Deep learning methods to aid lesion analysis in medical images

In this thesis, novel deep learning-based methods and extensions to existing methods that aid the segmentation and analysis of lesions have been presented. In the first half of this thesis (Chapter 2 and Chapter 3), we studied the role of uncertainty estimation methods in improving the performance of deep learning-based lesion segmentation models. Our work on false-positive reduction (Chapter 2) showed that the miscalibration present in the predictions prevents a meaningful interpretation of uncertainty estimates. We demonstrated the benefits of using more expressive distributions to model the latent space distribution to handle the segmentation of ambiguous images (Chapter 3). In the second half of the thesis (Chapter 4 and Chapter 5), we showed that the use of learned landmark correspondences can improve the registration of organs that exhibit a high degree of motion or deformation, with a focus on the clinical task of lesion co-localization. We extended an existing deep learning-based landmark correspondence prediction model, DCNN-Match, by introducing a soft mask loss term and demonstrated an improvement in lung CT registration in the absence of lung masks (Chapter 4). We also showed that using learned landmark correspondences, on or near vessels in the liver, can improve lesion co-localization over standard intensity-based image registration (Chapter 5)

Measurement of Λ (1520) production in pp collisions at √s=7TeV and p–Pb collisions at √sNN=5.02TeV

The production of the Λ (1520) baryonic resonance has been measured at midrapidity in inelastic pp collisions at s=7TeV and in p–Pb collisions at sNN=5.02TeV for non-single diffractive events and in multiplicity classes. The resonance is reconstructed through its hadronic decay channel Λ (1520) → pK - and the charge conjugate with the ALICE detector. The integrated yields and mean transverse momenta are calculated from the measured transverse momentum distributions in pp and p–Pb collisions. The mean transverse momenta follow mass ordering as previously observed for other hyperons in the same collision systems. A Blast-Wave function constrained by other light hadrons (π, K, KS0, p, Λ) describes the shape of the Λ (1520) transverse momentum distribution up to 3.5GeV/c in p–Pb collisions. In the framework of this model, this observation suggests that the Λ (1520) resonance participates in the same collective radial flow as other light hadrons. The ratio of the yield of Λ (1520) to the yield of the ground state particle Λ remains constant as a function of charged-particle multiplicity, suggesting that there is no net effect of the hadronic phase in p–Pb collisions on the Λ (1520) yield

Measurement of prompt D0, D+, D*+, and DS+ production in p–Pb collisions at √sNN = 5.02 TeV

The measurement of the production of prompt D0, D+, D*+, and DS+ mesons in proton–lead (p–Pb) collisions at the centre-of-mass energy per nucleon pair of sNN = 5.02 TeV, with an integrated luminosity of 292 ± 11 μb−1, are reported. Differential production cross sections are measured at mid-rapidity (−0.96 < ycms< 0.04) as a function of transverse momentum (pT) in the intervals 0 < pT< 36 GeV/c for D0, 1 < pT< 36 GeV/c for D+ and D*+, and 2 < pT< 24 GeV/c for D+ mesons. For each species, the nuclear modification factor RpPb is calculated as a function of pT using a proton-proton (pp) ref- erence measured at the same collision energy. The results are compatible with unity in the whole pT range. The average of the non-strange D mesons RpPb is compared with theoretical model predictions that include initial-state effects and parton transport model predictions. The pT dependence of the D0, D+, and D*+ nuclear modification factors is also reported in the interval 1 < pT< 36 GeV/c as a function of the collision centrality, and the central-to-peripheral ratios are computed from the D-meson yields measured in different centrality classes. The results are further compared with charged-particle measurements and a similar trend is observed in all the centrality classes. The ratios of the pT-differential cross sections of D0, D+, D*+, and DS+ mesons are also reported. The DS+ and D+ yields are compared as a function of the charged-particle multiplicity for several pT intervals. No modification in the relative abundances of the four species is observed with respect to pp collisions within the statistical and systematic uncertainties. [Figure not available: see fulltext.]

