Publications

Sum and Tensor of Quantitative Effects
Giorgio Bacci
Radu Mardare
Prakash Panangaden
Gordon Plotkin
2024-10-28
Logical Methods in Computer Science (publié)
doi.org
arxiv.org
The Case for Globalizing Fairness: A Mixed Methods Study on Colonialism, AI, and Health in Africa
Mercy Nyamewaa Asiedu
Awa Dieng
Iskandar Haykel
Negar Rostamzadeh
Stephen R. Pfohl
Chirag Nagpal
Maria Nagawa
Abigail Oppong
Sanmi Koyejo
Katherine Heller
With growing application of machine learning (ML) technologies in healthcare, there have been calls for developing techniques to understand … (voir plus)and mitigate biases these systems may exhibit. Fair-ness considerations in the development of ML-based solutions for health have particular implications for Africa, which already faces inequitable power imbalances between the Global North and South.This paper seeks to explore fairness for global health, with Africa as a case study. We conduct a scoping review to propose axes of disparities for fairness consideration in the African context and delineate where they may come into play in different ML-enabled medical modalities. We then conduct qualitative research studies with 672 general population study participants and 28 experts inML, health, and policy focused on Africa to obtain corroborative evidence on the proposed axes of disparities. Our analysis focuses on colonialism as the attribute of interest and examines the interplay between artificial intelligence (AI), health, and colonialism. Among the pre-identified attributes, we found that colonial history, country of origin, and national income level were specific axes of disparities that participants believed would cause an AI system to be biased.However, there was also divergence of opinion between experts and general population participants. Whereas experts generally expressed a shared view about the relevance of colonial history for the development and implementation of AI technologies in Africa, the majority of the general population participants surveyed did not think there was a direct link between AI and colonialism. Based on these findings, we provide practical recommendations for developing fairness-aware ML solutions for health in Africa.
2024-10-28
Proceedings of the 4th ACM Conference on Equity and Access in Algorithms, Mechanisms, and Optimization (publié)
doi.org
arxiv.org
Doctoral Symposium Committee
Anthony Cleve
Christian Lange
Silvia Breu
Manar H. Alalfi
Mario Luca Bernardi
Cornelia Boldyreff
Marco D'Ambros
Simon Denier
Natalia Dragan
Ekwa Duala-Ekoko
Fausto Fasano
Adnane Ghannem
Carmine Gravino
Maen Hammad
Imed Hammouda
Salima Hassaine
Yue Jia
Zhen Ming (Jack) Jiang
Foutse Khomh
Adam Kiezun … (voir 11 de plus)
Jay Kothari
Jonathan Memaitre
Naouel Moha
Rocco Oliveto
Denys Poshyvanyk
Michele Risi
Giuseppe Scanniello
Bonita Sharif
Andrew Sutton
Anis Yousefi
Eugenio Zimeo
Manar H. Alalfi Mario Luca Bernardi Cornelia Boldyreff Anthony Cleve Marco D'Ambros Simon Denier Natalia Dragan Ekwa Duala-Ekoko Fausto Fasa… (voir plus)no Adnane Ghannem Carmine Gravino Maen Hammad Imed Hammouda Salima Hassaine Yue Jia Zhen Ming Jiang Foutse Khomh Adam Kiezun Jay Kothari Jonathan Memaitre Naouel Moha Rocco Oliveto Denys Poshyvanyk Michele Risi Giuseppe Scanniello Bonita Sharif Andrew Sutton Anis Yousefi Eugenio Zimeo
2024-10-27
2024 IEEE 35th International Symposium on Software Reliability Engineering Workshops (ISSREW) (publié)
doi.org
Investigating the Benefits of Nonlinear Action Maps in Data-Driven Teleoperation
Michael Przystupa
Gauthier Gidel
Matthew E. Taylor
Martin Jagersand
Justus Piater
Samuele Tosatto
As robots become more common for both able-bodied individuals and those living with a disability, it is increasingly important that lay peop… (voir plus)le be able to drive multi-degree-of-freedom platforms with low-dimensional controllers. One approach is to use state-conditioned action mapping methods to learn mappings between low-dimensional controllers and high DOF manipulators -- prior research suggests these mappings can simplify the teleoperation experience for users. Recent works suggest that neural networks predicting a local linear function are superior to the typical end-to-end multi-layer perceptrons because they allow users to more easily undo actions, providing more control over the system. However, local linear models assume actions exist on a linear subspace and may not capture nuanced actions in training data. We observe that the benefit of these mappings is being an odd function concerning user actions, and propose end-to-end nonlinear action maps which achieve this property. Unfortunately, our experiments show that such modifications offer minimal advantages over previous solutions. We find that nonlinear odd functions behave linearly for most of the control space, suggesting architecture structure improvements are not the primary factor in data-driven teleoperation. Our results suggest other avenues, such as data augmentation techniques and analysis of human behavior, are necessary for action maps to become practical in real-world applications, such as in assistive robotics to improve the quality of life of people living with w disability.
