Tue, 21 Jun 2022

14:00 - 15:00

Sequential Motifs in Observed Walks

Timothy LaRock
(Mathematical Institute (University of Oxford))

The structure of complex networks can be characterized by counting and analyzing network motifs, which are small graph structures that occur repeatedly in a network, such as triangles or chains. Recent work has generalized motifs to temporal and dynamic network data. However, existing techniques do not generalize to sequential or trajectory data, which represents entities walking through the nodes of a network, such as passengers moving through transportation networks. The unit of observation in these data is fundamentally different, since we analyze observations of walks (e.g., a trip from airport A to airport C through airport B), rather than independent observations of edges or snapshots of graphs over time. In this work, we define sequential motifs in trajectory data, which are small, directed, and sequenced-ordered graphs corresponding to patterns in observed sequences. We draw a connection between counting and analysis of sequential motifs and Higher-Order Network (HON) models. We show that by mapping edges of a HON, specifically a kth-order DeBruijn graph, to sequential motifs, we can count and evaluate their importance in observed data, and we test our proposed methodology with two datasets: (1) passengers navigating an airport network and (2) people navigating the Wikipedia article network. We find that the most prevalent and important sequential motifs correspond to intuitive patterns of traversal in the real systems, and show empirically that the heterogeneity of edge weights in an observed higher-order DeBruijn graph has implications for the distributions of sequential motifs we expect to see across our null models.

ArXiv link: https://arxiv.org/abs/2112.05642

Tue, 14 Jun 2022

14:00 - 15:00


Luc Rocher
(Oxford Internet Institute)
Tue, 07 Jun 2022

14:00 - 15:00

Homological analysis of network dynamics

Dane Taylor
(Department of Mathematics - University at Buffalo)

Social, biological and physical systems are widely studied through the modeling of dynamical processes over networks, and one commonly investigates the interplay between structure and dynamics. I will discuss how cyclic patterns in networks can influence models for collective and diffusive processes, including generalized models in which dynamics are defined over simplicial complexes and multiplex networks. Our approach relies on homology theory, which is the subfield of mathematics that formally studies cycles (and more generally, k-dimensional holes). We will make use of techniques including persistent homology and Hodge theory to examine the role of cycles in helping organize dynamics onto low-dimensional manifolds. This pursuit represents an emerging interface between the fields of network-coupled dynamical systems and topological data analysis.

Mon, 02 May 2022

16:00 - 17:00

Random matrices with integer entries

Valeriya Kovaleva

Many classical arithmetic problems ranging from the elementary ones such as the density of square-free numbers to more difficult such as the density of primes, can be extended to integer matrices. Arithmetic problems over higher dimensions are typically much more difficult. Indeed, the Bateman-Horn conjecture predicting the density of numbers giving prime values of multivariate polynomials is very much open. In this talk I give an overview of the unfortunately brief history of integer random matrices.

Tue, 31 May 2022

14:00 - 15:00

Physics-inspired machine learning

Konstantin Rusch
(ETH Zurich)

Combining physics with machine learning is a rapidly growing field of research. Thereby, most work focuses on leveraging machine learning methods to solve problems in physics. Here, however, we focus on the reverse direction of leveraging structure of physical systems (e.g. dynamical systems modeled by ODEs or PDEs) to construct novel machine learning algorithms, where the existence of highly desirable properties of the underlying method can be rigorously proved. In particular, we propose several physics-inspired deep learning architectures for sequence modelling as well as for graph representation learning. The proposed architectures mitigate central problems in each corresponding domain, such as the vanishing and exploding gradients problem for recurrent neural networks or the oversmoothing problem for graph neural networks. Finally, we show that this leads to state-of-the-art performance on several widely used benchmark problems.

Tue, 24 May 2022

14:00 - 15:00

A Mechanism for the Emergence of Chimera States

Adilson Motter
(Northwestern University)

Chimera states have attracted significant attention as symmetry-broken states exhibiting the coexistence of coherence and incoherence. Despite the valuable insights gained by analyzing specific systems, the understanding of the physical mechanism underlying the emergence of chimeras has been incomplete. In this presentation, I will argue that an important class of stable chimeras arise because coherence in part of the system is sustained by incoherence in the rest of the system. This mechanism may be regarded as a deterministic analog of noise-induced synchronization and is shown to underlie the emergence of so-called strong chimeras. These are chimera states whose coherent domain is formed by identically synchronized oscillators. The link between coherence and incoherence revealed by this mechanism also offers insights into the dynamics of a broader class of states, including switching chimera states and incoherence-mediated remote synchronization.

Tue, 17 May 2022

14:00 - 15:00

Epidemics, synchronization and rumors spreading in complex networks

Angélica Sousa da Mata
(Federal University of Lavras)

Synchronization, epidemic processes and information spreading are natural processes that emerge from the interaction between people. Mathematically, all of them can be described by models that, despite their simplicity, they can predict collective behaviors. In addition, they have in common a very interesting feature: a phase transition from an active state to an absorbing state. For example, the spread of an epidemic is characterized by the infection rate, the control parameter, which basically determines whether the epidemic will spread in the network or, if this rate is very low, few people become infected and the system falls into an absorbing state where there are no more infected people. In this presentation we will present the analytical and computational approaches used to investigate these classical models of statistical physics that present phase transitions and we will also show how the network topology influences such dynamical processes. The behavior of such dynamics can be much richer than we imagine.