Measurement of electrons from heavy-flavour hadron decays as a function of multiplicity in p-Pb collisions at √sNN = 5.02 TeV

The multiplicity dependence of electron production from heavy-flavour hadron decays as a function of transverse momentum was measured in p-Pb collisions at sNN = 5.02 TeV using the ALICE detector at the LHC. The measurement was performed in the centre-of-mass rapidity interval −1.07 < ycms< 0.14 and transverse momentum interval 2 < pT< 16 GeV/c. The multiplicity dependence of the production of electrons from heavy-flavour hadron decays was studied by comparing the pT spectra measured for different multiplicity classes with those measured in pp collisions (QpPb) and in peripheral p-Pb collisions (Qcp). The QpPb results obtained are consistent with unity within uncertainties in the measured pT interval and event classes. This indicates that heavy-flavour decay electron production is consistent with binary scaling and independent of the geometry of the collision system. Additionally, the results suggest that cold nuclear matter effects are negligible within uncertainties, in the production of heavy-flavour decay electrons at midrapidity in p-Pb collisions. [Figure not available: see fulltext.

Measurement of ϒ(1S) Elliptic Flow at Forward Rapidity in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV.

The first measurement of the ϒ(1S) elliptic flow coefficient (v_{2}) is performed at forward rapidity (2.

Inclusive J/ψ production at mid-rapidity in pp collisions at √s = 5.02 TeV

Inclusive J/ψ production is studied in minimum-bias proton-proton collisions at a centre-of-mass energy of s = 5.02 TeV by ALICE at the CERN LHC. The measurement is performed at mid-rapidity (|y| < 0.9) in the dielectron decay channel down to zero transverse momentum pT, using a data sample corresponding to an integrated luminosity of Lint = 19.4 ± 0.4 nb−1. The measured pT-integrated inclusive J/ψ production cross sec- tion is dσ/dy = 5.64 ± 0.22(stat.) ± 0.33(syst.) ± 0.12(lumi.) μb. The pT-differential cross section d2σ/dpTdy is measured in the pT range 0–10 GeV/c and compared with state-of- the-art QCD calculations. The J/ψ 〈pT〉 and 〈pT2〉 are extracted and compared with results obtained at other collision energies. [Figure not available: see fulltext.]

Studies of J/ψ production at forward rapidity in Pb–Pb collisions at √sNN = 5.02 TeV

The inclusive J/ψ production in Pb–Pb collisions at the center-of-mass energy per nucleon pair sNN = 5.02 TeV, measured with the ALICE detector at the CERN LHC, is reported. The J/ψ meson is reconstructed via the dimuon decay channel at forward rapidity (2.5 < y < 4) down to zero transverse momentum. The suppression of the J/ψ yield in Pb–Pb collisions with respect to binary-scaled pp collisions is quantified by the nuclear modification factor (RAA). The RAA at sNN = 5.02 TeV is presented and compared with previous measurements at sNN = 2.76 TeV as a function of the centrality of the collision, and of the J/ψ transverse momentum and rapidity. The inclusive J/ψ RAA shows a suppression increasing toward higher transverse momentum, with a steeper dependence for central collisions. The modification of the J/ψ average transverse momentum and average squared transverse momentum is also studied. Comparisons with the results of models based on a transport equation and on statistical hadronization are carried out. [Figure not available: see fulltext.

Multiplicity dependence of (multi-)strange hadron production in proton-proton collisions at √s = 13 TeV

The production rates and the transverse momentum distribution of strange hadrons at mid-rapidity (| y| < 0.5) are measured in proton-proton collisions at s = 13 TeV as a function of the charged particle multiplicity, using the ALICE detector at the LHC. The production rates of KS0, Λ , Ξ , and Ω increase with the multiplicity faster than what is reported for inclusive charged particles. The increase is found to be more pronounced for hadrons with a larger strangeness content. Possible auto-correlations between the charged particles and the strange hadrons are evaluated by measuring the event-activity with charged particle multiplicity estimators covering different pseudorapidity regions. When comparing to lower energy results, the yields of strange hadrons are found to depend only on the mid-rapidity charged particle multiplicity. Several features of the data are reproduced qualitatively by general purpose QCD Monte Carlo models that take into account the effect of densely-packed QCD strings in high multiplicity collisions. However, none of the tested models reproduce the data quantitatively. This work corroborates and extends the ALICE findings on strangeness production in proton-proton collisions at 7 TeV