Romeo Rizzi

Francisco Sena, Aleksandr Politov, Corentin Moumard et al.

A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph. These correspond to regions of genetic variation and are useful in analyzing collections of genomes. We present the first linear-time algorithms for identifying all snarls and all ultrabubbles, resolving problems open since 2018. The algorithm for snarls relies on a new linear-size representation of all snarls with respect to the number of vertices in the graph. We employ the well-known SPQR-tree decomposition, which encodes all 2-separators of a biconnected graph. After several dynamic-programming-style traversals of this tree, we maintain key properties (such as acyclicity) that allow us to decide whether a given 2-separator defines a subgraph to be reported. A crucial ingredient for linear-time complexity is that acyclicity of linearly many subgraphs can be tested simultaneously via the problem of computing all arcs in a directed graph whose removal renders it acyclic (so-called feedback arcs). As such, we prove a fundamental result for bidirected graphs, that may be of independent interest: all feedback arcs can be computed in linear time for tipless bidirected graphs, while in general this is at least as hard as matrix multiplication, assuming the k-Clique Conjecture. Our results form a unified framework that also yields a completely different linear-time algorithm for finding all superbubbles. Although some of the results are technically involved, the underlying ideas are conceptually simple, and may extend to other bubble-like subgraphs. More broadly, our work contributes to the theoretical foundations of computational biology and advances a growing line of research that uses SPQR-tree decompositions as a general tool for designing efficient algorithms, beyond their traditional role in graph drawing.

Massimo Cairo, Gabriele Farina, Romeo Rizzi

In this paper, we present a novel algorithm for the maximum a posteriori decoding (MAPD) of time-homogeneous Hidden Markov Models (HMM), improving the worst-case running time of the classical Viterbi algorithm by a logarithmic factor. In our approach, we interpret the Viterbi algorithm as a repeated computation of matrix-vector $(\max, +)$-multiplications. On time-homogeneous HMMs, this computation is online: a matrix, known in advance, has to be multiplied with several vectors revealed one at a time. Our main contribution is an algorithm solving this version of matrix-vector $(\max,+)$-multiplication in subquadratic time, by performing a polynomial preprocessing of the matrix. Employing this fast multiplication algorithm, we solve the MAPD problem in $O(mn^2/ \log n)$ time for any time-homogeneous HMM of size $n$ and observation sequence of length $m$, with an extra polynomial preprocessing cost negligible for $m > n$. To the best of our knowledge, this is the first algorithm for the MAPD problem requiring subquadratic time per observation, under the only assumption -- usually verified in practice -- that the transition probability matrix does not change with time.

Carlo Comin, Romeo Rizzi

Conditional Simple Temporal Network (CSTN) is a constraint-based graph-formalism for conditional temporal planning. It offers a more flexible formalism than the equivalent CSTP model of Tsamardinos, Vidal and Pollack, from which it was derived mainly as a sound formalization. Three notions of consistency arise for CSTNs and CSTPs: weak, strong, and dynamic. Dynamic consistency is the most interesting notion, but it is also the most challenging and it was conjectured to be hard to assess. Tsamardinos, Vidal and Pollack gave a doubly-exponential time algorithm for deciding whether a CSTN is dynamically-consistent and to produce, in the positive case, a dynamic execution strategy of exponential size. In the present work we offer a proof that deciding whether a CSTN is dynamically-consistent is coNP-hard and provide the first singly-exponential time algorithm for this problem, also producing a dynamic execution strategy whenever the input CSTN is dynamically-consistent. The algorithm is based on a novel connection with Mean Payoff Games, a family of two-player combinatorial games on graphs well known for having applications in model-checking and formal verification. The presentation of such connection is mediated by the Hyper Temporal Network model, a tractable generalization of Simple Temporal Networks whose consistency checking is equivalent to determining Mean Payoff Games. In order to analyze the algorithm we introduce a refined notion of dynamic-consistency, named ε-dynamic-consistency, and present a sharp lower bounding analysis on the critical value of the reaction time \hat{\varepsilon} where the CSTN transits from being, to not being, dynamically-consistent. The proof technique introduced in this analysis of \hat{\varepsilon} is applicable more in general when dealing with linear difference constraints which include strict inequalities.

Carlo Comin, Roberto Posenato, Romeo Rizzi

Simple Temporal Networks (STNs) provide a powerful and general tool for representing conjunctions of maximum delay constraints over ordered pairs of temporal variables. In this paper we introduce Hyper Temporal Networks (HyTNs), a strict generalization of STNs, to overcome the limitation of considering only conjunctions of constraints but maintaining a practical efficiency in the consistency check of the instances. In a Hyper Temporal Network a single temporal hyperarc constraint may be defined as a set of two or more maximum delay constraints which is satisfied when at least one of these delay constraints is satisfied. HyTNs are meant as a light generalization of STNs offering an interesting compromise. On one side, there exist practical pseudo-polynomial time algorithms for checking consistency and computing feasible schedules for HyTNs. On the other side, HyTNs offer a more powerful model accommodating natural constraints that cannot be expressed by STNs like Trigger off exactly delta min before (after) the occurrence of the first (last) event in a set., which are used to represent synchronization events in some process aware information systems/workflow models proposed in the literature.