arXiv subjects
Publications and source records attributed to Paul Kirk.
I provide a detailed exposition of the fundamental group calculations in the ``reverse engineering" construction of an exotic $\CP ^2\#3\overline{\CP }^2$ and of an exotic $\CP ^2\#2\overline{\CP }^2$.
We provide a proof that the $SU(2)$ character variety of a genus two surface, $\chi(F_2)$, is a closed compact manifold, and a proof of the Narasimhan-Ramanan theorem that $\chi(F_2)$ is homeomorphic to ${\mathbb C} P^3$. This is done entirely in the language of $SU(2)$ representations, differential topology and elementary algebraic topology. It avoids the Narasimhan-Seshadri correspondence, clarifying the nature of Lagrangian immersions into $\chi(F_2)$ induced by 3-manifolds with genus two boundary. We give examples of such Lagrangian immersions and describe a correspondence from multicurves in the pillowcase to Lagrangian immersions in $\chi(F_2)$, induced by a 2-stranded tangle in a punctured genus 2 handlebody. We give an example of a non-transverse pair of smooth Lagrangians in $\chi(F_2)$ induced by a genus 2 Heegaard splitting of $(S^3,W)$ for the ``linked eyeglasses" web $W$, which are made transverse, and hence the corresponding Chern-Simons function Morse, using Goldman flows/holonomy perturbations along embedded curves in the Heegaard surface.
Legacy software systems, written in outdated languages like MUMPS and mainframe assembly, pose challenges in efficiency, maintenance, staffing, and security. While LLMs offer promise for modernizing these systems, their ability to understand legacy languages is largely unknown. This paper investigates the utilization of LLMs to generate documentation for legacy code using two datasets: an electronic health records (EHR) system in MUMPS and open-source applications in IBM mainframe Assembly Language Code (ALC). We propose a prompting strategy for generating line-wise code comments and a rubric to evaluate their completeness, readability, usefulness, and hallucination. Our study assesses the correlation between human evaluations and automated metrics, such as code complexity and reference-based metrics. We find that LLM-generated comments for MUMPS and ALC are generally hallucination-free, complete, readable, and useful compared to ground-truth comments, though ALC poses challenges. However, no automated metrics strongly correlate with comment quality to predict or measure LLM performance. Our findings highlight the limitations of current automated measures and the need for better evaluation metrics for LLM-generated documentation in legacy systems.
We examine the holonomy-perturbed traceless SU(2) character variety of the trivial four-stranded tangle {p_1,p_2,p_3,p_4} X [0,1] in S^2 X [0,1] equipped with a strong marking, either an earring or a bypass. Viewing these marked tangles as endomorphisms in the cobordism category from the four-punctured sphere to itself, we identify the images of these endomorphisms in the Weinstein symplectic partial category under the partially defined holonomy-perturbed traceless character variety functor. We express these endomorphisms on immersed curves in the pillowcase in terms of doubling and figure eight operations and prove they have the same image.
We construct two homology 3-spheres for which the (unperturbed) $SU(2)$ Chern-Simons function is not Morse-Bott. In one case, there is a degenerate isolated critical point. In the other, a path component of the critical set is not homeomorphic to a manifold. The examples are $+1$ surgeries on connected sums of torus knots.
The earring tangle consists of four strands 4pt x [0,1] inside S^2 x [0,1] and one meridian around one of the strands. Equipping this tangle with a nontrivial SO(3) bundle, we show that its traceless SU(2) flat moduli space is topologically a smooth genus three surface. We also show that the restriction map from this surface to the traceless flat moduli space of the boundary of the earring tangle is a particular Lagrangian immersion into the product of two pillowcases. The latter computation suggests that figure eight bubbling -- a subtle degeneration phenomenon predicted by Bottman and Wehrheim -- appears in the context of traceless character varieties.
We prove that the restriction map from the subspace of regular points of the holonomy perturbed SU(2) traceless flat moduli space of a tangle in a 3-manifold to the traceless flat moduli space of its boundary marked surface is a Lagrangian immersion. A key ingredient in our proof is the use of composition in the Weinstein category, combined with the fact that SU(2) holonomy perturbations in a cylinder induce Hamiltonian isotopies. In addition, we show that $(S^2,4)$, the 2-sphere with four marked points, is its own traceless flat SU(2) moduli space.
