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1. Efficient Computation of Sequence Mappability

   https://doi.org/10.1007/s00453-022-00934-y  

   Charalampopoulos, Panagiotis ; Iliopoulos, Costas S. ; Kociumaka, Tomasz ; Pissis, Solon P. ; Radoszewski, Jakub ; Straszyński, Juliusz ( February 2022 , Algorithmica)

   Sequence mappability is an important task in genome resequencing. In the (k, m)-mappability problem, for a given sequenceTof lengthn, the goal is to compute a table whoseith entry is the number of indices$$j \ne i$$$j\ne i$such that the length-msubstrings ofTstarting at positionsiandjhave at mostkmismatches. Previous works on this problem focused on heuristics computing a rough approximation of the result or on the case of$$k=1$$$k=1$. We present several efficient algorithms for the general case of the problem. Our main result is an algorithm that, for$$k=O(1)$$$k=O\left(1\right)$, works in$$O(n)$$$O\left(n\right)$space and, with high probability, in$$O(n \cdot \min \{m^k,\log ^k n\})$$$O(n·min\{m^k,{log}^{k}n\})$time. Our algorithm requires a careful adaptation of thek-errata trees of Cole et al. [STOC 2004] to avoid multiple counting of pairs of substrings. Our technique can also be applied to solve the all-pairs Hamming distance problem introduced by Crochemore et al. [WABI 2017]. We further develop$$O(n^2)$$$O\left(n^2\right)$-time algorithms to computeall(k, m)-mappability tables for a fixedmand all$$k\in \{0,\ldots ,m\}$$$k\in \{0,\dots ,m\}$or a fixedkand all$$m\in \{k,\ldots ,n\}$$$m\in \{k,\dots ,n\}$. Finally, we show that, for$$k,m = \Theta (\log n)$$$k,m=\Theta (logn)$, the (k, m)-mappability problem cannot be solved in strongly subquadratic time unless the Strong Exponential Time Hypothesis fails. This is an improved and extended version of a paper presented at SPIRE 2018.
2. Lower Bounds Against Sparse Symmetric Functions of ACC Circuits: Expanding the Reach of #SAT Algorithms

   https://doi.org/10.1007/s00224-022-10106-8  

   Vyas, Nikhil ; Williams, R. Ryan ( November 2022 , Theory of Computing Systems)

   We continue the program of proving circuit lower bounds via circuit satisfiability algorithms. So far, this program has yielded several concrete results, proving that functions in$\mathsf {Quasi}\text {-}\mathsf {NP} = \mathsf {NTIME}[n^{(\log n)^{O(1)}}]$$\mathrm{Quasi}-\mathrm{NP}=\mathrm{NTIME}\left[n^{{\left(\log n\right)}^{O\left(1\right)}}\right]$and other complexity classes do not have small circuits (in the worst case and/or on average) from various circuit classes$\mathcal { C}$$C$, by showing that$\mathcal { C}$$C$admits non-trivial satisfiability and/or#SAT algorithms which beat exhaustive search by a minor amount. In this paper, we present a new strong lower bound consequence of having a non-trivial#SAT algorithm for a circuit class${\mathcal C}$$C$. Say that a symmetric Boolean functionf(x₁,…,x_n) issparseif it outputs 1 onO(1) values of${\sum }_{i} x_{i}$${\sum }_i{x}_i$. We show that for every sparsef, and for all “typical”$\mathcal { C}$$C$, faster#SAT algorithms for$\mathcal { C}$$C$circuits imply lower bounds against the circuit class$f \circ \mathcal { C}$$f\circ C$, which may bestrongerthan$\mathcal { C}$$C$itself. In particular:

   #SAT algorithms forn^k-size$\mathcal { C}$$C$-circuits running in 2ⁿ/n^ktime (for allk) implyNEXPdoes not have$(f \circ \mathcal { C})$$(f\circ C)$-circuits of polynomial size.

   #SAT algorithms for$2^{n^{{\varepsilon }}}$$2^{n^{\epsilon }}$-size$\mathcal { C}$$C$-circuits running in$2^{n-n^{{\varepsilon }}}$$2^{n-n^{\epsilon }}$time (for someε> 0) implyQuasi-NPdoes not have$(f \circ \mathcal { C})$$(f\circ C)$-circuits of polynomial size.

