Publications

Towards Causal Deep Learning for Vulnerability Detection
Md Mahbubur Rahman
Ira Ceka
Chengzhi Mao
Saikat Chakraborty
Baishakhi Ray
Wei Le
Deep learning vulnerability detection has shown promising results in recent years. However, an important challenge that still blocks it from… (see more) being very useful in practice is that the model is not robust under perturbation and it cannot generalize well over the out-of-distribution (OOD) data, e.g., applying a trained model to unseen projects in real world. We hypothesize that this is because the model learned non-robust features, e.g., variable names, that have spurious correlations with labels. When the perturbed and OOD datasets no longer have the same spurious features, the model prediction fails. To address the challenge, in this paper, we introduced causality into deep learning vulnerability detection. Our approach CausalVul consists of two phases. First, we designed novel perturbations to discover spurious features that the model may use to make predictions. Second, we applied the causal learning algorithms, specifically, do-calculus, on top of existing deep learning models to systematically remove the use of spurious features and thus promote causal based prediction. Our results show that CausalVul consistently improved the model accuracy, robustness and OOD performance for all the state-of-the-art models and datasets we experimented. To the best of our knowledge, this is the first work that introduces do calculus based causal learning to software engineering models and shows it's indeed useful for improving the model accuracy, robustness and generalization. Our replication package is located at https://figshare.com/s/0ffda320dcb96c249ef2.
2024-04-12
Proceedings of the IEEE/ACM 46th International Conference on Software Engineering (published)
doi.org
arxiv.org
Deep learning for high-resolution dose prediction in high dose rate brachytherapy for breast cancer treatment.
Sébastien Quetin
Boris Bahoric
Farhad Maleki
Shirin A. Enger
OBJECTIVE Monte Carlo (MC) simulations are the benchmark for accurate radiotherapy dose calculations, notably in patient-specific high dose … (see more)rate brachytherapy (HDR BT), in cases where considering tissue heterogeneities is critical. However, the lengthy computational time limits the practical application of MC simulations. Prior research used Deep Learning (DL) for dose prediction as an alternative to MC simulations. While accurate dose predictions akin to MC were attained, GPU limitations constrained these predictions to large voxels of 3mm × 3mm × 3mm. This study aimed to enable dose predictions as accurate as MC simulations in 1mm × 1mm × 1mm voxels within a clinically acceptable timeframe. Approach: Computed tomography scans of 98 breast cancer patients treated with Iridium-192-based HDR BT were used: 70 for training, 14 for validation, and 14 for testing. A new cropping strategy based on the distance to the seed was devised to reduce the volume size, enabling efficient training of 3D DL models using 1 mm × 1 mm × 1 mm dose grids. Additionally, novel DL architecture with layer-level fusion were proposed to predict MC simulated dose to medium-in-medium (Dm,m). These architectures fuse information from TG-43 dose to water-in-water (Dw,w) with patient tissue composition at the layer-level. Different inputs describing patient body composition were investigated. Main results: The proposed approach demonstrated state-of-the-art performance, on par with the MC Dm,m maps, but 300 times faster. The mean absolute percent error for dosimetric indices between the MC and DL-predicted complete treatment plans was 0.17%±0.15% for the planning target volume V100, 0.30%±0.32% for the skin D2cc, 0.82%±0.79% for the lung D2cc, 0.34%±0.29% for the chest wall D2cc and 1.08%±0.98% for the heart D2cc. Significance: Unlike the time-consuming MC simulations, the proposed novel strategy efficiently converts TG-43 Dw,w maps into precise Dm,m maps at high resolution, enabling clinical integration.
