School of Mathematics and Statistics - Research Publications
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ItemA representation learning framework for detection and characterization of dead versus strain localization zones from pre-to post-failure(SPRINGER, 2022-08-01)Abstract Experiments have long shown that zones of near vanishing deformation, so-called “dead zones”, emerge and coexist with strain localization zones inside deforming granular media. To date, a method that can disentangle these dynamically coupled structures from each other, from pre- to post- failure, is lacking. Here we develop a framework that learns a new representation of the kinematic data, based on the complexity of a grain’s neighborhood structure in the kinematic-state-space, as measured by a recently introduced metric called s-LID. Dead zones (DZ) are first distinguished from strain localization zones (SZ) throughout loading history. Next the coupled dynamics of DZ and SZ are characterized using a range of discriminative features representing: local nonaffine deformation, contact topology and force transmission properties. Data came from discrete element simulations of biaxial compression tests. The deformation is found to be essentially dual in nature. DZ and SZ exhibit distinct yet coupled dynamics, with the separation in dynamics increasing in the lead up to failure. Force congestion and plastic deformation mainly concentrate in SZ. Although the 3-core of the contact network is highly prone to damage in SZ, it is robust to pre-failure microbands but is decimated in the shearband, leaving a fragmented 3-core in DZ at failure. We also show how loading condition and rolling resistance influence SZ and DZ differently, thus casting new light on controls on plasticity from the perspective of emergent deformation structures. Graphic abstract
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ItemEstimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.(Springer Science and Business Media LLC, 2022-11)Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, have so far impeded at-scale pan-cancer examination of total mRNA content. Here we present a method to quantify tumor-specific total mRNA expression (TmS) from bulk sequencing data, taking into account tumor transcript proportion, purity and ploidy, which are estimated through transcriptomic/genomic deconvolution. We estimate and validate TmS in 6,590 patient tumors across 15 cancer types, identifying significant inter-tumor variability. Across cancers, high TmS is associated with increased risk of disease progression and death. TmS is influenced by cancer-specific patterns of gene alteration and intra-tumor genetic heterogeneity as well as by pan-cancer trends in metabolic dysregulation. Taken together, our results indicate that measuring cell-type-specific total mRNA expression in tumor cells predicts tumor phenotypes and clinical outcomes.
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ItemSpin-Ruijsenaars, q-Deformed Haldane-Shastry and Macdonald Polynomials(SPRINGER, 2022-05-13)Abstract We study the -analogue of the Haldane–Shastry model, a partially isotropic (xxz-like) long-range spin chain that by construction enjoys quantum-affine (really: quantum-loop) symmetries at finite system size. We derive the pairwise form of the Hamiltonian, found by one of us building on work of D. Uglov, via ‘freezing’ from the affine Hecke algebra. To this end we first obtain explicit expressions for the spin-Macdonald operators of the (trigonometric) spin-Ruijsenaars model. Through freezing these give rise to the higher Hamiltonians of the spin chain, including another Hamiltonian of the opposite ‘chirality’. The sum of the two chiral Hamiltonians has a real spectrum also when $$|\mathsf {q}|=1$$ | q | = 1 , so in particular when is a root of unity. For generic $$\mathsf {q}$$ q the eigenspaces are known to be labelled by ‘motifs’. We clarify the relation between these patterns and the corresponding degeneracies (multiplicities) in the crystal limit $$\textsf {q}\rightarrow \infty $$ q → ∞ . For each motif we obtain an explicit expression for the exact eigenvector, valid for generic , that has (‘pseudo’ or ‘l-’) highest weight in the sense that, in terms of the operators from the monodromy matrix, it is an eigenvector of A and D and annihilated by C. It has a simple component featuring the ‘symmetric square’ of the -Vandermonde polynomial times a Macdonald polynomial—or more precisely its quantum spherical zonal special case. All other components of the eigenvector are obtained from this through the action of the Hecke algebra, followed by ‘evaluation’ of the variables to roots of unity. We prove that our vectors have highest weight upon evaluation. Our description of the exact spectrum is complete. The entire model, including the quantum-loop action, can be reformulated in terms of polynomials. Our main tools are the Y-operators from the affine Hecke algebra. From a more mathematical perspective the key step in our diagonalisation is as follows. We show that on a subspace of suitable polynomials the first M ‘classical’ (i.e. no difference part) Y-operators in N variables reduce, upon evaluation as above, to Y-operators in M variables with parameters at the quantum zonal spherical point.
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ItemNON-PERVERSE PARITY SHEAVES ON THE FLAG VARIETY(CAMBRIDGE UNIV PRESS, 2022-08-23)Abstract We give examples of non-perverse parity sheaves on Schubert varieties for all primes.
