United States

Signed networks (networks with positive and negative edges) commonly arise in various domains from molecular biology to social media. 
The edge signs -- i.e., the graph signage -- represent the interaction pattern between the nodes and can provide insights into the underlying system formation process. Generative models considering signage formation are essential for testing hypotheses about the emergence of interactions and for creating synthetic datasets for algorithm benchmarking (especially in areas where obtaining real-world datasets is difficult).

In this work, we pose a novel Maximum-Likelihood-based optimization problem for modeling signages given their topology and showcase it in the context of gene regulation. Regulatory interactions of genes play a key role in the process of organism development, and when broken can lead to serious organism abnormalities and diseases.  Our contributions are threefold: First, we design a new class of signage models for a given topology, and, based on the parameter setting, we discuss its biological interpretations for gene regulatory networks (GRNs). Second, we design algorithms computing the Maximum Likelihood -- depending on the parameter setting, our algorithms range from closed-form expressions to MCMC sampling. Third, we evaluated the results of our algorithms on synthetic datasets and real-world large GRNs. Our work can lead to the prediction of unknown gene regulations, novel biological hypotheses, and realistic benchmark datasets in the realm of gene regulation.

AAAI 2023

GRASMOS: Graph Signage Model Selection for Gene Regulatory Networks

maximum-likelihood markov chains

gene regulatory networks

model fitting

signed networks

bioinformatics

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. AAAI-23 is the Thirty-Seventh AAAI Conference on Artificial Intelligence. The theme of this conference is to create collaborative bridges within and beyond AI. Like previous AAAI conferences, AAAI-23 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and two new activities: a Bridge Program and a Lab Program. Many of these activities are tailored to the theme of bridges and all are selected according to the highest standards, with additional programs for students and young researchers. 
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The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines.

poster

We study the algorithm configuration (AC) problem, in which one seeks to find an optimal parameter configuration of a given target algorithm in an automated way. Although this field of research has experienced much progress recently regarding approaches satisfying strong theoretical guarantees, there is still a gap between the practical performance of these approaches and the heuristic state-of-the-art approaches. Recently, there has been significant progress in designing AC approaches that satisfy strong theoretical guarantees. However, a significant gap still remains between the practical performance of these approaches and state-of-the-art heuristic methods. To this end, we introduce AC-Band, a general approach for the AC problem based on multi-armed bandits that provides theoretical guarantees while exhibiting strong practical performance. We show that AC-Band requires significantly less computation time than other AC approaches providing theoretical guarantees while still yielding high-quality configurations.

AC-Band: A Combinatorial Bandit-Based Approach to Algorithm Configuration

The use of neural networks in safety-critical systems requires safe and robust models, due to the existence of adversarial attacks. Knowing the minimal adversarial perturbation of any input x, or, equivalently, knowing the distance of x from the classification boundary, allows evaluating the classification robustness, providing certifiable predictions. Unfortunately, state-of-the-art techniques for computing such a distance are computationally expensive and hence not suited for online applications. This work proposes a novel family of classifiers, namely Signed Distance Classifiers (SDCs), that, from a theoretical perspective, directly output the exact distance of x from the classification boundary, rather than a probability score (e.g., SoftMax). SDCs represent a family of robust-by-design classifiers. To practically address the theoretical requirements of a SDC, a novel network architecture named Unitary-Gradient Neural Network is presented. Experimental results show that the proposed architecture approximates a signed distance classifier, hence allowing an online certifiable classification of x at the cost of a single inference.

Robust-by-Design Classification via Unitary-Gradient Neural Networks

Power grids, across the world, play an important societal and economical role by providing uninterrupted, reliable and transient-free power to several industries, businesses and household consumers. With the advent of renewable power resources and EVs resulting into uncertain generation and highly dynamic load demands, it has become ever so important to ensure robust operation of power networks through suitable management of transient stability issues and localize the events of blackouts. In the light of ever increasing stress on the modern grid infrastructure and the grid operators, this paper presents a reinforcement learning (RL) framework, PowRL, to mitigate the effects of unexpected network events, as well as reliably maintain electricity everywhere on the network at all times. The PowRL leverages a novel heuristic for overload management, along with the RL-guided decision making on optimal topology selection to ensure that the grid is operated safely and reliably (with no overloads). PowRL is benchmarked on a variety of competition datasets hosted by the L2RPN (Learning to Run a Power Network). Even with its reduced action space, PowRL tops the leaderboard in the L2RPN NeurIPS 2020 challenge (Robustness track) at an aggregate level, while also being the top performing agent in the L2RPN WCCI 2020 challenge. Moreover, detailed analysis depicts state-of-the-art performances by the PowRL agent in some of the test scenarios.

PowRL: A Reinforcement Learning Framework for Robust Management of Power Networks

Adversarial attacks on Graph Neural Networks (GNNs) reveal their security vulnerabilities, limiting their adoption in safety-critical applications. However, existing attack strategies rely on the knowledge of either the GNN model being used or the predictive task being attacked. Is this knowledge necessary? For example, a graph may be used for multiple downstream tasks unknown to a practical attacker. It is thus important to test the vulnerability of GNNs to adversarial perturbations in a model and task agnostic setting. In this work, we study this problem and show that Gnns remain vulnerable even when the downstream task and model are unknown. The proposed algorithm, TANDIS (Targeted Attack via Neighborhood DIStortion) shows that distortion of node neighborhoods is effective in drastically compromising prediction performance. Although neighborhood distortion is an NP-hard problem, Tandis designs an effective heuristic through a novel combination of Graph Isomorphism Network with deep Q-learning. Extensive experiments on real datasets show that, on average, Tandis is up to 50% more effective than state-of-the-art techniques, while being more than 100 times faster.

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GRASMOS: Graph Signage Model Selection for Gene Regulatory Networks

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AC-Band: A Combinatorial Bandit-Based Approach to Algorithm Configuration

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