Search

We introduce a new algorithm for finding robust circular coordinates on data that is expected to exhibit recurrence, such as that which appears in neuronal recordings of C. elegans. Techniques exist to create circular coordinates on a simplicial complex from a dimension 1 cohomology class, and these can be applied to the Rips complex of a dataset when it has a prominent class in its dimension 1 cohomology. However, it is known this approach is extremely sensitive to uneven sampling density. Our algorithm comes with a new method to correct for uneven sampling density, adapting our prior work on averaging coordinates in manifold learning. We use rejection sampling to correct for inhomogeneous sampling and then apply Procrustes matching to align and average the subsamples. In addition to providing a more robust coordinate than other approaches, this subsampling and averaging approach has better efficiency. We validate our technique on both synthetic data sets and neuronal activity recordings. Our results reveal a topological model of neuronal trajectories for C. elegans that is constructed from loops in which different regions of the brain state space can be mapped to specific and interpretable macroscopic behaviors in the worm.

This paper studies the foundations of the geometric fixed point functor in multiplicative equivariant stable homotopy theory. We introduce a new class of equivariant orthogonal spectra called generalized orbit desuspension spectra and analyze their homotopical behavior with respect to the geometric fixed point functor and especially the interaction with smash products and symmetric powers. This analysis leads to several new foundational results, including the construction of the derived functor of geometric fixed points on equivariant commutative ring orthogonal spectra and its comparison to the derived functor on the underlying equivariant orthogonal spectra. In addition this theory provides foundations for the category of commutative ring pre-cyclotomic spectra and a formula for the derived space of maps in this category (a formula needed in the authors' paper with Yuan on relative TC). Finally, we prove a new multiplicative tom Dieck splitting for equivariant commutative ring spectra obtained as the pushforward of non-equivariant commutative ring spectra.

We introduce ORC-ManL, a new algorithm to prune spurious edges from nearest neighbor graphs using a criterion based on Ollivier-Ricci curvature and estimated metric distortion. Our motivation comes from manifold learning: we show that when the data generating the nearest-neighbor graph consists of noisy samples from a low-dimensional manifold, edges that shortcut through the ambient space have more negative Ollivier-Ricci curvature than edges that lie along the data manifold. We demonstrate that our method outperforms alternative pruning methods and that it significantly improves performance on many downstream geometric data analysis tasks that use nearest neighbor graphs as input. Specifically, we evaluate on manifold learning, persistent homology, dimension estimation, and others. We also show that ORC-ManL can be used to improve clustering and manifold learning of single-cell RNA sequencing data. Finally, we provide empirical convergence experiments that support our theoretical findings.

We introduce algorithms for robustly computing intrinsic coordinates on point clouds. Our approach relies on generating many candidate coordinates by subsampling the data and varying hyperparameters of the embedding algorithm (e.g., manifold learning). We then identify a subset of representative embeddings by clustering the collection of candidate coordinates and using shape descriptors from topological data analysis. The final output is the embedding obtained as an average of the representative embeddings using generalized Procrustes analysis. We validate our algorithm on both synthetic data and experimental measurements from genomics, demonstrating robustness to noise and outliers.

We construct a stable infinity category with objects flow categories and morphisms flow bimodules; our construction has many flavors, related to a choice of bordism theory, and we discuss in particular framed bordism and the bordism theory of complex oriented derived orbifolds. In this setup, the construction of homotopy types associated to Floer-theoretic data is immediate: the moduli spaces of solutions to Floer's equation assemble into a flow category with respect to the appropriate bordism theory, and the associated Floer homotopy types arise as suitable mapping spectra in this category. The definition of these mapping spectra is sufficiently explicit to allow a direct interpretation of the Floer homotopy groups as Floer bordism groups. In the setting of framed bordism, we show that the category we construct is a model for the category of spectra. We implement the construction of Floer homotopy types in this new formalism for the case of Hamiltonian Floer theory., Comment: Various clarifications and corrections

A classical question about a metric space is whether Borel measures on the space are determined by their values on balls. We show that for any given measure this property is stable under Gromov-Wasserstein convergence of metric measure spaces. We then use this result to show that suitable bounded subspaces of the space of persistence diagrams have the property that any Borel measure is determined by its values on balls. This justifies the use of empirical ball volumes for statistical testing in topological data analysis (TDA). Our intended application is to deploy the statistical foundations of van Delft and Blumberg (2023) for time series of random geometric objects in the context of TDA invariants, specifically persistent homology and zigzag persistence.

