We formulate a structure-informed multiple sequence alignment problem, denoted MSA-S. The model abstracts biological sequences as strings and structural information as designated position-pairs. It augments a fixed pairwise string score, defined by a fixed non-gap symbol-pair scoring rule and fixed affine gap penalties, with a binary overlap score on designated position-pairs, which can be interpreted as a contact-map overlap score in structural applications. This yields a fixed-score, integer-valued optimization model suitable for complexity-theoretic analysis.
Under this formulation, we show that the decision problem MSA-S-DEC is NP-complete for a broad class of fixed pairwise string scoring schemes. We also show that NP-hardness persists even under the restriction that every designated position-pair set is nonempty and the pair-overlap threshold is strictly positive. For the associated scalarized optimization problem MSA-S-OPT(lambda) with any fixed rational constant lambda >= 1, we further show that, under the canonical unit scheme for the non-gap symbol-pair scoring rule, MSA-S-OPT(lambda) admits no polynomial-time approximation scheme (PTAS) even for two input strings (k = 2), unless P = NP.
These results establish a formal complexity-theoretic baseline for structure-informed multiple sequence alignment.
We propose a new conjecture on hardness of low-degree $2$-CSP's, and show that new hardness of approximation results for Densest $k$-Subgraph and several other problems, including a graph partitioning problem, and a variation of the Graph Crossing Number problem, follow from this conjecture. The conjecture can be viewed as occupying a middle ground between the $d$-to-$1$ conjecture, and hardness results for $2$-CSP's that can be obtained via standard techniques, such as Parallel Repetition combined with standard $2$-prover protocols for the 3SAT problem. We hope that this work will motivate fu…
We study the computational complexity of the non-preemptive scheduling problem of a list of independent jobs on a set of identical parallel processors with a makespan minimization objective. We make a maiden attempt to explore the combinatorial structure showing the exhaustive solution space of the problem by defining the \textit{Scheduling Solution Space Tree (SSST)} data structure. The properties of the \textit{SSST} are formally defined and characterized through our analytical results. We develop a unique technique to show the problem $\mathcal{NP}$ using the SSST and the \textit{Weighted S…
The problem of optimizing over random structures emerges in many areas of science and engineering, ranging from statistical physics to machine learning and artificial intelligence. For many such structures finding optimal solutions by means of fast algorithms is not known and often is believed not possible. At the same time the formal hardness of these problems in form of say complexity-theoretic $NP$-hardness is lacking. In this introductory article a new approach for algorithmic intractability in random structures is described, which is based on the topological disconnectivity property of th…
The recent emergence of fine-grained cryptography strongly motivates developing an average-case analogue of Fine-Grained Complexity (FGC). This paper defines new versions of OV, $k$SUM and zero-$k$-clique that are both worst-case and average-case fine-grained hard assuming the core hypotheses of FGC. We then use these as a basis for fine-grained hardness and average-case hardness of other problems. The new problems represent their inputs in a certain ``factored'' form. We call them ``factored''-OV, ``factored''-zero-$k$-clique and ``factored''-$3$SUM. We show that factored-$k$-OV and factored …
These notes survey and explore an emerging method, which we call the low-degree method, for predicting and understanding statistical-versus-computational tradeoffs in high-dimensional inference problems. In short, the method posits that a certain quantity -- the second moment of the low-degree likelihood ratio -- gives insight into how much computational time is required to solve a given hypothesis testing problem, which can in turn be used to predict the computational hardness of a variety of statistical inference tasks. While this method originated in the study of the sum-of-squares (SoS) hi…
Recent attempts to explain the effectiveness of Boolean satisfiability (SAT) solvers based on conflict-driven clause learning (CDCL) on large industrial benchmarks have focused on the concept of community structure. Specifically, industrial benchmarks have been empirically found to have good community structure, and experiments seem to show a correlation between such structure and the efficiency of CDCL. However, in this paper we establish hardness results suggesting that community structure is not sufficient to explain the success of CDCL in practice. First, we formally characterize a propert…
Blömer and Seifert showed that $\mathsf{SIVP}_2$ is NP-hard to approximate by giving a reduction from $\mathsf{CVP}_2$ to $\mathsf{SIVP}_2$ for constant approximation factors as long as the $\mathsf{CVP}$ instance has a certain property. In order to formally define this requirement on the $\mathsf{CVP}$ instance, we introduce a new computational problem called the Gap Closest Vector Problem with Bounded Minima. We adapt the proof of Blömer and Seifert to show a reduction from the Gap Closest Vector Problem with Bounded Minima to $\mathsf{SIVP}$ for any $\ell_p$ norm for some constant approxima…
We say that two given polynomials $f, g \in R[X]$, over a ring $R$, are equivalent under shifts if there exists a vector $a \in R^n$ such that $f(X+a) = g(X)$. Grigoriev and Karpinski (FOCS 1990), Lakshman and Saunders (SICOMP, 1995), and Grigoriev and Lakshman (ISSAC 1995) studied the problem of testing polynomial equivalence of a given polynomial to any $t$-sparse polynomial, over the rational numbers, and gave exponential time algorithms. In this paper, we provide hardness results for this problem. Formally, for a ring $R$, let $\mathrm{SparseShift}_R$ be the following decision problem. Giv…
We study the problem of efficiently refuting the k-colorability of a graph, or equivalently certifying a lower bound on its chromatic number. We give formal evidence of average-case computational hardness for this problem in sparse random regular graphs, showing optimality of a simple spectral certificate. This evidence takes the form of a computationally-quiet planting: we construct a distribution of d-regular graphs that has significantly smaller chromatic number than a typical regular graph drawn uniformly at random, while providing evidence that these two distributions are indistinguishabl…
Community detection in graphs is the problem of finding groups of vertices which are more densely connected than they are to the rest of the graph. This problem has a long history, but it is undergoing a resurgence of interest due to the need to analyze social and biological networks. While there are many ways to formalize it, one of the most popular is as an inference problem, where there is a "ground truth" community structure built into the graph somehow. The task is then to recover the ground truth knowing only the graph. Recently it was discovered, first heuristically in physics and then …
Harvard University（哈佛大学）；Carnegie Mellon University（卡内基梅隆大学）；University of Washington（华盛顿大学）；Columbia University（哥伦比亚大学）；Princeton University（普林斯顿大学）；Institute for Advanced Study（高等研究院）
For a function $\mathsf{K} : \mathbb{R}^{d} \times \mathbb{R}^{d} \to \mathbb{R}_{\geq 0}$, and a set $P = \{ x_1, \ldots, x_n\} \subset \mathbb{R}^d$ of $n$ points, the $\mathsf{K}$ graph $G_P$ of $P$ is the complete graph on $n$ nodes where the weight between nodes $i$ and $j$ is given by $\mathsf{K}(x_i, x_j)$. In this paper, we initiate the study of when efficient spectral graph theory is possible on these graphs. We investigate whether or not it is possible to solve the following problems in $n^{1+o(1)}$ time for a $\mathsf{K}$-graph $G_P$ when $d < n^{o(1)}$: $\bullet$ Multiply a given v…
