arXiv subjects

Bruno Coutinho

Publications and source records attributed to Bruno Coutinho.

10 recordsLinked to original sources

arXiv2025

Network-based prediction of drug combinations with quantum annealing

The systematic discovery of effective drug combinations is a challenging problem in modern pharmacology, driven by the combinatorial growth of potential pairings and dosage configurations. Network medicine, modeling diseases and drugs as interconnected modules of the human protein-protein interactome, has emerged as a new paradigm for understanding disease mechanisms and drug action. In this work, we propose a quantum annealing-based algorithm for identifying effective drug combinations. Underlying our approach is the biologically motivated principle of `Complementary Exposure', which posits that therapeutic drug combinations target distinct yet complementary regions of a disease module. We translate this into a quadratic unconstrained binary optimisation problem. We test our method for Diabetes Mellitus, Rheumatoid Arthritis, Asthma, and Brain Neoplasms, relying on experimentally validated drug combinations for these diseases. Our simulated quantum annealing experiments reveal that low-energy configurations align with biologically plausible combinations, demonstrating the algorithm's ability to generate novel predictions for drug combinations.

quant-ph↗

arXiv2025

Quantum Network-Based Prediction of Cancer Driver Genes

Identification of cancer driver genes is fundamental for the development of targeted therapeutic interventions. The integration of mutational profiles with protein-protein interaction (PPI) networks offers a promising avenue for their detection [ 1, 2], but scaling to large network datasets is computationally demanding. Quantum computing offers compact representations and potential complexity reductions. Motivated by the classical method of Gumpinger et al. [3], in this work we introduce a supervised quantum framework that combines mutation scores with network topology via a novel state preparation scheme, Quantum Multi-order Moment Embedding (QMME). QMME encodes low-order statistical moments over the mutation scores of a node's immediate and second-order neighbors, and encodes this information into quantum states. These are used as inputs to a kernel-based quantum binary classifier that discriminates known driver genes from others. Simulations on an empirical PPI network demonstrate competitive performance, with a 12.6% recall gain over a classical baseline. The pipeline performs explicit quantum state preparation and requires no classical training, enabling an efficient, nearly end-to-end quantum workflow. A brief complexity analysis suggests the approach could achieve a quantum speedup in network-based cancer gene prediction. This work underscores the potential of supervised quantum graph learning frameworks to advance biological discovery.

quant-ph↗

arXiv2025

GPU-Accelerated Syndrome Decoding for Quantum LDPC Codes below the 63 $\mu$s Latency Threshold

This paper presents a GPU-accelerated decoder for quantum low-density parity-check (QLDPC) codes that achieves sub-$63$ $\mu$s latency, below the surface code decoder's real-time threshold demonstrated on Google's Willow quantum processor. While surface codes have demonstrated below-threshold performance, the encoding rates approach zero as code distances increase, posing challenges for scalability. Recently proposed QLDPC codes, such as those by Panteleev and Kalachev, offer constant-rate encoding and asymptotic goodness but introduce higher decoding complexity. To address such limitation, this work presents a parallelized belief propagation decoder leveraging syndrome information on commodity GPU hardware. Parallelism was exploited to maximize performance within the limits of target latency, allowing decoding latencies under $50$ $\mu$s for [[$784$, $24$, $24$]] codes and as low as $23.3$ $\mu$s for smaller codes, meeting the tight timing constraints of superconducting qubit cycles. These results show that real-time, scalable decoding of asymptotically good quantum codes is achievable using widely available commodity hardware, advancing the feasibility of fault-tolerant quantum computation beyond surface codes.

quant-ph↗

arXiv2023

On the quantum simulation of complex networks

Quantum walks provide a natural framework to approach graph problems with quantum computers, exhibiting speedups over their classical counterparts for tasks such as the search for marked nodes or the prediction of missing links. Continuous-time quantum walk algorithms assume that we can simulate the dynamics of quantum systems where the Hamiltonian is given by the adjacency matrix of the graph. It is known that such can be simulated efficiently if the underlying graph is row-sparse and efficiently row-computable. While this is sufficient for many applications, it limits the applicability for this class of algorithms to study real world complex networks, which, among other properties, are characterized by the existence of a few densely connected nodes, called hubs. In other words, complex networks are typically not row-sparse, even though the average connectivity over all nodes can be very small. In this work, we extend the state-of-the-art results on quantum simulation to graphs that contain a small number of hubs, but that are otherwise sparse. Hopefully, our results may lead to new applications of quantum computing to network science.

quant-ph↗

arXiv2022

On the complexity of quantum link prediction in complex networks

Link prediction methods use patterns in known network data to infer which connections may be missing. Previous work has shown that continuous-time quantum walks can be used to represent path-based link prediction, which we further study here to develop a more optimized quantum algorithm. Using a sampling framework for link prediction, we analyze the query access to the input network required to produce a certain number of prediction samples. Considering both well-known classical path-based algorithms using powers of the adjacency matrix as well as our proposed quantum algorithm for path-based link prediction, we argue that there is a polynomial quantum advantage on the dependence on $N$, the number of nodes in the network. We further argue that the complexity of our algorithm, although sub-linear in $N$, is limited by the complexity of performing a quantum simulation of the network's adjacency matrix, which may prove to be an important problem in the development of quantum algorithms for network science in general.