We describe a structure on a commutative ring (pre)cyclotomic spectrum $R$ that gives rise to a (pre)cyclotomic structure on topological Hochschild homology ($THH$) relative to its underlying commutative ring spectrum. This lets us construct $TC$ relative to $R$, denoted $TC^{R}$, and we prove some descent results relating $TC^{R}$ and $TC$. We explore several examples of this structure on familiar $\mathbb{T}$-equivariant commutative ring spectra including the periodic $\mathbb{T}$-equivariant complex cobordism spectrum $MUP_{\mathbb{T}}$ and a new (connective) equivariant version of the complex cobordism spectrum $MU$., Comment: Updated references to now finalized [8] (formerly, [Cyc23]) with requisite minor changes

We introduce an intrinsic estimator for the scalar curvature of a data set presented as a finite metric space. Our estimator depends only on the metric structure of the data and not on an embedding in $\mathbb{R}^n$. We show that the estimator is consistent in the sense that for points sampled from a probability measure on a compact Riemannian manifold, the estimator converges to the scalar curvature as the number of points increases. To justify its use in applications, we show that the estimator is stable with respect to perturbations of the metric structure, e.g., noise in the sample or error estimating the intrinsic metric. We validate our estimator experimentally on synthetic data that is sampled from manifolds with specified curvature., Comment: 37 pages, 5 figures

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is {\em persistent homology}, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. In particular, a central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on {\em decompositions} of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

We introduce a new framework to analyze shape descriptors that capture the geometric features of an ensemble of point clouds. At the core of our approach is the point of view that the data arises as sampled recordings from a metric space-valued stochastic process, possibly of nonstationary nature, thereby integrating geometric data analysis into the realm of functional time series analysis. Our framework allows for natural incorporation of spatial-temporal dynamics, heterogeneous sampling, and the study of convergence rates. Further, we derive complete invariants for classes of metric space-valued stochastic processes in the spirit of Gromov, and relate these invariants to so-called ball volume processes. Under mild dependence conditions, a weak invariance principle in $D([0,1]\times [0,\mathscr{R}])$ is established for sequential empirical versions of the latter, assuming the probabilistic structure possibly changes over time. Finally, we use this result to introduce novel test statistics for topological change, which are distribution-free in the limit under the hypothesis of stationarity. We explore these test statistics on time series of single-cell mRNA expression data, using shape descriptors coming from topological data analysis., Comment: revised version

We propose a construction of an analogue of the Hill-Hopkins-Ravenel relative norm $N_{H}^{G}$ in the context of a positive dimensional compact Lie group $G$ and closed subgroup $H$. We explore expected properties of the construction. We show that in the case when $G$ is the circle group (the unit complex numbers), the proposed construction here agrees with the relative norm constructed by Angeltveit, Gerhardt, Lawson, and the authors using the cyclic bar construction. Our construction is based on a new perspective on equivariant factorization homology, using framings to convert from actions of one group to another.

In this article, we introduce a new parameterized family of topological invariants, taking the form of candidate decompositions, for multi-parameter persistence modules. We prove that our candidate decompositions are controllable approximations: when restricting to modules that can be decomposed into interval summands, we establish theoretical results about the approximation error between our candidate decompositions and the true underlying module in terms of the standard interleaving and bottleneck distances. Moreover, even when the underlying module does not admit such a decomposition, our candidate decompositions are nonetheless stable invariants; small perturbations in the underlying module lead to small perturbations in the candidate decomposition. Then, we introduce MMA (Multipersistence Module Approximation): an algorithm for computing stable instances of such invariants, which is based on fibered barcodes and exact matchings, two constructions that stem from the theory of single-parameter persistence. By design, MMA can handle an arbitrary number of filtrations, and has bounded complexity and running time. Finally, we present empirical evidence validating the generalization capabilities and running time speed-ups of MMA on several data sets.

We show that the map from $K({\mathbb S})$ to its chromatic completion is a connective cover and identify the fiber in $K$-theoretic terms. We combine this with recent work of Land-Mathew-Meier-Tamme to prove a form of "Waldhausen's Chromatic Convergence Conjecture": we show that the map $K({\mathbb S}_{(p)})_{(p)}\to \mathop{\rm holim} K(L^{f}_{n}{\mathbb S})_{(p)}$ is the inclusion of a wedge summand.