For a diagram of a 2-stranded tangle in the 3-ball we define a twisted complex of compact Lagrangians in the triangulated envelope of the Fukaya category of the smooth locus of the pillowcase. We show that this twisted complex is a functorial invariant of the isotopy class of the tangle, and that it provides a factorization of Bar-Natan's functor from the tangle cobordism category to chain complexes. In particular, the hom set of our invariant with a particular non-compact Lagrangian associated to the trivial tangle is naturally isomorphic to the reduced Khovanov chain complex of the closure of the tangle. Our construction comes from the geometry of traceless SU(2) character varieties associated to resolutions of the tangle diagram, and was inspired by Kronheimer and Mrowka's singular instanton link homology.
We present the complete classification of the subgroup of the classical knot concordance group generated by knots with eight or fewer crossings. Proofs are presented in summary. We also describe extensions of this work to the case of nine crossing knots.
We exhibit the traceless $SU(2)$ character variety of a 6-punctured 2-sphere as a 2-fold branched cover of ${\mathbb{C}}P^3$, branched over the singular Kummer surface, with the branch locus in $R(S^2,6)$ corresponding to the binary dihedral representations. This follows from an analysis of the map induced on $SU(2)$ character varieties by the 2-fold branched cover $F_{n-1}\to S^2$ branched over $2n$ points, combined with the theorem of Narasimhan-Ramanan which identifies $R(F_2)$ with ${\mathbb{C}} P^3$. The singular points of $R(S^2,6)$ correspond to abelian representations, and we prove that each has a neighborhood in $R(S^2,6)$ homeomorphic to a cone on $S^2\times S^3$.
The traceless $SU(2)$ character variety $R(S^2,\{a_i,b_i\}_{i=1}^n)$ of a $2n$-punctured 2-sphere is the symplectic reduction of a Hamiltonian $n$-torus action on the $SU(2)$ character variety of a closed surface of genus $n$. It is stratified with a finite singular stratum and a top smooth symplectic stratum of dimension $4n-6$. For generic holonomy perturbations $π$, the traceless $SU(2)$ character variety $R_π(Y,L)$ of an $n$-stranded tangle $L$ in a homology 3-ball $Y$ is stratified with a finite singular stratum and top stratum a smooth manifold. The restriction to $R(S^2, 2n)$ is a Lagrangian immersion which preserves the cone neighborhood structure near the singular stratum. For generic holonomy perturbations $π$, the variant $R_π^\natural(Y,L)$, obtained by taking the connected sum of $L$ with a Hopf link and considering $SO(3)$ representations with $w_2$ supported near the extra component, is a smooth compact manifold without boundary of dimension $2n-3$, which Lagrangian immerses into the smooth stratum of $R(S^2,\{a_i,b_i\}_{i=1}^n)$. The proofs of these assertions consist of stratified transversality arguments to eliminate non-generic strata in the character variety and to insure that the restriction map to the boundary character variety is also generic. The main tool introduced to establish abundance of holonomy perturbations is the use of holonomy perturbations along curves $C$ in a cylinder $F\times I$, where $F$ is a closed surface. When $C$ is obtained by pushing an embedded curve on $F$ into the cylinder, we prove that the corresponding holonomy perturbation induces one of Goldman's generalized Hamiltonian twist flows on the $SU(2)$ character variety $\mathcal{M}(F)$ associated to the curve $C$.
There has been a long-standing and at times fractious debate whether complex and large systems can be stable. In ecology, the so-called `diversity-stability debate' arose because mathematical analyses of ecosystem stability were either specific to a particular model (leading to results that were not general), or chosen for mathematical convenience, yielding results unlikely to be meaningful for any interesting realistic system. May's work, and its subsequent elaborations, relied upon results from random matrix theory, particularly the circular law and its extensions, which only apply when the strengths of interactions between entities in the system are assumed to be independent and identically distributed (i.i.d.). Other studies have optimistically generalised from the analysis of very specific systems, in a way that does not hold up to closer scrutiny. We show here that this debate can be put to rest, once these two contrasting views have been reconciled --- which is possible in the statistical framework developed here. Here we use a range of illustrative examples of dynamical systems to demonstrate that (i) stability probability cannot be summarily deduced from any single property of the system (e.g. its diversity), and (ii) our assessment of stability depends on adequately capturing the details of the systems analysed. Failing to condition on the structure of dynamical systems will skew our analysis and can, even for very small systems, result in an unnecessarily pessimistic diagnosis of their stability.
