Publications

Lower Bounds for Active Automata Learning.
Loes Kruger
Bharat Garhewal
François Coste
Frits W. Vaandrager
Faissal Ouardi
Guillaume Rabusseau
2022-12-31
ICGI (publié)
dblp.uni-trier.de
Maintenance Cost of Software Ecosystem Updates
Solomon Berhe
M. Maynard
Foutse Khomh
2022-12-31
ANT/EDI40 (publié)
doi.org
MARSY: a multitask deep-learning framework for prediction of drug combination synergy scores
Mohamed Reda El Khili
Safyan Aman Memon
Amin Emad
Combination therapies have emerged as a treatment strategy for cancers to reduce the probability of drug resistance and to improve outcomes.… (voir plus) Large databases curating the results of many drug screening studies on preclinical cancer cell lines have been developed, capturing the synergistic and antagonistic effects of combination of drugs in different cell lines. However, due to the high cost of drug screening experiments and the sheer size of possible drug combinations, these databases are quite sparse. This necessitates the development of transductive computational models to accurately impute these missing values. Here, we developed MARSY, a deep-learning multitask model that incorporates information on the gene expression profile of cancer cell lines, as well as the differential expression signature induced by each drug to predict drug-pair synergy scores. By utilizing two encoders to capture the interplay between the drug pairs, as well as the drug pairs and cell lines, and by adding auxiliary tasks in the predictor, MARSY learns latent embeddings that improve the prediction performance compared to state-of-the-art and traditional machine-learning models. Using MARSY, we then predicted the synergy scores of 133 722 new drug-pair cell line combinations, which we have made available to the community as part of this study. Moreover, we validated various insights obtained from these novel predictions using independent studies, confirming the ability of MARSY in making accurate novel predictions. An implementation of the algorithms in Python and cleaned input datasets are provided in https://github.com/Emad-COMBINE-lab/MARSY.
2022-12-31
Bioinformatics (publié)
doi.org
Membership Inference Attacks Against Temporally Correlated Data in Deep Reinforcement Learning
Maziar Gomrokchi
Susan Amin
Hossein Aboutalebi
Alexander Wong
Doina Precup
While significant research advances have been made in the field of deep reinforcement learning, there have been no concrete adversarial atta… (voir plus)ck strategies in literature tailored for studying the vulnerability of deep reinforcement learning algorithms to membership inference attacks. In such attacking systems, the adversary targets the set of collected input data on which the deep reinforcement learning algorithm has been trained. To address this gap, we propose an adversarial attack framework designed for testing the vulnerability of a state-of-the-art deep reinforcement learning algorithm to a membership inference attack. In particular, we design a series of experiments to investigate the impact of temporal correlation, which naturally exists in reinforcement learning training data, on the probability of information leakage. Moreover, we compare the performance of \emph{collective} and \emph{individual} membership attacks against the deep reinforcement learning algorithm. Experimental results show that the proposed adversarial attack framework is surprisingly effective at inferring data with an accuracy exceeding
2022-12-31
IEEE Access (publié)
doi.org
arxiv.org
Motor cortex latent dynamics 1 encode arm movement direction and 2 urgency independently 3
Andrea Colins Rodriguez
Matthew G Perich
Lee Miller
Mark D. Humphries
10 The fluid movement of an arm is controlled by multiple parameters that can be set 11 independently. Recent studies argue that arm moveme… (voir plus)nts are generated by the collective 12 dynamics of neurons in motor cortex. But how these collective dynamics simultaneously encode 13 and control multiple parameters of movement is an open question. Using a task where monkeys 14 made sequential, varied arm movements, we show that the direction and urgency of arm 15 movements are simultaneously encoded in the low-dimensional trajectories of population 16 activity: each movement’s direction by a fixed, looped neural trajectory and its urgency by how 17 quickly that trajectory was traversed. Network models showed this latent coding is potentially 18 advantageous as it allows the direction and urgency of arm movement to be independently 19 controlled. Our results suggest how low-dimensional neural dynamics can define multiple 20 parameters of goal-directed movement simultaneously. 21
2022-12-31
(publié)
www.semanticscholar.org
Multi-view manifold learning of human brain-state trajectories.