The map $TC(\mathbb{S})^{\wedge}_{p}\to \text{holim } TC(L_{n}\mathbb{S})^{\wedge}_{p}$ is a weak equivalence.

For an equivariant commutative ring spectrum $R$, $\pi_0 R$ has algebraic structure reflecting the presence of both additive transfers and multiplicative norms. The additive structure gives rise to a Mackey functor and the multiplicative structure yields the additional structure of a Tambara functor. If $R$ is an $N_\infty$ ring spectrum in the category of genuine $G$-spectra, then all possible additive transfers are present and $\pi_0 R$ has the structure of an incomplete Tambara functor. However, if $R$ is an $N_\infty$ ring spectrum in a category of incomplete $G$-spectra, the situation is more subtle. In this paper, we study the algebraic theory of Tambara structures on incomplete Mackey functors, which we call bi-incomplete Tambara functors. Just as incomplete Tambara functors have compatibility conditions that control which systems of norms are possible, bi-incomplete Tambara functors have algebraic constraints arising from the possible interactions of transfers and norms. We give a complete description of the possible interactions between the additive and multiplicative structures.

We prove that the rank of the cohomology of a closed symplectic manifold with coefficients in a field of characteristic $p$ is smaller than the number of periodic orbits of any non-degenerate Hamiltonian flow. Following Floer, the proof relies on constructing a homology group associated to each such flow, and comparing it with the homology of the ambient symplectic manifold. The proof does not proceed by constructing a version of Floer's complex with characteristic $p$ coefficients, but uses instead the canonical (stable) complex orientations of moduli spaces of Floer trajectories to construct a version of Floer homology with coefficients in Morava's $K$-theories, and can thus be seen as an implementation of Cohen, Jones, and Segal's vision for a Floer homotopy theory. The key feature of Morava K-theory that allows the construction to be carried out is the fact that the corresponding homology and cohomology groups of classifying spaces of finite groups satisfy Poincar\'e duality.

Let $p\in \mathbb Z$ be an odd prime. We show that the fiber sequence for the cyclotomic trace of the sphere spectrum $\mathbb S$ admits an "eigensplitting" that generalizes known splittings on $K$-theory and $TC$. We identify the summands in the fiber as the covers of $\mathbb Z_{p}$-Anderson duals of summands in the $K(1)$-localized algebraic $K$-theory of $\mathbb Z$. Analogous results hold for the ring $\mathbb Z$ where we prove that the $K(1)$-localized fiber sequence is self-dual for $\mathbb Z_{p}$-Anderson duality, with the duality permuting the summands by $i\mapsto p-i$ (indexed mod $p-1$). We explain an intrinsic characterization of the summand we call $Z$ in the splitting $TC(\mathbb Z)^{\wedge}_{p}\simeq j \vee \Sigma j'\vee Z$ in terms of units in the $p$-cyclotomic tower of $\mathbb Q_{p}$., Comment: Minor corrections and improvements

The \v{C}ech and Rips constructions of persistent homology are stable with respect to perturbations of the input data. However, neither is robust to outliers, and both can be insensitive to topological structure of high-density regions of the data. A natural solution is to consider 2-parameter persistence. This paper studies the stability of 2-parameter persistent homology: We show that several related density-sensitive constructions of bifiltrations from data satisfy stability properties accommodating the addition and removal of outliers. Specifically, we consider the multicover bifiltration, Sheehy's subdivision bifiltrations, and the degree bifiltrations. For the multicover and subdivision bifiltrations, we get 1-Lipschitz stability results closely analogous to the standard stability results for 1-parameter persistent homology. Our results for the degree bifiltrations are weaker, but they are tight, in a sense. As an application of our theory, we prove a law of large numbers for subdivision bifiltrations of random data., Comment: 46 pages

Comparing and aligning large datasets is a pervasive problem occurring across many different knowledge domains. We introduce and study MREC, a recursive decomposition algorithm for computing matchings between data sets. The basic idea is to partition the data, match the partitions, and then recursively match the points within each pair of identified partitions. The matching itself is done using black box matching procedures that are too expensive to run on the entire data set. Using an absolute measure of the quality of a matching, the framework supports optimization over parameters including partitioning procedures and matching algorithms. By design, MREC can be applied to extremely large data sets. We analyze the procedure to describe when we can expect it to work well and demonstrate its flexibility and power by applying it to a number of alignment problems arising in the analysis of single cell molecular data.

