Publications

Inferring dynamic regulatory interaction graphs from time series data with perturbations
Dhananjay Bhaskar
Sumner Magruder
Edward De Brouwer
Matheo Morales
Aarthi Venkat
Frederik Wenkel
Guy Wolf
Smita Krishnaswamy
Complex systems are characterized by intricate interactions between entities that evolve dynamically over time. Accurate inference of these … (see more)dynamic relationships is crucial for understanding and predicting system behavior. In this paper, we propose Regulatory Temporal Interaction Network Inference (RiTINI) for inferring time-varying interaction graphs in complex systems using a novel combination of space-and-time graph attentions and graph neural ordinary differential equations (ODEs). RiTINI leverages time-lapse signals on a graph prior, as well as perturbations of signals at various nodes in order to effectively capture the dynamics of the underlying system. This approach is distinct from traditional causal inference networks, which are limited to inferring acyclic and static graphs. In contrast, RiTINI can infer cyclic, directed, and time-varying graphs, providing a more comprehensive and accurate representation of complex systems. The graph attention mechanism in RiTINI allows the model to adaptively focus on the most relevant interactions in time and space, while the graph neural ODEs enable continuous-time modeling of the system's dynamics. We evaluate RiTINI's performance on various simulated and real-world datasets, demonstrating its state-of-the-art capability in inferring interaction graphs compared to previous methods.
2022-12-31
LoG (published)
doi.org
proceedings.mlr.press
Inferring multiple consensus trees and supertrees using clustering: a review
Vladimir Makarenkov
Gayane S. Barseghyan
Nadia Tahiri
2022-12-31
ArXiv (preprint)
doi.org
arxiv.org
An Intentional Forgetting-Driven Self-Healing Method for Deep Reinforcement Learning Systems
Ahmed Haj Yahmed
Rached Bouchoucha
Houssem Ben Braiek
Foutse Khomh
Deep reinforcement learning (DRL) is increasingly applied in large-scale productions like Netflix and Facebook. As with most data-driven sys… (see more)tems, DRL systems can exhibit undesirable behaviors due to environmental drifts, which often occur in constantly-changing production settings. Continual Learning (CL) is the inherent self-healing approach for adapting the DRL agent in response to the environment's conditions shifts. However, successive shifts of considerable magnitude may cause the production environment to drift from its original state. Recent studies have shown that these environmental drifts tend to drive CL into long, or even unsuccessful, healing cycles, which arise from inefficiencies such as catastrophic forgetting, warm-starting failure, and slow convergence. In this paper, we propose Dr. DRL, an effective self-healing approach for DRL systems that integrates a novel mechanism of intentional forgetting into vanilla CL (i.e., standard CL) to overcome its main issues. Dr. DRL deliberately erases the DRL system's minor behaviors to systematically prioritize the adaptation of the key problem-solving skills. Using well-established DRL algorithms, Dr. DRL is compared with vanilla CL on various drifted environments. Dr. DRL is able to reduce, on average, the healing time and fine-tuning episodes by, respectively, 18.74% and 17.72%. Dr. DRL successfully helps agents to adapt to 19.63% of drifted environments left unsolved by vanilla CL while maintaining and even enhancing by up to 45% the obtained rewards for drifted environments that are resolved by both approaches.
2022-12-31
2023 38th IEEE/ACM International Conference on Automated Software Engineering (ASE) (published)
doi.org
arxiv.org
Interpretable deep learning architectures for improving drug response prediction performance: myth or reality?
Yihui Li
David Earl Hostallero
Amin Emad
Motivation: Recent advances in deep learning model development have enabled more accurate prediction of drug response in cancer. However, th… (see more)e black-box nature of these models still remains a hurdle in their adoption for precision cancer medicine. Recent efforts have focused on making these models interpretable by incorporating signaling pathway information in model architecture. While these models improve interpretability, it is unclear whether this higher interpretability comes at the cost of less accurate predictions, or a prediction improvement can also be obtained. Results: In this study, we comprehensively and systematically assessed four state-of-the-art interpretable models developed for drug response prediction to answer this question using three pathway collections. Our results showed that models that explicitly incorporate pathway information in the form of a latent layer perform worse compared to models that incorporate this information implicitly. Moreover, in most evaluation setups the best performance is achieved using a simple black-box model. In addition, replacing the signaling pathways with randomly generated pathways shows a comparable performance for the majority of these interpretable models. Our results suggest that new interpretable models are necessary to improve the drug response prediction performance. In addition, the current study provides different baseline models and evaluation setups necessary for such new models to demonstrate their superior prediction performance. Availability and Implementation: Implementation of all methods are provided inhttps://github.com/Emad-COMBINE-lab/InterpretableAI_for_DRP. Generated uniform datasets are inhttps://zenodo.org/record/7101665#.YzS79HbMKUk. Contact:amin.emad@mcgill.caSupplementary Information: Online-only supplementary data is available at the journal’s website.
2022-12-31
Bioinform. (published)
doi.org
Invasion of Ukraine Discourse on TikTok Dataset
Benjamin D. Steel
Sara J. Parker
Derek Ruths
We present a dataset of videos and comments from the social media platform TikTok, centred around the invasion of Ukraine in 2022, an event … (see more)that launched TikTok into the geopolitical arena. The discourse around the invasion exposed myriad political behaviours and dynamics that are unexplored on this platform. To this end we provide a mass scale language and interaction dataset for further research into these processes. An initial investigation of language and social interaction dynamics are explored in this paper. The dataset and the library used to collect it are open sourced to the public.