   Applying#SAT algorithms from the literature, one immediate corollary of our results is thatQuasi-NPdoes not haveEMAJ∘ACC⁰∘THRcircuits of polynomialmore »size, whereEMAJis the “exact majority” function, improving previous lower bounds againstACC⁰[Williams JACM’14] andACC⁰∘THR[Williams STOC’14], [Murray-Williams STOC’18]. This is the first nontrivial lower bound against such a circuit class.

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3. Improved Merlin–Arthur Protocols for Central Problems in Fine-Grained Complexity

   https://doi.org/10.1007/s00453-023-01102-6  

   Akmal, Shyan ; Chen, Lijie ; Jin, Ce ; Raj, Malvika ; Williams, Ryan ( February 2023 , Algorithmica)

   In a Merlin–Arthur proof system, the proof verifier (Arthur) accepts valid proofs (from Merlin) with probability 1, and rejects invalid proofs with probability arbitrarily close to 1. The running time of such a system is defined to be the length of Merlin’s proof plus the running time of Arthur. We provide new Merlin–Arthur proof systems for some key problems in fine-grained complexity. In several cases our proof systems have optimal running time. Our main results include:

   Certifying that a list ofnintegers has no 3-SUM solution can be done in Merlin–Arthur time$$\tilde{O}(n)$$$\tilde{O}\left(n\right)$. Previously, Carmosino et al. [ITCS 2016] showed that the problem has a nondeterministic algorithm running in$$\tilde{O}(n^{1.5})$$$\tilde{O}\left(n^{1.5}\right)$time (that is, there is a proof system with proofs of length$$\tilde{O}(n^{1.5})$$$\tilde{O}\left(n^{1.5}\right)$and a deterministic verifier running in$$\tilde{O}(n^{1.5})$$$\tilde{O}\left(n^{1.5}\right)$time).

   Counting the number ofk-cliques with total edge weight equal to zero in ann-node graph can be done in Merlin–Arthur time$${\tilde{O}}(n^{\lceil k/2\rceil })$$$\tilde{O}\left(n^{\lceil k/2\rceil }\right)$(where$$k\ge 3$$$k\ge 3$). For oddk, this bound can be further improved for sparse graphs: for example, counting the number of zero-weight triangles in anm-edge graph can be done in Merlin–Arthur time$${\tilde{O}}(m)$$$\tilde{O}\left(m\right)$. Previous Merlin–Arthur protocols by Williams [CCC’16] and Björklund and Kaski [PODC’16] could only countk-cliques in unweighted graphs, and had worse running times for smallk.

   Computing the All-Pairsmore »Shortest Distances matrix for ann-node graph can be done in Merlin–Arthur time$$\tilde{O}(n^2)$$$\tilde{O}\left(n^2\right)$. Note this is optimal, as the matrix can have$$\Omega (n^2)$$$\Omega \left(n^2\right)$nonzero entries in general. Previously, Carmosino et al. [ITCS 2016] showed that this problem has an$$\tilde{O}(n^{2.94})$$$\tilde{O}\left(n^{2.94}\right)$nondeterministic time algorithm.

   Certifying that ann-variablek-CNF is unsatisfiable can be done in Merlin–Arthur time$$2^{n/2 - n/O(k)}$$$2^{n/2-n/O\left(k\right)}$. We also observe an algebrization barrier for the previous$$2^{n/2}\cdot \textrm{poly}(n)$$$2^{n/2}·\text{poly}\left(n\right)$-time Merlin–Arthur protocol of R. Williams [CCC’16] for$$\#$$$\#$SAT: in particular, his protocol algebrizes, and we observe there is no algebrizing protocol fork-UNSAT running in$$2^{n/2}/n^{\omega (1)}$$$2^{n/2}/n^{\omega \left(1\right)}$time. Therefore we have to exploit non-algebrizing properties to obtain our new protocol.

   Certifying a Quantified Boolean Formula is true can be done in Merlin–Arthur time$$2^{4n/5}\cdot \textrm{poly}(n)$$$2^{4n/5}·\text{poly}\left(n\right)$. Previously, the only nontrivial result known along these lines was an Arthur–Merlin–Arthur protocol (where Merlin’s proof depends on some of Arthur’s coins) running in$$2^{2n/3}\cdot \textrm{poly}(n)$$$2^{2n/3}·\text{poly}\left(n\right)$time.