quant-ph↗

arXiv2022

Quantum Link Prediction in Complex Networks

Predicting new links in physical, biological, social, or technological networks has a significant scientific and societal impact. Path-based link prediction methods utilize explicit counting of even and odd-length paths between nodes to quantify a score function and infer new or unobserved links. Here, we propose a quantum algorithm for path-based link prediction, QLP, using a controlled continuous-time quantum walk to encode even and odd path-based prediction scores. Through classical simulations on a few real networks, we confirm that the quantum walk scoring function performs similarly to other path-based link predictors. In a brief complexity analysis we identify the potential of our approach in uncovering a quantum speedup for path-based link prediction.

quant-ph↗

arXiv2022

Predicting the Future of AI with AI: High-quality link prediction in an exponentially growing knowledge network

A tool that could suggest new personalized research directions and ideas by taking insights from the scientific literature could significantly accelerate the progress of science. A field that might benefit from such an approach is artificial intelligence (AI) research, where the number of scientific publications has been growing exponentially over the last years, making it challenging for human researchers to keep track of the progress. Here, we use AI techniques to predict the future research directions of AI itself. We develop a new graph-based benchmark based on real-world data -- the Science4Cast benchmark, which aims to predict the future state of an evolving semantic network of AI. For that, we use more than 100,000 research papers and build up a knowledge network with more than 64,000 concept nodes. We then present ten diverse methods to tackle this task, ranging from pure statistical to pure learning methods. Surprisingly, the most powerful methods use a carefully curated set of network features, rather than an end-to-end AI approach. It indicates a great potential that can be unleashed for purely ML approaches without human knowledge. Ultimately, better predictions of new future research directions will be a crucial component of more advanced research suggestion tools.

cs.AI↗

arXiv2022

Network-based link prediction of scientific concepts -- a Science4Cast competition entry

We report on a model built to predict links in a complex network of scientific concepts, in the context of the Science4Cast 2021 competition. We show that the network heavily favours linking nodes of high degree, indicating that new scientific connections are primarily made between popular concepts, which constitutes the main feature of our model. Besides this notion of popularity, we use a measure of similarity between nodes quantified by a normalized count of their common neighbours to improve the model. Finally, we show that the model can be further improved by considering a time-weighted adjacency matrix with both older and newer links having higher impact in the predictions, representing rooted concepts and state of the art research, respectively.

cs.SI↗

arXiv2019

Continuous-time quantum walk spatial search on the Bollobás scale-free network

The scale-free property emerges in various real-world networks and is an essential property which characterizes the dynamics or features of such networks. In this work we investigate the effect of this scale-free property on a quantum information processing task of finding a marked node in the network, known as the quantum spatial search. We analyze the quantum spatial search algorithm using continuous-time quantum walk on the Bollobás network, and evaluate the time $T$ to localize the quantum walker on the marked node starting from an unbiased initial state. Our main finding is that $T$ is determined by the global structure around the marked node, while some local information of the marked node such as degree does not identify $T$. We discuss this by examining the correlation between $T$ and some centrality measures of the network, and show that the closeness centrality of the marked node is highly correlated with $T$. We also characterize the distribution of $T$ by marking different nodes in the network, which displays a multi-mode lognormal distribution. Especially on the Bollobás network, $T$ is magnitude of orders shorter depending whether the marked node is adjacent to the largest degree hub node or not. However, as $T$ depends on the property of the marked node, one requires some amount of prior knowledge about such property of the marked node in order to identify the optimal time to measure the quantum walker and achieve fast search. These results indicate that the existence of the hub node in the scale-free network is playing a crucial role on the quantum spatial search.

quant-ph↗

arXiv2016

Discriminating Topology in Galaxy Distributions using Network Analysis

(abridged) The large-scale distribution of galaxies is generally analyzed using the two-point correlation function. However, this statistic does not capture the topology of the distribution, and it is necessary to resort to higher order correlations to break degeneracies. We demonstrate that an alternate approach using network analysis can discriminate between topologically different distributions that have similar two-point correlations. We investigate two galaxy point distributions, one produced by a cosmological simulation and the other by a Lévy walk. For the cosmological simulation, we adopt the redshift $z = 0.58$ slice from Illustris (Vogelsberger et al. 2014A) and select galaxies with stellar masses greater than $10^8$$M_\odot$. The two point correlation function of these simulated galaxies follows a single power-law, $ξ(r) \sim r^{-1.5}$. Then, we generate Lévy walks matching the correlation function and abundance with the simulated galaxies. We find that, while the two simulated galaxy point distributions have the same abundance and two point correlation function, their spatial distributions are very different; most prominently, \emph{filamentary structures}, absent in Lévy fractals. To quantify these missing topologies, we adopt network analysis tools and measure diameter, giant component, and transitivity from networks built by a conventional friends-of-friends recipe with various linking lengths. Unlike the abundance and two point correlation function, these network quantities reveal a clear separation between the two simulated distributions; therefore, the galaxy distribution simulated by Illustris is not a Lévy fractal quantitatively. We find that the described network quantities offer an efficient tool for discriminating topologies and for comparing observed and theoretical distributions.

astro-ph.CO↗