2022-12-31
arXiv.org (preprint)
doi.org
Invited commentary on Stoehr J et al: The personal impact of involvement in international global health outreach: A national survey of former operation smile student volunteers.
Dan Poenaru
2022-12-31
Journal of Pediatric Surgery (published)
doi.org
Iorl: Inductive-Offline-Reinforcement-Learning for Traffic Signal Control Warmstarting
François-Xavier Devailly
Denis Larocque
Laurent Charlin
2022-12-31
Social Science Research Network (published)
doi.org
A Kernel Perspective on Behavioural Metrics for Markov Decision Processes
Pablo Samuel Castro
Tyler Kastner
Prakash Panangaden
Mark Rowland
We present a novel perspective on behavioural metrics for Markov decision processes via the use of positive definite kernels. We define a ne… (see more)w metric under this lens that is provably equivalent to the recently introduced MICo distance (Castro et al., 2021). The kernel perspective enables us to provide new theoretical results, including value-function bounds and low-distortion finite-dimensional Euclidean embeddings, which are crucial when using behavioural metrics for reinforcement learning representations. We complement our theory with strong empirical results that demonstrate the effectiveness of these methods in practice.
2022-12-31
Trans. Mach. Learn. Res. (published)
doi.org
openreview.net
LEAD: Min-Max Optimization from a Physical Perspective
Reyhane Askari Hemmat
Amartya Mitra
Guillaume Lajoie
Ioannis Mitliagkas
Adversarial formulations have rekindled interest in two-player min-max games. A central obstacle in the optimization of such games is the ro… (see more)tational dynamics that hinder their convergence. In this paper, we show that game optimization shares dynamic properties with particle systems subject to multiple forces, and one can leverage tools from physics to improve optimization dynamics. Inspired by the physical framework, we propose LEAD, an optimizer for min-max games. Next, using Lyapunov stability theory from dynamical systems as well as spectral analysis, we study LEAD’s convergence properties in continuous and discrete time settings for a class of quadratic min-max games to demonstrate linear convergence to the Nash equilibrium. Finally, we empirically evaluate our method on synthetic setups and CIFAR-10 image generation to demonstrate improvements in GAN training.
2022-12-31
Trans. Mach. Learn. Res. (published)
openreview.net
openreview.net
Learning GFlowNets From Partial Episodes For Improved Convergence And Stability
Kanika Madan
Jarrid Rector-Brooks
Maksym Korablyov
Emmanuel Bengio
Moksh Jain
Andrei Nica
Tom Bosc
Yoshua Bengio
Nikolay Malkin
Generative flow networks (GFlowNets) are a family of algorithms for training a sequential sampler of discrete objects under an unnormalized … (see more)target density and have been successfully used for various probabilistic modeling tasks. Existing training objectives for GFlowNets are either local to states or transitions, or propagate a reward signal over an entire sampling trajectory. We argue that these alternatives represent opposite ends of a gradient bias-variance tradeoff and propose a way to exploit this tradeoff to mitigate its harmful effects. Inspired by the TD(
2022-12-31
ICML (published)
doi.org
proceedings.mlr.press
Learning Lyapunov-Stable Polynomial Dynamical Systems Through Imitation
Amin Abyaneh
Hsiu-Chin Lin
Imitation learning is a paradigm to address complex motion planning problems by learning a policy to imitate an expert’s behavior. However… (see more), relying solely on the expert’s data might lead to unsafe actions when the robot deviates from the demonstrated trajectories. Stability guarantees have previously been provided utilizing nonlinear dynamical systems, acting as high-level motion planners, in conjunction with the Lyapunov stability theorem. Yet, these methods are prone to inaccurate policies, high computational cost, sample inefficiency, or quasi stability when replicating complex and highly nonlinear trajectories. To mitigate this problem, we present an approach for learning a globally stable nonlinear dynamical system as a motion planning policy. We model the nonlinear dynamical system as a parametric polynomial and learn the polynomial’s coefficients jointly with a Lyapunov candidate. To showcase its success, we compare our method against the state of the art in simulation and conduct real-world experiments with the Kinova Gen3 Lite manipulator arm. Our experiments demonstrate the sample efficiency and reproduction accuracy of our method for various expert trajectories, while remaining stable in the face of perturbations.
2022-12-31
CoRL (published)
doi.org
proceedings.mlr.press
Learning Syntactic Monoids from Samples by extending known Algorithms for learning State Machines
Simon Dieck
Sicco Verwer
François Coste
Faissal Ouardi
Guillaume Rabusseau
For the inference of regular languages, most current methods learn a version of deterministic finite automata. Syntactic monoids are an alte… (see more)rnative representation of regular languages, which have some advantages over automata. For example, traces can be parsed starting from any index and the star-freeness of the language they represent can be checked in polynomial time. But, to date, there existed no passive learning algorithm for syntactic monoids. In this paper, we prove that known state-merging algorithms for learning deterministic finite automata can be instrumented to learn syntactic monoids instead, by using as the input a special structure proposed in this paper: the interfix-graph. Further, we introduce a method to encode frequencies on the interfix-graph, such that models can also be learned from only positive traces. We implemented this structure and performed experiments with both traditional data and data containing only positive traces. As such this work answers basic theoretical and experimental questions regarding a novel passive learning algorithm for syntactic monoids.
2022-12-31
International Conference on Graphics and Interaction (published)
dblp.uni-trier.de