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ItemInferring rheology from free-surface observations(CAMBRIDGE UNIV PRESS, 2022-03-03)We develop direct inversion methods for inferring the rheology of a fluid from observations of its shallow flow. First, the evolution equation for the free-surface flow of an inertia-less current with general constitutive law is derived. The relationship between the volume flux of fluid and the basal stress, $\tau _b$ , is encapsulated by a single function $F(\tau _b)$ , which depends only on the constitutive law. The inversion method consists of (i) determining the flux and basal stress from the free-surface evolution, (ii) comparing the flux with the basal stress to constrain $F$ and (iii) inferring the constitutive law from $F$ . Examples are presented for both steady and transient free-surface flows demonstrating that a wide range of constitutive laws can be directly obtained. For flows in which the free-surface velocity is known, we derive a different method, which circumvents the need to calculate the flux.
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ItemDistributed forward-backward methods for ring networks(Springer Science and Business Media LLC, 2022-01-01)Abstract In this work, we propose and analyse forward-backward-type algorithms for finding a zero of the sum of finitely many monotone operators, which are not based on reduction to a two operator inclusion in the product space. Each iteration of the studied algorithms requires one resolvent evaluation per set-valued operator, one forward evaluation per cocoercive operator, and two forward evaluations per monotone operator. Unlike existing methods, the structure of the proposed algorithms are suitable for distributed, decentralised implementation in ring networks without needing global summation to enforce consensus between nodes.
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ItemCritical scaling of lattice polymers confined to a box without endpoint restriction(SPRINGER, 2022-08-21)Abstract We study self-avoiding walks on the square lattice restricted to a square box of side L weighted by a length fugacity without restriction of their end points. This is a natural model of a confined polymer in dilute solution such as polymers in mesoscopic pores. The model admits a phase transition between an ‘empty’ phase, where the average length of walks are finite and the density inside large boxes goes to zero, to a ‘dense’ phase, where there is a finite positive density. We prove various bounds on the free energy and develop a scaling theory for the phase transition based on the standard theory for unconstrained polymers. We compare this model to unrestricted walks and walks that whose endpoints are fixed at the opposite corners of a box, as well as Hamiltonian walks. We use Monte Carlo simulations to verify predicted values for three key exponents: the density exponent $$\alpha =1/2$$ α = 1 / 2 , the finite size crossover exponent $$1/\nu =4/3$$ 1 / ν = 4 / 3 and the critical partition function exponent $$2-\eta =43/24$$ 2 - η = 43 / 24 . This implies that the theoretical framework relating them to the unconstrained SAW problem is valid.
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Itempropeller: testing for differences in cell type proportions in single cell data(OXFORD UNIV PRESS, 2022-08-25)MOTIVATION: Single cell RNA-Sequencing (scRNA-seq) has rapidly gained popularity over the last few years for profiling the transcriptomes of thousands to millions of single cells. This technology is now being used to analyse experiments with complex designs including biological replication. One question that can be asked from single cell experiments, which has been difficult to directly address with bulk RNA-seq data, is whether the cell type proportions are different between two or more experimental conditions. As well as gene expression changes, the relative depletion or enrichment of a particular cell type can be the functional consequence of disease or treatment. However, cell type proportion estimates from scRNA-seq data are variable and statistical methods that can correctly account for different sources of variability are needed to confidently identify statistically significant shifts in cell type composition between experimental conditions. RESULTS: We have developed propeller, a robust and flexible method that leverages biological replication to find statistically significant differences in cell type proportions between groups. Using simulated cell type proportions data, we show that propeller performs well under a variety of scenarios. We applied propeller to test for significant changes in cell type proportions related to human heart development, ageing and COVID-19 disease severity. AVAILABILITY AND IMPLEMENTATION: The propeller method is publicly available in the open source speckle R package (https://github.com/phipsonlab/speckle). All the analysis code for the article is available at the associated analysis website: https://phipsonlab.github.io/propeller-paper-analysis/. The speckle package, analysis scripts and datasets have been deposited at https://doi.org/10.5281/zenodo.7009042. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Itemsgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data(OXFORD UNIV PRESS, 2022-09-15)Profiling gametes of an individual enables the construction of personalised haplotypes and meiotic crossover landscapes, now achievable at larger scale than ever through the availability of high-throughput single-cell sequencing technologies. However, high-throughput single-gamete data commonly have low depth of coverage per gamete, which challenges existing gamete-based haplotype phasing methods. In addition, haplotyping a large number of single gametes from high-throughput single-cell DNA sequencing data and constructing meiotic crossover profiles using existing methods requires intensive processing. Here, we introduce efficient software tools for the essential tasks of generating personalised haplotypes and calling crossovers in gametes from single-gamete DNA sequencing data (sgcocaller), and constructing, visualising, and comparing individualised crossover landscapes from single gametes (comapr). With additional data pre-possessing, the tools can also be applied to bulk-sequenced samples. We demonstrate that sgcocaller is able to generate impeccable phasing results for high-coverage datasets, on which it is more accurate and stable than existing methods, and also performs well on low-coverage single-gamete sequencing datasets for which current methods fail. Our tools achieve highly accurate results with user-friendly installation, comprehensive documentation, efficient computation times and minimal memory usage.
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ItemDefining the Fetal Gene Program at Single-Cell Resolution in Pediatric Dilated Cardiomyopathy.(Ovid Technologies (Wolters Kluwer Health), 2022-10-04)