Erica L. Busch
Jessie Huang
Andrew Benz
Tom Wallenstein
Guillaume Lajoie
Guy Wolf
Smita Krishnaswamy
Nicholas B. Turk-Browne
The complexity of the human brain gives the illusion that brain activity is intrinsically high-dimensional. Nonlinear dimensionality-reducti… (voir plus)on methods such as uniform manifold approximation and t-distributed stochastic neighbor embedding have been used for high-throughput biomedical data. However, they have not been used extensively for brain activity data such as those from functional magnetic resonance imaging (fMRI), primarily due to their inability to maintain dynamic structure. Here we introduce a nonlinear manifold learning method for time-series data—including those from fMRI—called temporal potential of heat-diffusion for affinity-based transition embedding (T-PHATE). In addition to recovering a low-dimensional intrinsic manifold geometry from time-series data, T-PHATE exploits the data’s autocorrelative structure to faithfully denoise and unveil dynamic trajectories. We empirically validate T-PHATE on three fMRI datasets, showing that it greatly improves data visualization, classification, and segmentation of the data relative to several other state-of-the-art dimensionality-reduction benchmarks. These improvements suggest many potential applications of T-PHATE to other high-dimensional datasets of temporally diffuse processes.
2022-12-31
Nature Computational Science (publié)
doi.org
Network Design for Ultra-fast Delivery Services via Probabilistic Envelope Constrained Programs
Xin Wang
Okan Arslan
Jean-François Cordeau
Erick Delage
2022-12-31
SSRN Electronic Journal (publié)
doi.org
NEURAL MANIFOLDS AND GRADIENT-BASED ADAPTATION IN NEURAL-INTERFACE TASKS
Alexandre Payeur
Amy L. Orsborn
Guillaume Lajoie
. Neural activity tends to reside on manifolds whose dimension is much lower than the dimension of the whole neural state space. Experiments… (voir plus) using brain-computer interfaces with microelectrode arrays implanted in the motor cortex of nonhuman primates tested the hypothesis that external perturbations should produce different adaptation strategies depending on how “aligned” the perturbation is with respect to a pre-existing intrinsic manifold. On the one hand, perturbations within the manifold (WM) evoked fast reassociations of existing patterns for rapid adaptation. On the other hand, perturbations outside the manifold (OM) triggered the slow emergence of new neural patterns underlying a much slower—and, without adequate training protocols, inconsistent or virtually impossible—adaptation. This suggests that the time scale and the overall difficulty of the brain to adapt depend fundamentally on the structure of neural activity. Here, we used a simplified static Gaussian model to show that gradient-descent learning could explain the differences between adaptation to WM and OM perturbations. For small learning rates, we found that the adaptation speeds were different but the model eventually adapted to both perturbations. Moreover, sufficiently large learning rates could entirely prohibit adaptation to OM perturbations while preserving adaptation to WM perturbations, in agreement with experiments. Adopting an incremental training protocol, as has been done in experiments, permitted a swift recovery of a full adaptation in the cases where OM perturbations were previously impossible to relearn. Finally, we also found that gradient descent was compatible with the reassociation mechanism on short adaptation time scales. Since gradient descent has many biologically plausible variants, our findings thus establish gradient-based learning as a plausible mechanism for adaptation under network-level constraints, with a central role for the learning rate.