In this paper, we construct incomplete versions of the equivariant stable category; i.e., equivariant stabilization of the category of $G$-spaces with respect to incomplete systems of transfers encoded by an $N_\infty$ operad $\mathcal{O}$. These categories are built from the categories of $\mathcal{O}$-algebras in $G$-spaces. Using this operadic formulation, we establish incomplete versions of the usual structural properties of the equivariant stable category, notably the tom Dieck splitting. Our work is motivated in part by the examples arising from the equivariant units and Picard space functors.

The development of single-cell technologies provides the opportunity to identify new cellular states and reconstruct novel cell-to-cell relationships. Applications range from understanding the transcriptional and epigenetic processes involved in metazoan development to characterizing distinct cells types in heterogeneous populations like cancers or immune cells. However, analysis of the data is impeded by its unknown intrinsic biological and technical variability together with its sparseness; these factors complicate the identification of true biological signals amidst artifact and noise. Here we show that, across technologies, roughly 95% of the eigenvalues derived from each single-cell data set can be described by universal distributions predicted by Random Matrix Theory. Interestingly, 5% of the spectrum shows deviations from these distributions and present a phenomenon known as eigenvector localization, where information tightly concentrates in groups of cells. Some of the localized eigenvectors reflect underlying biological signal, and some are simply a consequence of the sparsity of single cell data; roughly 3% is artifactual. Based on the universal distributions and a technique for detecting sparsity induced localization, we present a strategy to identify the residual 2% of directions that encode biological information and thereby denoise single-cell data. We demonstrate the effectiveness of this approach by comparing with standard single-cell data analysis techniques in a variety of examples with marked cell populations., Comment: Main text has 18 pages and 5 figures. Supplementary material (methods) has 21 pages and 16 figures

We define twisted Hochschild homology for Green functors. This construction is the algebraic analogue of the relative topological Hochschild homology $THH_{C_n}(-)$, and it describes the $E_2$ term of the K\"unneth spectral sequence for relative $THH$. Applied to ordinary rings, we obtain new algebraic invariants. Extending Hesselholt's construction of the Witt vectors of noncommutative rings, we interpret our construction as providing Witt vectors for Green functors., Comment: Minor revisions. Published version

We study the problem of distinguishing between two distributions on a metric space; i.e., given metric measure spaces $({\mathbb X}, d, \mu_1)$ and $({\mathbb X}, d, \mu_2)$, we are interested in the problem of determining from finite data whether or not $\mu_1$ is $\mu_2$. The key is to use pairwise distances between observations and, employing a reconstruction theorem of Gromov, we can perform such a test using a two sample Kolmogorov--Smirnov test. A real analysis using phylogenetic trees and flu data is presented.

We construct an equivalence of $E_{2}$ algebras between two models for the Thom spectrum of the free loop space that are related by derived Koszul duality. To do this, we describe the functoriality and invariance properties of topological Hochschild cohomology.

For $N_\infty$ operads $\mathcal O$ and $\mathcal O'$ such that there is an inclusion of the associated indexing systems, there is a forgetful functor from incomplete Tambara functors over $\mathcal O'$ to incomplete Tambara functors over $\mathcal O$. Roughly speaking, this functor forgets the norms in $\mathcal O'$ that are not present in $\mathcal O$. The forgetful functor has both a left and a right adjoint; the left adjoint is an operadic tensor product, but the right adjoint is more mysterious. We explicitly compute the right adjoint for finite cyclic groups of prime order., Comment: Updated the exposition based on the helpful comments of a referee

Topological periodic cyclic homology (i.e., $\mathbb{T}$-Tate fixed points of $THH$) has the structure of a strong symmetric monoidal functor of smooth and proper dg categories over a perfect field of finite characteristic., Comment: Final version

