In this paper we combine many of the standard and more recent algebraic techniques for testing isomorphism of finite groups (GpI) with combinatorial techniques that have typically been applied to Graph Isomorphism. In particular, we show how to combine several state-of-the-art GpI algorithms for specific group classes into an algorithm for general GpI, namely: composition series isomorphism (Rosenbaum-Wagner, Theoret. Comp. Sci., 2015; Luks, 2015), recursively-refineable filters (Wilson, J. Group Theory, 2013), and low-genus GpI (Brooksbank-Maglione-Wilson, J. Algebra, 2017). Recursively-refineable filters -- a generalization of subgroup series -- form the skeleton of this framework, and we refine our filter by building a hypergraph encoding low-genus quotients, to which we then apply a hypergraph variant of the k-dimensional Weisfeiler-Leman technique. Our technique is flexible enough to readily incorporate additional hypergraph invariants or additional characteristic subgroups.

We study unitary property testing, where a quantum algorithm is given query access to a black-box unitary and has to decide whether it satisfies some property. In addition to containing the standard quantum query complexity model (where the unitary encodes a binary string) as a special case, this model contains "inherently quantum" problems that have no classical analogue. Characterizing the query complexity of these problems requires new algorithmic techniques and lower bound methods. Our main contribution is a generalized polynomial method for unitary property testing problems. By leveraging connections with invariant theory, we apply this method to obtain lower bounds on problems such as determining recurrence times of unitaries, approximating the dimension of a marked subspace, and approximating the entanglement entropy of a marked state. We also present a unitary property testing-based approach towards an oracle separation between $\mathsf{QMA}$ and $\mathsf{QMA(2)}$, a long standing question in quantum complexity theory.

We show that any Algebraic Branching Program (ABP) computing the polynomial ∑_{i=1}^n xⁿ_i has at least Ω(n²) vertices. This improves upon the lower bound of Ω(nlog n), which follows from the classical result of Baur and Strassen [Volker Strassen, 1973; Walter Baur and Volker Strassen, 1983], and extends the results of Kumar [Mrinal Kumar, 2019], which showed a quadratic lower bound for homogeneous ABPs computing the same polynomial. Our proof relies on a notion of depth reduction which is reminiscent of similar statements in the context of matrix rigidity, and shows that any small enough ABP computing the polynomial ∑_{i=1}^n xⁿ_i can be depth reduced to essentially a homogeneous ABP of the same size which computes the polynomial ∑_{i=1}^n xⁿ_i + ε(𝐱), for a structured "error polynomial" ε(𝐱). To complete the proof, we then observe that the lower bound in [Mrinal Kumar, 2019] is robust enough and continues to hold for all polynomials ∑_{i=1}^n xⁿ_i + ε(𝐱), where ε(𝐱) has the appropriate structure.

Schur Polynomials are families of symmetric polynomials that have been classically studied in Combinatorics and Algebra alike. They play a central role in the study of Symmetric functions, in Representation theory [Stanley, 1999], in Schubert calculus [Ledoux and Malham, 2010] as well as in Enumerative combinatorics [Gasharov, 1996; Stanley, 1984; Stanley, 1999]. In recent years, they have also shown up in various incarnations in Computer Science, e.g, Quantum computation [Hallgren et al., 2000; Ryan O'Donnell and John Wright, 2015] and Geometric complexity theory [Ikenmeyer and Panova, 2017]. However, unlike some other families of symmetric polynomials like the Elementary Symmetric polynomials, the Power Symmetric polynomials and the Complete Homogeneous Symmetric polynomials, the computational complexity of syntactically computing Schur polynomials has not been studied much. In particular, it is not known whether Schur polynomials can be computed efficiently by algebraic formulas. In this work, we address this question, and show that unless every polynomial with a small algebraic branching program (ABP) has a small algebraic formula, there are Schur polynomials that cannot be computed by algebraic formula of polynomial size. In other words, unless the algebraic complexity class VBP is equal to the complexity class VF, there exist Schur polynomials which do not have polynomial size algebraic formulas. As a consequence of our proof, we also show that computing the determinant of certain generalized Vandermonde matrices is essentially as hard as computing the general symbolic determinant. To the best of our knowledge, these are one of the first hardness results of this kind for families of polynomials which are not multilinear. A key ingredient of our proof is the study of composition of well behaved algebraically independent polynomials with a homogeneous polynomial, and might be of independent interest.

UNLABELLED: Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. AVAILABILITY AND IMPLEMENTATION: PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.