Deep Learning for Nanoscience Scanning Electron Microscope Image Recognition

In this thesis, part of the NFFA-Europe project, different deep learning techniques are used in order to train several neural networks on high performance computing facilities with the goal of classifying images of nanoscience structures captured by SEM (scanning electron microscope). Using TensorFlow and TF-Slim as deep learning frameworks, we train on multiple and different GPU cards several state-of-the-art convolutional neural network (CNN) architectures (i.e. AlexNet, Inception, ResNet, DenseNet) and test their performances in terms of training time and accuracy on our SEM dataset. Furthermore, we coded a DenseNet implementation in TF-Slim. Moreover, we apply and benchmark transfer learning, which consists of retraining some pre-trained models. We then present some preliminary results, obtained in collaboration with Intel and CINECA, about several tests on Neon, the deep learning framework by Intel and Nervana-Systems optimized on Intel CPUs. Lastly, Inceptionv3 was ported from TF-Slim to Neon for future investigations

Entanglement entropy and negativity of disjoint intervals in CFT: Some numerical extrapolations

The entanglement entropy and the logarithmic negativity can be computed in quantum field theory through a method based on the replica limit. Performing these analytic continuations in some cases is beyond our current knowledge, even for simple models. We employ a numerical method based on rational interpolations to extrapolate the entanglement entropy of two disjoint intervals for the conformal field theories given by the free compact boson and the Ising model. The case of three disjoint intervals is studied for the Ising model and the non compact free massless boson. For the latter model, the logarithmic negativity of two disjoint intervals has been also considered. Some of our findings have been checked against existing numerical results obtained from the corresponding lattice models

Deep Learning, Feature Learning, and Clustering Analysis for SEM Image Classification

In this paper, we report upon our recent work aimed at improving and adapting machine learning algorithms to automatically classify nanoscience images acquired by the Scanning Electron Microscope (SEM). This is done by coupling supervised and unsupervised learning approaches. We first investigate supervised learning on a ten-category data set of images and compare the performance of the different models in terms of training accuracy. Then, we reduce the dimensionality of the features through autoencoders to perform unsupervised learning on a subset of images in a selected range of scales (from 1 $\mu$m to 2 $\mu$m). Finally, we compare different clustering methods to uncover intrinsic structures in the images

The Benefit of Sleeve Gastrectomy in Obese Adolescents on Nonalcoholic Steatohepatitis and Hepatic Fibrosis

Objective To determine whether bariatric surgery is effective for the treatment of nonalcoholic steatohepatitis (NASH) in adolescence, we compared the efficacy of laparoscopic sleeve gastrectomy (LSG) with that of lifestyle intervention (nonsurgical weight loss [NSWL]) for NASH reversal in obese adolescents. Study design Obese (body mass index ≥ 35 kg/m2) adolescents (13-17 years of age) with biopsy-proven NAFLD underwent LSG, lifestyle intervention plus intragastric weight loss devices (IGWLD), or only NSWL. At baseline and 1 year after treatment, patients underwent clinical and psychosocial evaluation, blood tests, liver biopsy, polysomnography, and 24-hour ambulatory blood pressure estimation. Results Twenty patients (21%) underwent LSG, 20 (21%) underwent IGWLD, and 53 (58%) received lifestyle intervention alone (NSWL). One year after treatment, patients who underwent LSG lost 21.5% of their baseline body weight, whereas patients who underwent IGWLD lost 3.4%, and patients who underwent NSWL increase 1.7%. In patients who underwent LSG, NASH reverted completely in all patients and hepatic fibrosis stage 2 disappeared in 18 patients (90%). After IGWLD, NASH reverted in 6 patients (24%) and fibrosis in 7 (37%). Patients who received the NSWL intervention did not improve significantly. Hypertension resolved in all patients who underwent LSG with preoperative hypertension (12/12) versus 50% (4/8) of the patients who underwent IGWLD (P = .02). The cohort-specific changes in impaired glucose metabolism were similar: 100% (9/9) of affected patients who underwent LSG versus 50% (1/2) of patients who underwent IGWLD (P = .02). LSG was also more affective in resolving dyslipidemia (55% [7/12] vs 26% [10/19]; P = .05) and sleep apnea (78% [2/9] vs 30% [11/20]; P = .001). Conclusion LSG was more effective than lifestyle intervention, even when combined with intragastric devices, for reducing NASH and liver fibrosis in obese adolescents after 1 year of treatment

LPS-induced TNF-α factor mediates pro-inflammatory and pro-fibrogenic pattern in non-alcoholic fatty liver disease