2024-10-27
ArXiv (prépublication)
doi.org
arxiv.org
In-Simulation Testing of Deep Learning Vision Models in Autonomous Robotic Manipulators
Dmytro Humeniuk
Houssem Ben Braiek
Thomas Reid
Foutse Khomh
2024-10-26
Proceedings of the 39th IEEE/ACM International Conference on Automated Software Engineering (publié)
doi.org
arxiv.org
Parameter Efficient Fine-tuning of Transformer-Based Language Models Using Dataset Pruning
Sayed Mohammadreza Tayaranian Hosseini
Seyyed Hasan Mozafari
James Clark
Brett Meyer
Warren Gross
The widespread use of transformer-based language models is in part owed to their ease of adaptation to various tasks. Fine-tuning is a metho… (voir plus)d of adapting pre-trained language models to a downstream task. The resource requirements for fine-tuning, although still less than pre-training, has been increasing due to the significant growth in the number of parameters of language models. Parameter efficient fine-tuning methods limit the set of model parameters that are updated during fine-tuning, leading to reductions in both memory usage and fine-tuning time. Dataset pruning is another method of efficient fine-tuning which removes training data points, thus reducing training time, while maintaining the evaluation performance of the fine-tuned model. In this work, we apply dataset pruning on top of parameter efficient fine-tuning to further reduce the hardware requirements of the fine-tuning. Our approach benefits from lower memory usage of parameter efficient methods while addressing their long fine-tuning time with dataset pruning. On average, our proposed method uses 22% of the fine-tuning dataset while updating only 0.5% of model parameters. As a result, while achieving an evaluation performance similar to full fine-tuning, our method reduces the peak memory usage of the fine-tuning by 40% and its wall clock time by 83%.
2024-10-26
Asilomar Conference on Signals, Systems and Computers (publié)
doi.org
ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
Siddharth Viswanath
Dhananjay Bhaskar
David R. Johnson
João Felipe Rocha
Egbert Castro
Jackson Grady
Alex T. Grigas
Michael Perlmutter
Corey S. O'Hern
Smita Krishnaswamy
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress… (voir plus) has been made in predicting static folded structures, modeling protein motions on microsecond to millisecond scales remains challenging. To address these challenges, we introduce a novel deep learning architecture, Protein Transformer with Scattering, Attention, and Positional Embedding (ProtSCAPE), which leverages the geometric scattering transform alongside transformer-based attention mechanisms to capture protein dynamics from molecular dynamics (MD) simulations. ProtSCAPE utilizes the multi-scale nature of the geometric scattering transform to extract features from protein structures conceptualized as graphs and integrates these features with dual attention structures that focus on residues and amino acid signals, generating latent representations of protein trajectories. Furthermore, ProtSCAPE incorporates a regression head to enforce temporally coherent latent representations.
2024-10-26
ArXiv (prépublication)
doi.org
arxiv.org
Sharpness-Aware Minimization Scaled by Outlier Normalization for Robust DNNs on In-Memory Computing Accelerators
Sébastien Henwood
Goncalo Mordido
Yvon Savaria
A. Chandar
François Leduc-Primeau
Many deep neural network (DNN) models consume a significant amount of energy at inference time, in large part due to energy consumed by memo… (voir plus)ry access. In-memory computing addresses this problem by eliminating many memory accesses, but exposes model weights to noise and circuit variations. While several methods have been proposed to train DNNs robust to weight noise they typically require knowledge of the noise distribution, or degrade the DNN performance in noiseless setting. In this work, we first show that applying sharpness-aware training, by optimizing for both the loss value and loss sharpness, significantly improves robustness to noisy weights at inference time. Then, we propose a new adaptive sharpness-aware method that conditions the worst-case perturbation of a given weight not only on its magnitude but also on the range of the weight distribution. This is achieved by performing sharpness-aware minimization scaled by outlier normalization (SAMSON). Results on computer-vision benchmarks show that SAMSON increases model robustness to noisy weights without compromising generalization performance in noiseless regimes.