Tue, 10 May 2022

14:00 - 15:00

Extracting backbones from bipartite projections: comparing hard and soft constraints

Zachary Neal
(Michigan State University)

Co-occurrence networks formed by bipartite projection are widely studied in many contexts, including politics (bill co-sponsorship), bibliometrics (paper co-authorship), ecology (species co-habitation), and genetics (protein co-expression). It is often useful to focus on the backbone, a binary representation that includes only the most important edges, however many different backbone extraction models exist. In this talk, I will demonstrate the "backbone" package for R, which implements many such models. I will also use it to compare two promising null models: the fixed degree sequence model (FDSM) that imposes hard constraints, and the stochastic degree sequence model (SDSM) that imposes soft constraints, on the bipartite degree sequences. While FDSM is more statistically powerful, SDSM is more efficient and offers a close approximation.

Tue, 03 May 2022

14:00 - 15:00

How Network Filtering can extract knowledge from data

Tiziana Di Matteo
(King's College London)

In this talk I will present network-theoretic tools [1-2] to filter information in large-scale datasets and I will show that these are powerful tools to study complex datasets. In particular I will introduce correlation-based information filtering networks and the planar filtered graphs (PMFG) and I will show that applications to financial data-sets can meaningfully identify industrial activities and structural market changes [3-4].

It has been shown that by making use of the 3-clique structure of the PMFG a clustering can be extracted allowing dimensionality reduction that keeps both local information and global hierarchy in a deterministic manner without the use of any prior information [5-6]. However, the algorithm so far proposed to construct the PMFG is numerically costly with O(N3) computational complexity and cannot be applied to large-scale data. There is therefore scope to search for novel algorithms that can provide, in a numerically efficient way, such a reduction to planar filtered graphs. I will introduce a new algorithm, the TMFG (Triangulated Maximally Filtered Graph), that efficiently extracts a planar subgraph which optimizes an objective function. The method is scalable to very large datasets and it can take advantage of parallel and GPUs computing [7]. Filtered graphs are valuable tools for risk management and portfolio optimization too [8-9] and they allow to construct probabilistic sparse modeling for financial systems that can be used for forecasting, stress testing and risk allocation [10].

Filtered graphs can be used not only to extract relevant and significant information but more importantly to extract knowledge from an overwhelming quantity of unstructured and structured data. I will provide a practitioner example by a successful Silicon Valley start-up, Yewno. The key idea underlying Yewno’s products is the concept of the Knowledge Graph, a framework based on filtered graph research, whose goal is to extract signals from evolving corpus of data. The common principle is that a methodology leveraging on developments in Computational linguistics and graph theory is used to build a graph representation of knowledge [11], which can be automatically analysed to discover hidden relations between components in many different complex systems. This Knowledge Graph based framework and inference engine has a wide range of applications, including finance, economics, biotech, law, education, marketing and general research.


[1] T. Aste, T. Di Matteo, S. T. Hyde, Physica A 346 (2005) 20.

[2] T. Aste, Ruggero Gramatica, T. Di Matteo, Physical Review E 86 (2012) 036109.

[3] M. Tumminello, T. Aste, T. Di Matteo, R. N. Mantegna, PNAS 102, n. 30 (2005) 10421.

[4] N. Musmeci, Tomaso Aste, T. Di Matteo, Journal of Network Theory in Finance 1(1) (2015) 1-22.

[5] W.-M. Song, T. Di Matteo, and T. Aste, PLoS ONE 7 (2012) e31929.

[6] N. Musmeci, T. Aste, T. Di Matteo, PLoS ONE 10(3): e0116201 (2015).

[7] Guido Previde Massara, T. Di Matteo, T. Aste, Journal of Complex networks 5 (2), 161 (2016).

[8] F. Pozzi, T. Di Matteo and T. Aste, Scientific Reports 3 (2013) 1665.

[9] N. Musmeci, T. Aste and T. Di Matteo, Scientific Reports 6 (2016) 36320.

[10] Wolfram Barfuss, Guido Previde Massara, T. Di Matteo, T. Aste, Phys.Rev. E 94 (2016) 062306.

[11] Ruggero Gramatica, T. Di Matteo, Stefano Giorgetti, Massimo Barbiani, Dorian Bevec and Tomaso Aste, PLoS One (2014) PLoS ONE 9(1): e84912.

Tue, 26 Apr 2022

14:00 - 15:00

Drug Pair Scoring Theory, Models and Software

Benedek Rozemberczki
Further Information

Dr. Benedek Rozemberczki is currently a machine learning engineer at AstraZeneca.


Pair combination repurposing of drugs is a common challenge faced by researchers in the pharmaceutical industry. Network biology and molecular machine learning based drug pair scoring techniques offer computation tools to predict the interaction, polypharmacy side effects and synergy of drugs. In this talk we overview of three things: (a) the theory and unified model of drug pair scoring (b) a relational machine learning model that can solve the pair scoring task (c) the design of large-scale machine learning systems needed to tackle the pair scoring task.

ArXiv links: https://arxiv.org/abs/2111.02916https://arxiv.org/abs/2110.15087https://arxiv.org/abs/2202.05240.

ML library: https://github.com/AstraZeneca/chemicalx

Subscribe to C6