Lipopolysaccharide (LPS) is currently considered one of the major players in non-alcoholic fatty liver disease (NAFLD) pathogenesis and progression. Here, we aim to investigate the possible role of LPS-induced TNF-α factor (LITAF) in inducing a pro-inflammatory and pro-fibrogenic phenotype of non-alcoholic steatohepatitis (NASH).We found that children with NAFLD displayed, in different liver-resident cells, an increased expression of LITAF which correlated with histological traits of hepatic inflammation and fibrosis. Total and nuclear LITAF expression increased in mouse and human hepatic stellate cells (HSCs). Moreover, LPS induced LITAF-dependent transcription of IL-1β, IL-6 and TNF-α in the clonal myofibroblastic HSC LX-2 cell line, and this effect was hampered by LITAF silencing. We showed, for the first time in HSCs, that LITAF recruitment to these cytokine promoters is LPS dependent. However, preventing LITAF nuclear translocation by p38MAPK inhibitor, the expression of IL-6 and TNF-α was significantly reduced with the aid of p65NF-ĸB, while IL-1β transcription exclusively required LITAF expression/activity. Finally, IL-1β levels in plasma mirrored those in the liver and correlated with LPS levels and LITAF-positive HSCs in children with NASH.In conclusion, a more severe histological profile in paediatric NAFLD is associated with LITAF over-expression in HSCs, which in turn correlates with hepatic and circulating IL-1β levels outlining a panel of potential biomarkers of NASH-related liver damage. The in vitro study highlights the role of LITAF as a key regulator of the LPS-induced pro-inflammatory pattern in HSCs and suggests p38MAPK inhibitors as a possible therapeutic approach against hepatic inflammation in NASH

Macrophage Activation in Pediatric Nonalcoholic Fatty Liver Disease (NAFLD) Correlates with Hepatic Progenitor Cell Response via Wnt3a Pathway

Non-alcoholic fatty liver disease is one of the most important causes of liver-related morbidity in children. In non-alcoholic fatty liver disease, the activation of liver resident macrophage pool is a central event in the progression of liver injury. The aims of the present study were to evaluate the polarization of liver macrophages and the possible role of Wnt3a production by macrophages in hepatic progenitor cell response in the progression of pediatric non-alcoholic fatty liver disease. 32 children with biopsy-proven non-alcoholic fatty liver disease were included. 20 out of 32 patients were treated with docosahexaenoic acid for 18 months and biopsies at the baseline and after 18 months were included. Hepatic progenitor cell activation, macrophage subsets and Wnt/β-catenin pathway were evaluated by immunohistochemistry and immunofluorescence. Our results indicated that in pediatric non-alcoholic fatty liver disease, pro-inflammatory macrophages were the predominant subset. Macrophage polarization was correlated with Non-alcoholic fatty liver disease Activity Score, ductular reaction, and portal fibrosis; docosahexaenoic acid treatment determined a macrophage polarization towards an anti-inflammatory phenotype in correlation with the reduction of serum inflammatory cytokines, with increased macrophage apoptosis, and with the up-regulation of macrophage Wnt3a expression; macrophage Wnt3a expression was correlated with β-catenin phosphorylation in hepatic progenitor cells and signs of commitment towards hepatocyte fate. In conclusion, macrophage polarization seems to have a key role in the progression of pediatric non-alcoholic fatty liver disease; the modulation of macrophage polarization could drive hepatic progenitor cell response by Wnt3a production

A contour for the entanglement entropies in harmonic lattices

We construct a contour function for the entanglement entropies in generic harmonic lattices. In one spatial dimension, numerical analysis are performed by considering harmonic chains with either periodic or Dirichlet boundary conditions. In the massless regime and for some configurations where the subsystem is a single interval, the numerical results for the contour function are compared to the inverse of the local weight function which multiplies the energy-momentum tensor in the corresponding entanglement hamiltonian, found through conformal field theory methods, and a good agreement is observed. A numerical analysis of the contour function for the entanglement entropy is performed also in a massless harmonic chain for a subsystem made by two disjoint intervals

Entanglement negativity in a two dimensional harmonic lattice: Area law and corner contributions

We study the logarithmic negativity and the moments of the partial transpose in the ground state of a two dimensional massless harmonic square lattice with nearest neighbour interactions for various configurations of adjacent domains. At leading order for large domains, the logarithmic negativity and the logarithm of the ratio between the generic moment of the partial transpose and the moment of the reduced density matrix at the same order satisfy an area law in terms of the length of the curve shared by the adjacent regions. We give numerical evidence that the coefficient of the area law term in these quantities is related to the coefficient of the area law term in the R\ue9nyi entropies. Whenever the curve shared by the adjacent domains contains vertices, a subleading logarithmic term occurs in these quantities and the numerical values of the corner function for some pairs of angles are obtained. In the special case of vertices corresponding to explementary angles, we provide numerical evidence that the corner function of the logarithmic negativity is given by the corner function of the R\ue9nyi entropy of order 1/2