As a step towards establishing homotopy-theoretic foundations for topological data analysis (TDA), we introduce and study homotopy interleavings between filtered topological spaces. These are homotopy-invariant analogues of interleavings, objects commonly used in TDA to articulate stability and inference theorems. Intuitively, whereas a strict interleaving between filtered spaces $X$ and $Y$ certifies that $X$ and $Y$ are approximately isomorphic, a homotopy interleaving between $X$ and $Y$ certifies that $X$ and $Y$ are approximately weakly equivalent. The main results of this paper are that homotopy interleavings induce an extended pseudometric $d_{HI}$ on filtered spaces, and that this is the universal pseudometric satisfying natural stability and homotopy invariance axioms. To motivate these axioms, we also observe that $d_{HI}$ (or more generally, any pseudometric satisfying these two axioms and an additional "homology bounding" axiom) can be used to formulate lifts of several fundamental TDA theorems from the algebraic (homological) level to the level of filtered spaces. Finally, we consider the problem of establishing a persistent Whitehead theorem in terms of homotopy interleavings. We provide a counterexample to a naive formulation of the result., Comment: Major revision: Improved exposition and expanded discussion of applications. 40 pages

The Gromov-Hausdorff distance provides a metric on the set of isometry classes of compact metric spaces. Unfortunately, computing this metric directly is believed to be computationally intractable. Motivated by applications in shape matching and point-cloud comparison, we study a semidefinite programming relaxation of the Gromov-Hausdorff metric. This relaxation can be computed in polynomial time, and somewhat surprisingly is itself a pseudometric. We describe the induced topology on the set of compact metric spaces. Finally, we demonstrate the numerical performance of various algorithms for computing the relaxed distance and apply these algorithms to several relevant data sets. In particular we propose a greedy algorithm for finding the best correspondence between finite metric spaces that can handle hundreds of points., Comment: 15 pages

Recently, an elegant approach in phylogenetics was introduced by Billera-Holmes-Vogtmann that allows a systematic comparison of different evolutionary histories using the metric geometry of tree spaces. In many problem settings one encounters heavily populated phylogenetic trees, where the large number of leaves encumbers visualization and analysis in the relevant evolutionary moduli spaces. To address this issue, we introduce tree dimensionality reduction, a structured approach to reducing large phylogenetic trees to a distribution of smaller trees. We prove a stability theorem ensuring that small perturbations of the large trees are taken to small perturbations of the resulting distributions. We then present a series of four biologically motivated applications to the analysis of genomic data, spanning cancer and infectious disease. The first quantifies how chemotherapy can disrupt the evolution of common leukemias. The second examines a link between geometric information and the histologic grade in relapsed gliomas, where longer relapse branches were specific to high grade glioma. The third concerns genetic stability of xenograft models of cancer, where heterogeneity at the single cell level increased with later mouse passages. The last studies genetic diversity in seasonal influenza A virus. We apply tree dimensionality reduction to 24 years of longitudinally collected H3N2 hemagglutinin sequences, generating distributions of smaller trees spanning between three and five seasons. A negative correlation is observed between the influenza vaccine effectiveness during a season and the variance of the distributions produced using preceding seasons' sequence data. We also show how tree distributions relate to antigenic clusters and choice of influenza vaccine. Our formalism exposes links between viral genomic data and clinical observables such as vaccine selection and efficacy.

For a "genuine" equivariant commutative ring spectrum $R$, $\pi_0(R)$ admits a rich algebraic structure known as a Tambara functor. This algebraic structure mirrors the structure on $R$ arising from the existence of multiplicative norm maps. Motivated by the surprising fact that Bousfield localization can destroy some of the norm maps, in previous work we studied equivariant commutative ring structures parametrized by $N_\infty$ operads. In a precise sense, these interpolate between "naive" and "genuine" equivariant ring structures. In this paper, we describe the algebraic analogue of $N_\infty$ ring structures. We introduce and study categories of incomplete Tambara functors, described in terms of certain categories of bispans. Incomplete Tambara functors arise as $\pi_0$ of $N_\infty$ algebras, and interpolate between Green functors and Tambara functors. We classify all incomplete Tambara functors in terms of a basic structural result about polynomial functors. This classification gives a conceptual justification for our prior description of $N_\infty$ operads and also allows us to easily describe the properties of the category of incomplete Tambara functors.