We define an elementary relatively $\mathbb Z/4$ graded Lagrangian-Floer chain complex for restricted immersions of compact 1-manifolds into the pillowcase, and apply it to the intersection diagram obtained by taking traceless $SU(2)$ character varieties of 2-tangle decompositions of knots. Calculations for torus knots are explained in terms of pictures in the punctured plane. The relation to the reduced instanton homology of knots is explored.
Given a 2-stranded tangle in a $\ZZ/2$ homology ball, $T\subset Y$, we investigate the character variety $R(Y,T)$ of conjugacy classes of traceless SU(2) representations of $π_1(Y\setminus T)$. In particular we completely determine the subspace of binary dihedral representations, and identify all of $R(Y,T)$ for many tangles naturally associated to knots in S^3. Moreover, we determine the image of the restriction map from $R(T,Y)$ to the traceless SU(2) character variety of the 4-punctured 2-sphere (the {\it pillowcase}). We give examples to show this image can be non-linear in general, and show it is linear for tangles associated to pretzel knots.
We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likely number of disease subtypes, given the data. We apply the method to 277 glioblastoma samples from The Cancer Genome Atlas, for which there are gene expression, copy number variation, methylation and microRNA data. We identify 8 distinct consensus subtypes and study their prognostic value for death, new tumour events, progression and recurrence. The consensus subtypes are prognostic of tumour recurrence (log-rank p-value of $3.6 \times 10^{-4}$ after correction for multiple hypothesis tests). This is driven principally by the methylation data (log-rank p-value of $2.0 \times 10^{-3}$) but the effect is strengthened by the other 3 data types, demonstrating the value of integrating multiple data types. Of particular note is a subtype of 47 patients characterised by very low levels of methylation. This subtype has very low rates of tumour recurrence and no new events in 10 years of follow up. We also identify a small gene expression subtype of 6 patients that shows particularly poor survival outcomes. Additionally, we note a consensus subtype that showly a highly distinctive data signature and suggest that it is therefore a biologically distinct subtype of glioblastoma. The code is available from https://sites.google.com/site/multipledatafusion/
Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities and which allows expansion up to any number of moments. For some chemical reaction systems, more than two moments are necessary to describe the dynamic properties of the system, which the linear noise approximation (LNA) is unable to provide. Moreover, also for systems for which the mean does not have a strong dependence on higher order moments, moment approximation methods give information about higher order moments of the underlying probability distribution. We demonstrate the method using a dimerisation reaction, Michaelis-Menten kinetics and a model of an oscillating p53 system. We show that for the dimerisation reaction and Michaelis-Menten enzyme kinetics system higher order moments have limited influence on the estimation of the mean, while for the p53 system, the solution for the mean can require several moments to converge to the average obtained from many stochastic simulations. We also find that agreement between lower order moments does not guarantee that higher moments will agree. Compared to stochastic simulations our approach is numerically highly efficient at capturing the behaviour of stochastic systems in terms of the average and higher moments, and we provide expressions for the computational cost for different system sizes and orders of approximation. {We show how the moment expansion method can be employed to efficiently {quantify parameter sensitivity}.} Finally we investigate the effects of using too few moments on parameter estimation, and provide guidance on how to estimate if the distribution can be accurately approximated using only a few moments.
We introduce explicit holonomy perturbations of the Chern-Simons functional on a 3-ball containing a pair of unknotted arcs. These perturbations give us a concrete local method for making the moduli spaces of flat singular SO(3) connections relevant to Kronheimer and Mrowka's singular instanton knot homology non-degenerate. The mechanism for this study is a (Lagrangian) intersection diagram which arises, through restriction of representations, from a tangle decomposition of a knot. When one of the tangles is trivial, our perturbations allow us to study isolated intersections of two Lagrangians to produce minimal generating sets for singular instanton knot homology. The (symplectic) manifold where this intersection occurs corresponds to the traceless character variety of the four-punctured 2-sphere, which we identify with the familiar pillowcase. We investigate the image in this pillowcase of the traceless representations of tangles obtained by removing a trivial tangle from 2-bridge knots and torus knots. Using this, we compute the singular instanton homology of a variety of torus knots. In many cases, our computations allow us to understand non-trivial differentials in the spectral sequence from Khovanov homology to singular instanton homology.
We introduce a surgery operation on symplectic manifolds called coisotropic Luttinger surgery, which generalizes Luttinger surgery on Lagrangian tori in symplectic 4-manifolds. We use it to produce infinitely many distinct symplectic non-Kahler 6-manifolds $X$ with $c_1(X)=0$ which are not of the form $M\times F$ for $M$ a symplectic 4-manifold and $F$ a closed surface.