   Due to the centrality of these problems in fine-grained complexity, our results have consequences for many other problems of interest. For example, our work implies that certifying there is no Subset Sum solution tonintegers can be done in Merlin–Arthur time$$2^{n/3}\cdot \textrm{poly}(n)$$$2^{n/3}·\text{poly}\left(n\right)$, improving on the previous best protocol by Nederlof [IPL 2017] which took$$2^{0.49991n}\cdot \textrm{poly}(n)$$$2^{0.49991n}·\text{poly}\left(n\right)$time.

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4. Hermitian–Yang–Mills Connections on Collapsing Elliptically Fibered K3 Surfaces

   https://doi.org/10.1007/s12220-021-00808-9  

   Datar, Ved ; Jacob, Adam ( January 2022 , The Journal of Geometric Analysis)

   Let$$X\rightarrow {{\mathbb {P}}}^1$$$X\to P^1$be an elliptically fiberedK3 surface, admitting a sequence$$\omega _{i}$$${\omega }_i$of Ricci-flat metrics collapsing the fibers. LetVbe a holomorphicSU(n) bundle overX, stable with respect to$$\omega _i$$${\omega }_i$. Given the corresponding sequence$$\Xi _i$$${\Xi }_i$of Hermitian–Yang–Mills connections onV, we prove that, ifEis a generic fiber, the restricted sequence$$\Xi _i|_{E}$$${\Xi }_i{|}_E$converges to a flat connection$$A_0$$$A_0$. Furthermore, if the restriction$$V|_E$$${V|}_E$is of the form$$\oplus _{j=1}^n{\mathcal {O}}_E(q_j-0)$$${\oplus }_{j=1}^n{O}_E(q_j-0)$forndistinct points$$q_j\in E$$$q_j\in E$, then these points uniquely determine$$A_0$$$A_0$.
5. Fast Barycentric-Based Evaluation Over Spectral/hp Elements

   https://doi.org/10.1007/s10915-021-01750-2  

   Laughton, Edward ; Zala, Vidhi ; Narayan, Akil ; Kirby, Robert M. ; Moxey, David ( January 2022 , Journal of Scientific Computing)

   As the use of spectral/hpelement methods, and high-order finite element methods in general, continues to spread, community efforts to create efficient, optimized algorithms associated with fundamental high-order operations have grown. Core tasks such as solution expansion evaluation at quadrature points, stiffness and mass matrix generation, and matrix assembly have received tremendous attention. With the expansion of the types of problems to which high-order methods are applied, and correspondingly the growth in types of numerical tasks accomplished through high-order methods, the number and types of these core operations broaden. This work focuses on solution expansion evaluation at arbitrary points within an element. This operation is core to many postprocessing applications such as evaluation of streamlines and pathlines, as well as to field projection techniques such as mortaring. We expand barycentric interpolation techniques developed on an interval to 2D (triangles and quadrilaterals) and 3D (tetrahedra, prisms, pyramids, and hexahedra) spectral/hpelement methods. We provide efficient algorithms for their implementations, and demonstrate their effectiveness using the spectral/hpelement libraryNektar++by running a series of baseline evaluations against the ‘standard’ Lagrangian method, where an interpolation matrix is generated and matrix-multiplication applied to evaluate a point at a given location. We present results from a rigorous seriesmore »of benchmarking tests for a variety of element shapes, polynomial orders and dimensions. We show that when the point of interest is to be repeatedly evaluated, the barycentric method performs at worst$$50\%$$$50\%$slower, when compared to a cached matrix evaluation. However, when the point of interest changes repeatedly so that the interpolation matrix must be regenerated in the ‘standard’ approach, the barycentric method yields far greater performance, with a minimum speedup factor of$$7\times $$$7\times$. Furthermore, when derivatives of the solution evaluation are also required, the barycentric method in general slightly outperforms the cached interpolation matrix method across all elements and orders, with an up to$$30\%$$$30\%$speedup. Finally we investigate a real-world example of scalar transport using a non-conformal discontinuous Galerkin simulation, in which we observe around$$6\times $$$6\times$speedup in computational time for the barycentric method compared to the matrix-based approach. We also explore the complexity of both interpolation methods and show that the barycentric interpolation method requires$${\mathcal {O}}(k)$$$O\left(k\right)$storage compared to a best case space complexity of$${\mathcal {O}}(k^2)$$$O\left(k^2\right)$for the Lagrangian interpolation matrix method.

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