We describe the multiplicative structures that arise on categories of equivariant modules over certain equivariant commutative ring spectra. Building on our previous work on N-infinity ring spectra, we construct categories of equivariant operadic modules over N-infinity rings that are structured by equivariant linear isometries operads. These categories of modules are endowed with equivariant symmetric monoidal structures, which amounts to the structure of an "incomplete Mackey functor in homotopical categories". In particular, we construct internal norms which satisfy the double coset formula. We regard the work of this paper as a first step towards equivariant derived algebraic geometry., Comment: Revised to include appendix on compact Lie groups, reflect referee comments

Let $p\in \mathbb{Z}$ be an odd prime. We prove a spectral version of Tate-Poitou duality for the algebraic $K$-theory spectra of number rings with $p$ inverted. This identifies the homotopy type of the fiber of the cyclotomic trace $K(\mathcal{O}_{F})^{\scriptscriptstyle\wedge}_{p} \to TC(\mathcal{O}_{F})^{\wedge}_{p}$ after taking a suitably connective cover. As an application, we identify the homotopy type at odd primes of the homotopy fiber of the cyclotomic trace for the sphere spectrum in terms of the algebraic $K$-theory of $\mathbb{Z}$., Comment: This draft omits material in previous drafts including: review of homotopy theory of presheaves of spectra (incl. hypercover descent and models for derived functors); review of pairings in localized and mod-p^n K-theory; proofs of some transfer and pairing folk results in the Thomason SS; details on duality in the splitting of the fiber sequence of the cyclotomic trace. For these and more, see v3

Malicious peripherals designed to attack their host computers are a growing problem. Inexpensive and powerful peripherals that attach to plug-and-play buses have made such attacks easy to mount. Making matters worse, commodity operating systems lack coherent defenses, and users are often unaware of the scope of the problem. We present Cinch, a pragmatic response to this threat. Cinch uses virtualization to attach peripheral devices to a logically separate, untrusted machine, and includes an interposition layer between the untrusted machine and the protected one. This layer regulates interaction with devices according to user-configured policies. Cinch integrates with existing OSes, enforces policies that thwart real-world attacks, and has low overhead., Comment: 18 pages, 7 figures

Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine specific genetic alterations driving disease progression. Genomic sampling of a patient's cancer provides a molecular history, represented by a phylogenetic tree. Cohorts of patients represent a forest of related phylogenetic structures. To extract clinically relevant information, one must represent and statistically compare these collections of trees. We propose a framework based on an application of the work by Billera, Holmes and Vogtmann on phylogenetic tree spaces to the case of unrooted trees of intra-individual cancer tissue samples. We observe that these tree spaces are globally nonpositively curved, allowing for statistical inference on populations of patient histories. A projective tree space is introduced, permitting visualizations of aggregate evolutionary behavior. Published data from three types of human malignancies are explored within our framework.

We calculate $\pi_*K(\mathbb S)[1/2]$, the homotopy groups of $K(\mathbb S)$ away from 2, in terms of the homotopy groups of $K(\mathbb Z)$, the homotopy groups of ${\mathbb C}P^\infty_{-1}$, and the homotopy groups of $\mathbb S$. This builds on the work of Waldhausen, who computed the rational homotopy groups (building on work of Quillen and Borel) and Rognes, who calculated the groups at regular primes in terms of the homotopy groups of ${\mathbb C}P^\infty_{-1}$, and the homotopy groups of $\mathbb S$., Comment: Last draft version of this 2018 paper, substantially similar (but not identical to) published version. Includes a correction on p.11

We prove that in the graded commutative ring $K_{*}(\mathbb{S})$, all positive degree elements are multiplicatively nilpotent. The analogous statements also hold for $TC_{*}(\mathbb{S};\mathbb{Z}^{\wedge}_p)$ and $K_{*}(\mathbb{Z})$.

We extend the theory of Thom spectra and the associated obstruction theory for orientations in order to support the construction of the string orientation of tmf, the spectrum of topological modular forms. We also develop the analogous theory of Thom spectra and orientations for associative ring spectra. Our work is based on a new model of the Thom spectrum as a derived smash product. An earlier version of this paper was part of arXiv:0810.4535., Comment: arXiv admin note: substantial text overlap with arXiv:0810.4535