2022-12-31
(publié)
www.semanticscholar.org
NEURAL NETWORK-BASED SOLVERS FOR PDES
M. Cameron
Ian G Goodfellow
Yoshua Bengio
(1) N (x; θ) = Ll+1 ○ σl ○Ll ○ σl−1 ○ . . . ○ σ1 ○L1. The symbol Lk denotes the k’s affine operator of the form Lk(x) = … (voir plus)Akx + bk, while σk denotes a nonlinear function called an activation function. The activation functions are chosen by the user. The matrices Ak and shift vectors (or bias vectors) bk are encoded into the argument θ: θ = {Ak, bk} l+1 k=1. The term training neural network means finding {Ak, bk} l+1 k=1 such that N (x; θ) satisfies certain conditions. These conditions are described by the loss function chosen by the user. For example, one might want the neural network to assume certain values fj at certain points xj , j = 1, . . . ,N . These points x are called the training data. In this case, a common choice of the loss function is the least squares error:
2022-12-31
(publié)
www.semanticscholar.org
Noisy Pairing and Partial Supervision for Stylized Opinion Summarization
Reinald Kim
Mirella Lapata. 2020
Un-611
David M. Krueger
Emmanuel Bengio
Maxinder S. Kan-620
Tegan Maharaj
Asja Fischer
Aaron Courville
Somnath Basu
Roy Chowdhury
Chao Zhao
Tanya Goyal
Junyi Jiacheng Xu
Jessy Li
Ivor W. Tsang
James T. Kwok
Neil Houlsby
Andrei Giurgiu
Stanisław Jastrzębski … (voir 22 de plus)
Bruna Morrone
Quentin de Laroussilhe
Mona Gesmundo
Attariyan Sylvain
Gelly
Thomas Wolf
Lysandre Debut
Julien Victor Sanh
Clement Chaumond
Anthony Delangue
Pier-339 Moi
Tim ric Cistac
R´emi Rault
Morgan Louf
Funtow-900 Joe
Sam Davison
Patrick Shleifer
Von Platen
Clara Ma
Yacine Jernite
Julien Plu
Canwen Xu
Opinion summarization research has primar-001 ily focused on generating summaries reflect-002 ing important opinions from customer reviews 0… (voir plus)03 without paying much attention to the writing 004 style. In this paper, we propose the stylized 005 opinion summarization task, which aims to 006 generate a summary of customer reviews in 007 the desired (e.g., professional) writing style. 008 To tackle the difficulty in collecting customer 009 and professional review pairs, we develop a 010 non-parallel training framework, Noisy Pair-011 ing and Partial Supervision ( NAPA ), which 012 trains a stylized opinion summarization sys-013 tem from non-parallel customer and profes-014 sional review sets. We create a benchmark P RO - 015 S UM by collecting customer and professional 016 reviews from Yelp and Michelin. Experimental 017 results on P RO S UM and FewSum demonstrate 018 that our non-parallel training framework con-019 sistently improves both automatic and human 020 evaluations, successfully building a stylized 021 opinion summarization model that can gener-022 ate professionally-written summaries from cus-023 tomer reviews. 024
2022-12-31
(publié)
www.semanticscholar.org
A Novel Deep Multi-head Attentive Vulnerable Line Detector
Miles Q. Li
Benjamin C. M. Fung
Ashita Diwan
2022-12-31
Procedia Computer Science (publié)
doi.org
An Online Newton’s Method for Time-Varying Linear Equality Constraints
Jean-Luc Lupien
Antoine Lesage-Landry
We consider online optimization problems with time-varying linear equality constraints. In this framework, an agent makes sequential decisio… (voir plus)ns using only prior information. At every round, the agent suffers an environment-determined loss and must satisfy time-varying constraints. Both the loss functions and the constraints can be chosen adversarially. We propose the Online Projected Equality-constrained Newton Method (OPEN-M) to tackle this family of problems. We obtain sublinear dynamic regret and constraint violation bounds for OPEN-M under mild conditions. Namely, smoothness of the loss function and boundedness of the inverse Hessian at the optimum are required, but not convexity. Finally, we show OPEN-M outperforms state-of-the-art online constrained optimization algorithms in a numerical network flow application.
2022-12-31
IEEE Control Systems Letters (publié)
doi.org
arxiv.org