Faster Algorithms for Integer Programs with Block Structure

We consider integer programming problems $\max \{ c^T x : \mathcal{A} x = b, l \leq x \leq u, x \in \mathbb{Z}^{nt}\}$ where $\mathcal{A}$ has a (recursive) block-structure generalizing "$n$-fold integer programs" which recently received considerable attention in the literature. An $n$-fold IP is an integer program where $\mathcal{A}$ consists of $n$ repetitions of submatrices $A \in \mathbb{Z}^{r \times t}$ on the top horizontal part and $n$ repetitions of a matrix $B \in \mathbb{Z}^{s \times t}$ on the diagonal below the top part. Instead of allowing only two types of block matrices, one for the horizontal line and one for the diagonal, we generalize the $n$-fold setting to allow for arbitrary matrices in every block. We show that such an integer program can be solved in time $n^2 t^2 {\phi} \cdot (rs{\Delta})^{\mathcal{O}(rs^2+ sr^2)}$ (ignoring logarithmic factors). Here ${\Delta}$ is an upper bound on the largest absolute value of an entry of $\mathcal{A}$ and ${\phi}$ is the largest binary encoding length of a coefficient of $c$. This improves upon the previously best algorithm of Hemmecke, Onn and Romanchuk that runs in time $n^3t^3 {\phi} \cdot {\Delta}^{\mathcal{O}(t^2s)}$. In particular, our algorithm is not exponential in the number $t$ of columns of $A$ and $B$. Our algorithm is based on a new upper bound on the $l_1$-norm of an element of the "Graver basis" of an integer matrix and on a proximity bound between the LP and IP optimal solutions tailored for IPs with block structure. These new bounds rely on the "Steinitz Lemma". Furthermore, we extend our techniques to the recently introduced "tree-fold IPs", where we again present a more efficient algorithm in a generalized setting

An Algorithmic Theory of Integer Programming

We study the general integer programming problem where the number of variables $n$ is a variable part of the input. We consider two natural parameters of the constraint matrix $A$: its numeric measure $a$ and its sparsity measure $d$. We show that integer programming can be solved in time $g(a,d)\textrm{poly}(n,L)$, where $g$ is some computable function of the parameters $a$ and $d$, and $L$ is the binary encoding length of the input. In particular, integer programming is fixed-parameter tractable parameterized by $a$ and $d$, and is solvable in polynomial time for every fixed $a$ and $d$. Our results also extend to nonlinear separable convex objective functions. Moreover, for linear objectives, we derive a strongly-polynomial algorithm, that is, with running time $g(a,d)\textrm{poly}(n)$, independent of the rest of the input data. We obtain these results by developing an algorithmic framework based on the idea of iterative augmentation: starting from an initial feasible solution, we show how to quickly find augmenting steps which rapidly converge to an optimum. A central notion in this framework is the Graver basis of the matrix $A$, which constitutes a set of fundamental augmenting steps. The iterative augmentation idea is then enhanced via the use of other techniques such as new and improved bounds on the Graver basis, rapid solution of integer programs with bounded variables, proximity theorems and a new proximity-scaling algorithm, the notion of a reduced objective function, and others. As a consequence of our work, we advance the state of the art of solving block-structured integer programs. In particular, we develop near-linear time algorithms for $n$-fold, tree-fold, and $2$-stage stochastic integer programs. We also discuss some of the many applications of these classes.Comment: Revision 2: - strengthened dual treedepth lower bound - simplified proximity-scaling algorith

New Bounds on Augmenting Steps of Block-Structured Integer Programs

Iterative augmentation has recently emerged as an overarching method for solving Integer Programs (IP) in variable dimension, in stark contrast with the volume and flatness techniques of IP in fixed dimension. Here we consider 4-block n-fold integer programs, which are the most general class considered so far. A 4-block n-fold IP has a constraint matrix which consists of n copies of small matrices A, B, and D, and one copy of C, in a specific block structure. Iterative augmentation methods rely on the so-called Graver basis of the constraint matrix, which constitutes a set of fundamental augmenting steps. All existing algorithms rely on bounding the ??- or ?_?-norm of elements of the Graver basis. Hemmecke et al. [Math. Prog. 2014] showed that 4-block n-fold IP has Graver elements of ?_?-norm at most ?_FPT(n^{2^{s_D}}), leading to an algorithm with a similar runtime; here, s_D is the number of rows of matrix D and ?_FPT hides a multiplicative factor that is only dependent on the small matrices A,B,C,D, However, it remained open whether their bounds are tight, in particular, whether they could be improved to ?_FPT(1), perhaps at least in some restricted cases. We prove that the ?_?-norm of the Graver elements of 4-block n-fold IP is upper bounded by ?_FPT(n^{s_D}), improving significantly over the previous bound ?_FPT(n^{2^{s_D}}). We also provide a matching lower bound of ?(n^{s_D}) which even holds for arbitrary non-zero lattice elements, ruling out augmenting algorithm relying on even more restricted notions of augmentation than the Graver basis. We then consider a special case of 4-block n-fold in which C is a zero matrix, called 3-block n-fold IP. We show that while the ?_?-norm of its Graver elements is ?(n^{s_D}), there exists a different decomposition into lattice elements whose ?_?-norm is bounded by ?_FPT(1), which allows us to provide improved upper bounds on the ?_?-norm of Graver elements for 3-block n-fold IP. The key difference between the respective decompositions is that a Graver basis guarantees a sign-compatible decomposition; this property is critical in applications because it guarantees each step of the decomposition to be feasible. Consequently, our improved upper bounds let us establish faster algorithms for 3-block n-fold IP and 4-block IP, and our lower bounds strongly hint at parameterized hardness of 4-block and even 3-block n-fold IP. Furthermore, we show that 3-block n-fold IP is without loss of generality in the sense that 4-block n-fold IP can be solved in FPT oracle time by taking an algorithm for 3-block n-fold IP as an oracle

biobambam: tools for read pair collation based algorithms on BAM files

Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. In this paper we introduce biobambam, an API for efficient BAM file reading supporting the efficient collation of alignments by read name without performing a complete resorting of the input file and some tools based on this API performing tasks like marking duplicate reads and conversion to the FastQ format. In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities in the Picard suite the approach of biobambam can often perform an equivalent task more efficiently in terms of the required main memory and run-time.Comment: 17 pages, 3 figures, 2 table

Survey on Combinatorial Register Allocation and Instruction Scheduling

Register allocation (mapping variables to processor registers or memory) and instruction scheduling (reordering instructions to increase instruction-level parallelism) are essential tasks for generating efficient assembly code in a compiler. In the last three decades, combinatorial optimization has emerged as an alternative to traditional, heuristic algorithms for these two tasks. Combinatorial optimization approaches can deliver optimal solutions according to a model, can precisely capture trade-offs between conflicting decisions, and are more flexible at the expense of increased compilation time. This paper provides an exhaustive literature review and a classification of combinatorial optimization approaches to register allocation and instruction scheduling, with a focus on the techniques that are most applied in this context: integer programming, constraint programming, partitioned Boolean quadratic programming, and enumeration. Researchers in compilers and combinatorial optimization can benefit from identifying developments, trends, and challenges in the area; compiler practitioners may discern opportunities and grasp the potential benefit of applying combinatorial optimization