We develop a generalization of the theory of Thom spectra using the language of infinity categories. This treatment exposes the conceptual underpinnings of the Thom spectrum functor: we use a new model of parametrized spectra, and our definition is motivated by the geometric definition of Thom spectra of May-Sigurdsson. For an associative ring spectrum $R$, we associate a Thom spectrum to a map of infinity categories from the infinity groupoid of a space $X$ to the infinity category of free rank one $R$-modules, which we show is a model for $BGL_1 R$; we show that $BGL_1 R$ classifies homotopy sheaves of rank one $R$-modules, which we call $R$-line bundles. We use our $R$-module Thom spectrum to define the twisted $R$-homology and cohomology of an $R$-line bundle over a space $X$, classified by a map from $X$ to $BGL_1 R$, and we recover the generalized theory of orientations in this context. In order to compare this approach to the classical theory, we characterize the Thom spectrum functor axiomatically, from the perspective of Morita theory. An earlier version of this paper was part of arXiv:0810.4535., Comment: arXiv admin note: substantial text overlap with arXiv:0810.4535

This paper lays the foundations of an approach to applying Gromov's ideas on quantitative topology to topological data analysis. We introduce the "contiguity complex", a simplicial complex of maps between simplicial complexes defined in terms of the combinatorial notion of contiguity. We generalize the Simplicial Approximation Theorem to show that the contiguity complex approximates the homotopy type of the mapping space as we subdivide the domain. We describe algorithms for approximating the rate of growth of the components of the contiguity complex under subdivision of the domain; this procedure allows us to computationally distinguish spaces with isomorphic homology but different homotopy types.

We study homotopy-coherent commutative multiplicative structures on equivariant spaces and spectra. We define N-infinity operads, equivariant generalizations of E-infinity operads. Algebras in equivariant spectra over an N-infinity operad model homotopically commutative equivariant ring spectra that only admit certain collections of Hill-Hopkins-Ravenel norms, determined by the operad. Analogously, algebras in equivariant spaces over an N-infinity operad provide explicit constructions of certain transfers. This characterization yields a conceptual explanation of the structure of equivariant infinite loop spaces. To explain the relationship between norms, transfers, and N-infinity operads, we discuss the general features of these operads, linking their properties to families of finite sets with group actions and analyzing their behavior under norms and geometric fixed points. A surprising consequence of our study is that in stark contract to the classical setting, equivariantly the little disks and linear isometries operads for a general universe $U$ need not determine the same algebras. Our work is motivated by the need to provide a framework to describe the flavors of commutativity seen in recent work of the second author and Hopkins on localization of equivariant commutative ring spectra., Comment: Revised in response to referee's comments

We describe spectral model category structures on the categories of cyclotomic spectra and $p$-cyclotomic spectra (in orthogonal spectra) with triangulated homotopy categories. We show that the functors $TR$ and $TC$ are corepresentable in these categories. Specifically, the derived mapping spectrum out of the sphere spectrum in the category of cyclotomic spectra corepresents the finite completion of $TC$ and the derived mapping spectrum out of the sphere spectrum in the category of $p$-cyclotomic spectra corepresents the $p$-completion of $TC(-;p)$., Comment: This is a last draft version (May 5, 2015) of an article whose final version was first published in Geometry & Topology in 2015, published by Mathematical Sciences Publishers

In this article we study the K-theory of endomorphisms using noncommutative motives. We start by extending the K-theory of endomorphisms functor from ordinary rings to (stable) infinity categories. We then prove that this extended functor KEnd(-) not only descends to the category of noncommutative motives but moreover becomes co-represented by the noncommutative motive associated to the tensor algebra S[t] of the sphere spectrum S. Using this co-representability result, we then classify all the natural transformations of KEnd(-) in terms of an integer plus a fraction between polynomials with constant term 1; this solves a problem raised by Almkvist in the seventies. Finally, making use of the multiplicative co-algebra structure of S[t], we explain how the (rational) Witt vectors can also be recovered from the symmetric monoidal category of noncommutative motives. Along the way we show that the K_0-theory of endomorphisms of a connective ring spectrum R equals the K_0-theory of endomorphisms of the underlying ordinary ring \pi_0(R).

Given an adjunction connecting reasonable categories with weak equivalences, we define a new derived bar and cobar construction associated to the adjunction. This yields homotopical models of the completion and cocompletion associated to the monad and comonad of the adjunction. We discuss applications of these resolutions to spectral sequences for derived completions and Goodwillie calculus in general model categories., Comment: 22 pages; v2 is the final journal version, with expository improvements suggested by the referee

We study distributions of persistent homology barcodes associated to taking subsamples of a fixed size from metric measure spaces. We show that such distributions provide robust invariants of metric measure spaces, and illustrate their use in hypothesis testing and providing confidence intervals for topological data analysis.