Related papers: Identifying bubble-like subgraphs in linear-time v…
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
Subgraph counting aims to count occurrences of a template T in a given network G(V, E). It is a powerful graph analysis tool and has found real-world applications in diverse domains. Scaling subgraph counting problems is known to be memory…
We develop two different methods to achieve subexponential time parameterized algorithms for problems on sparse directed graphs. We exemplify our approaches with two well studied problems. For the first problem, {\sc $k$-Leaf…
Designing algorithms that generate networks with a given degree sequence while varying both subgraph composition and distribution of subgraphs around nodes is an important but challenging research problem. Current algorithms lack control of…
Spiking Neural Networks (SNN). SNNs are based on a more biologically inspired approach than usual artificial neural networks. Such models are characterized by complex dynamics between neurons and spikes. These are very sensitive to the…
Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…
We apply deep recurrent neural networks, which are capable of learning complex sequential information, to classify supernovae\footnote{Code available at \href{https://github.com/adammoss/supernovae}{https://github.com/adammoss/supernovae}}.…
Multivariate time series anomaly detection technology plays an important role in many fields including aerospace, water treatment, cloud service providers, etc. Excellent anomaly detection models can greatly improve work efficiency and…
Deep Learning methods, specifically convolutional neural networks (CNNs), have seen a lot of success in the domain of image-based data, where the data offers a clearly structured topology in the regular lattice of pixels. This…
In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the…
Graph-based methods pervade the inference toolkits of numerous disciplines including sociology, biology, neuroscience, physics, chemistry, and engineering. A challenging problem encountered in this context pertains to determining the…
Lekkerkerker and Boland characterized the minimal forbidden induced subgraphs for the class of interval graphs. We give a linear-time algorithm to find one in any graph that is not an interval graph. Tucker characterized the minimal…
Nowadays, multivariate time series data are increasingly collected in various real world systems, e.g., power plants, wearable devices, etc. Anomaly detection and diagnosis in multivariate time series refer to identifying abnormal status in…
A graph is $k$-degenerate if any induced subgraph has a vertex of degree at most $k$. In this paper we prove new algorithms for cliques and similar structures for these graphs. We design linear time Fixed-Parameter Tractable algorithms for…
Detecting anomalies in dynamic graphs is a vital task, with numerous practical applications in areas such as security, finance, and social media. Previous network embedding based methods have been mostly focusing on learning good node…
Graph neural networks have pushed state-of-the-arts in graph classifications recently. Typically, these methods are studied within the context of supervised end-to-end training, which necessities copious task-specific labels. However, in…
Block graphs are graphs in which every block (biconnected component) is a clique. A graph $G=(V,E)$ is said to be an (unpartitioned) $k$-probe block graph if there exist $k$ independent sets $N_i\subseteq V$, $1\le i\le k$, such that the…
Butterflies are the smallest non-trivial subgraph in bipartite graphs, and therefore having efficient computations for analyzing them is crucial to improving the quality of certain applications on bipartite graphs. In this paper, we design…
Finding dense subnetworks, with density based on edges or more complex structures, such as subgraphs or $k$-cliques, is a fundamental algorithmic problem with many applications. While the problem has been studied extensively in static…
The identification of substructures within halos in cosmological hydrodynamical simulations is a fundamental step to identify the simulated counterparts of real objects, namely galaxies. For this reason, substructure finders play a crucial…