2024-10-26
Asilomar Conference on Signals, Systems and Computers (publié)
doi.org
Brain-like learning with exponentiated gradients
Jonathan Cornford
Roman Pogodin
Arna Ghosh
Kaiwen Sheng
Brendan A. Bicknell
Olivier Codol
Beverley A. Clark
Guillaume Lajoie
Blake A. Richards
Computational neuroscience relies on gradient descent (GD) for training artificial neural network (ANN) models of the brain. The advantage o… (voir plus)f GD is that it is effective at learning difficult tasks. However, it produces ANNs that are a poor phenomenological fit to biology, making them less relevant as models of the brain. Specifically, it violates Dale’s law, by allowing synapses to change from excitatory to inhibitory, and leads to synaptic weights that are not log-normally distributed, contradicting experimental data. Here, starting from first principles of optimisation theory, we present an alternative learning algorithm, exponentiated gradient (EG), that respects Dale’s Law and produces log-normal weights, without losing the power of learning with gradients. We also show that in biologically relevant settings EG outperforms GD, including learning from sparsely relevant signals and dealing with synaptic pruning. Altogether, our results show that EG is a superior learning algorithm for modelling the brain with ANNs.
2024-10-25
bioRxiv (prépublication)
doi.org
Baculovirus Expressing Tumor Growth Factor-β1 (TGFβ1) Nanoshuttle Augments Therapeutic Effects for Vascular Wound Healing: Design and In Vitro Analysis
Paromita Islam
Ahmed Abosalha
Sabrina Schaly
Jacqueline L. Boyajian
Madison Santos
Stephanie Makhlouf
Editha Renesteen
Amal Kassab
Cedrique Shum-Tim
Dominique Shum‐Tim
Satya Prakash
One of the major challenges in vascular tissue regeneration is effective wound healing that can be resolved by an innovative targeted nanosh… (voir plus)uttle that delivers growth factors to blood vessels. This study investigates the production and efficacy of transforming growth factor-β1 (TGFβ1) gene delivery using poly(lactic- co -glycolic acid) (PLGA) baculovirus (BV) nanoshuttles (NSs). They exhibited an encapsulation efficiency of 86.23% ± 0.65% and a negative zeta potential of −29.57 ± 1.27 mV. In vitro studies in human umbilical vein endothelial cells (HUVECs) revealed that a 12 h incubation period optimized virus transduction. The safety and superior intracellular uptake of NSs and BVs in HUVECs were observed. The NSs carrying 100 and 400 MOI exhibited the highest cell proliferation rates in HUVECs. These sustained-release NSs significantly improved vascular cell migration and wound closure compared to free TGFβ1 carrying BV and can be a groundbreaking find in regenerative medicine, cardiovascular diseases, and chronic ulcer conditions.
2024-10-24
ACS Pharmacology & Translational Science (publié)
doi.org
Efficient Biological Data Acquisition through Inference Set Design
Ihor Neporozhnii
Julien Roy
Emmanuel Bengio
Jason Hartford
In drug discovery, highly automated high-throughput laboratories are used to screen a large number of compounds in search of effective drugs… (voir plus). These experiments are expensive, so one might hope to reduce their cost by only experimenting on a subset of the compounds, and predicting the outcomes of the remaining experiments. In this work, we model this scenario as a sequential subset selection problem: we aim to select the smallest set of candidates in order to achieve some desired level of accuracy for the system as a whole. Our key observation is that, if there is heterogeneity in the difficulty of the prediction problem across the input space, selectively obtaining the labels for the hardest examples in the acquisition pool will leave only the relatively easy examples to remain in the inference set, leading to better overall system performance. We call this mechanism inference set design, and propose the use of a confidence-based active learning solution to prune out these challenging examples. Our algorithm includes an explicit stopping criterion that interrupts the acquisition loop when it is sufficiently confident that the system has reached the target performance. Our empirical studies on image and molecular datasets, as well as a real-world large-scale biological assay, show that active learning for inference set design leads to significant reduction in experimental cost while retaining high system performance.
2024-10-24
ArXiv (prépublication)
doi.org
arxiv.org
Investigating Alpha-DaRT Source Daughter Diffusion in Intra-Rectal Animal Models
Mélodie Cyr
Behnaz Behmand
Naim Chabaytah
Joud Babik
Mirta Dumancic
Joanna Li
Guillaume St-Jean
Shirin A. Enger
2024-10-24
Brachytherapy (publié)
doi.org