described previously. Cells were treated with MG132 at 2.5 µM or with DMSO, for 2 h, 4 h, 6 h or 8 h. Results correspond to the ratio between firefly luciferase (FLucif) and renilla luciferase (RLucif) activities and are the mean of three independent experiments +/− SD. (D) <i>Hsf1.2^−/−</i> iMEFs were co-transfected with 12.5 ng of pCR3.1-HSF2α, or pCR3.1-HSF2β, with the reporter genes as described in (A). Cells were treated with MG132 at 2.5 µM (black), or with DMSO (white), for 8 h. Results are expressed in percentage of empty vector and represent the mean of three independent experiments +/− SD (Student’s t test, ns: no significant). (E) Representative Western-blot showing the expression of HSF2 isoforms after transfection. <i>Hsf1.2^−/−</i> iMEFs were co-transfected with increasing quantity of pCR3.1-HSF2α (high panel) or pCR3.1-HSF2β (low panel) and pEGFP as control for efficiency. Cells were treated with MG132 at 2.5 µM and immunoblots for HSF2 and GFP were performed.</p

HSF2β interacts with HSF1β and inhibits its transcriptional activity.

<p>(A) <i>Hsf1.2^−/−</i> iMEFs were co-transfected with 12.5 ng of pCR3.1-HSF1α or pCR3.1-HSF1β in combination with 12.5 ng of pCR3.1-HSF2α, or pCR3.1-HSF2β. Transcriptional activity was followed with pHSE_x2-TATA-Luc, and pTK-Rluc was used as control for transfection efficiency. Cells were treated with MG132 at 2.5 µM (white), or with DMSO as control (black). Results correspond to the ratio between firefly luciferase (FLucif) and renilla luciferase (RLucif) activities and are a representative experiment made with three independent replicates (Student’s t test: HSF1α or β alone compared to others conditions. **p<0.01, ns: no significant). (B) Cells were transfected with the indicated expression vectors and the reporter genes, as described in (A). Cells were submitted to heat shock at 45°C for 20 min and put to recovery at 37°C for 6 h (grey). Untreated cells served as control (black). Results are the mean +/− SD of 9 to 12 independent transfections. (C) <i>Hsf1.2^−/−</i> iMEFs were co-transfected with pCR3.1-HSF1β (gray) and with an increase quantity of pCR3.1-HSF2α (white), or pCR3.1-HSF2β (black). Then, cells were treated with MG132 at 2.5 µM for 8 h. Results are expressed in percentage of HSF1β activity and are the mean of three independent experiments +/− SD (Student’s t test: HSF1β alone compare to others conditions. *p<0.05, **p<0.01, ns: no significant). (D) Representative co-immunoprecipitation experiments. <i>Hsf1.2^−/−</i> iMEFs were co-transfected with pEGFP or pHSF1β-EGFP, in combination with pCR3.1-HSF2α or pCR3.1-HSF2β. Cells were treated with MG132 at 1 µM for 8 h and nuclear protein extracts were submitted to EGFP immunoprecipitation, followed by immunoblotting for HSF2. The value of the IP/Input ratio is indicated below the panel.</p

Proteasome inhibition modifies the relative quantity of Hsf2α and Hsf2β at the mRNA level.

<p>(A) WT iMEFs were treated with MG132 at 1 µM or with DMSO for 10 h, or were heat shocked 20 min at 45°C and allowed to recover during 6 h. The relative quantity of Hsf2α and Hsf2β transcripts was assessed by RT-PCR using primers flanking the alternative exon. Gapdh RT-PCR served as control for efficient retrotranscritpion and amplification. (B) WT iMEFs were treated during 2 h, 4 h, 6 h or 10 h with MG132 at 1 µM or with DMSO before being harvested. In addition, WT iMEFs exposed to MG132 during 10 h were allowed to recover during 1 h, 6 h or 24 h before collection. Relative quantity of Hsf2α and Hsf2β was assessed by RT-PCR, as described above. Quantity one software (Bio Rad) was used to assess band intensity. Results were expressed in mean of percentage of each isoform +/− SD from four independent experiments. (C) WT iMEFs treated as described in (B) were harvested for protein analysis. Protein extracts were loaded on 12% polyacrylamide gel and submitted to a long migration to separate efficiently HSF2 isoforms. HSF2 was revealed by immunoblotting. Ponceau staining was used to verify the equal loading.</p

Ratio between HSF2α and HSF2β controls HSF1β transcriptional activity.

<p>(A) Representative Western-blot showing the expression of HSF2 isoforms after transfection. <i>Hsf1.2−/−</i> iMEFs were co-transfected with pCR3.1-HSF1β and pCR3.1-HSF2α/β to obtain the expression of equivalent amounts of HSF1 and HSF2, and increasing concentration of HSF2β relatively to HSF2α. Cells were treated with 2.5 µM MG132 for 8 h. Protein extracts were loaded on 12% polyacrylamide gel and submitted to a long migration to separate efficiently HSF2 isoforms. HSF2 was revealed by immunobloting. (B) Transcriptional activity induced, with fixed concentrations of HSF1 and total HSF2, but varying combinations of HSF2β/HSF2α. <i>Hsf1.2−/−</i> iMEFs were co-transfected with 12.5 ng of pCR3.1-HSF1β and with the same quantity of pCR3.1-HSF2α/β, as previously described. Diamonds correspond to the experimental data obtained in independent triplicates, and expressed as percentage of maximal activity. Solid line drawn to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056085#pone.0056085.e013" target="_blank">equation 2</a> with random multimerization and considering that HSF1 is active only in absence of HSF2β in the trimer. (C) HSE-driven transcriptional activities expected from Eq. 2, with a constant and identical amounts of HSF₁ and total HSF₂, and when increasing the ratio HSF₂β/HSF₂α. The transcriptional strength of a trimer is assumed to be proportional to the number of HSF₁ monomers present, and the unit of transcriptional strength (<i>k</i> = 1) corresponds to that of an HSF₁ monomer. The strength of trimerization is considered as either (i) identical between hetero- and homodimers (plain line), (ii) 10 fold higher for homodimers (dashed line), or (iii) 10 fold higher for heterodimers (dotted line). (D) HSE-driven transcriptional activities drawn to Eq. 2, with constant and equivalent amounts of HSF1 and HSF2, capable to either randomly homo- or heterotrimerize. Plain line: as for panel C, the transcriptional strength of a trimer is proportional to the number of HSF₁ monomers included in the trimer and the strength of a HSF₁ monomer is set to 1 (<i>k</i>₃ = 3 <i>k</i>₁ and <i>k</i>₂ = 2 <i>k</i>₁ and <i>k</i>₁ = 1). Dashed line: Transcriptional strength independent on whether the trimer contains 1, 2 or 3 HSF₁ monomers (<i>k</i>₁ = <i>k</i>₂ = <i>k</i>₃ = 1). Dotted line: same rule with <i>k</i>₁ = <i>k</i>₂ = <i>k</i>₃ = 3.</p