2024-04-11
Physics in Medicine and Biology (published)
doi.org
From the Lab to the Theater: An Unconventional Field Robotics Journey
Ali Imran
Vivek Shankar Vardharajan
Rafael Gomes Braga
Yann Bouteiller
Abdalwhab Abdalwhab
Matthis Di-Giacomo
Alexandra Mercader
Giovanni Beltrame
David St-Onge
2024-04-11
ArXiv (preprint)
doi.org
arxiv.org
Deep Generative Sampling in the Dual Divergence Space: A Data-efficient&Interpretative Approach for Generative AI
Sahil Garg
Anderson Schneider
Anant Raj
Kashif Rasul
Yuriy Nevmyvaka
S. Gopal
Amit Dhurandhar
Guillermo A. Cecchi
Irina Rish
Building on the remarkable achievements in generative sampling of natural images, we propose an innovative challenge, potentially overly amb… (see more)itious, which involves generating samples of entire multivariate time series that resemble images. However, the statistical challenge lies in the small sample size, sometimes consisting of a few hundred subjects. This issue is especially problematic for deep generative models that follow the conventional approach of generating samples from a canonical distribution and then decoding or denoising them to match the true data distribution. In contrast, our method is grounded in information theory and aims to implicitly characterize the distribution of images, particularly the (global and local) dependency structure between pixels. We achieve this by empirically estimating its KL-divergence in the dual form with respect to the respective marginal distribution. This enables us to perform generative sampling directly in the optimized 1-D dual divergence space. Specifically, in the dual space, training samples representing the data distribution are embedded in the form of various clusters between two end points. In theory, any sample embedded between those two end points is in-distribution w.r.t. the data distribution. Our key idea for generating novel samples of images is to interpolate between the clusters via a walk as per gradients of the dual function w.r.t. the data dimensions. In addition to the data efficiency gained from direct sampling, we propose an algorithm that offers a significant reduction in sample complexity for estimating the divergence of the data distribution with respect to the marginal distribution. We provide strong theoretical guarantees along with an extensive empirical evaluation using many real-world datasets from diverse domains, establishing the superiority of our approach w.r.t. state-of-the-art deep learning methods.
2024-04-10
ArXiv (preprint)
doi.org
arxiv.org
Zero-shot Logical Query Reasoning on any Knowledge Graph
Mikhail Galkin
Jincheng Zhou
Bruno Ribeiro
Jian Tang
Zhaocheng Zhu
Complex logical query answering (CLQA) in knowledge graphs (KGs) goes beyond simple KG completion and aims at answering compositional querie… (see more)s comprised of multiple projections and logical operations. Existing CLQA methods that learn parameters bound to certain entity or relation vocabularies can only be applied to the graph they are trained on which requires substantial training time before being deployed on a new graph. Here we present UltraQuery, an inductive reasoning model that can zero-shot answer logical queries on any KG. The core idea of UltraQuery is to derive both projections and logical operations as vocabulary-independent functions which generalize to new entities and relations in any KG. With the projection operation initialized from a pre-trained inductive KG reasoning model, UltraQuery can solve CLQA on any KG even if it is only finetuned on a single dataset. Experimenting on 23 datasets, UltraQuery in the zero-shot inference mode shows competitive or better query answering performance than best available baselines and sets a new state of the art on 14 of them.
2024-04-10
ArXiv (preprint)
doi.org
arxiv.org
AI healthcare research: Pioneering iSMART Lab
Narges Armanfard
Dr Narges Armanfard, Professor, talks us through the AI healthcare research at McGill University which is spearheading a groundbreaking init… (see more)iative – the iSMART Lab. Access to high-quality healthcare is not just a fundamental human right; it is the bedrock of our societal wellbeing, with the crucial roles played by doctors, nurses, and hospitals. Yet, healthcare systems globally face mounting challenges, particularly from aging populations. Dr Narges Armanfard, affiliated with McGill University and Mila Quebec AI Institute in Montreal, Canada, has spearheaded a groundbreaking initiative – the iSMART Lab. This laboratory represents a revolutionary leap into the future of healthcare, with its pioneering research in AI for health applications garnering significant attention. Renowned for its innovative integration of AI across diverse domains, iSMART Lab stands at the forefront of harnessing Artificial Intelligence to elevate and streamline health services.
2024-04-09
Open Access Government (published)
doi.org
Interpretable Machine Learning for Finding Intermediate-mass Black Holes
Mario Pasquato
Piero Trevisan
Abbas Askar
Pablo Lemos
Gaia Carenini
Michela Mapelli
Yashar Hezaveh
2024-04-09
The Astrophysical Journal (published)
doi.org
arxiv.org
LLM2Vec: Large Language Models Are Secretly Powerful Text Encoders
Parishad BehnamGhader
Vaibhav Adlakha
Marius Mosbach
Dzmitry Bahdanau
Nicolas Chapados
Siva Reddy
2024-04-09
ArXiv (preprint)
doi.org
arxiv.org
Structure-function coupling and decoupling during movie-watching and resting-state: Novel insights bridging EEG and structural imaging
Venkatesh Subramani
Giulia Lioi
Karim Jerbi
Nicolas Farrugia
2024-04-09
bioRxiv (preprint)
doi.org
Learning Heuristics for Transit Network Design and Improvement with Deep Reinforcement Learning
Andrew Holliday
A. El-geneidy
Gregory Dudek
2024-04-08
ArXiv (preprint)
doi.org
arxiv.org
Learning Minimal NAP Specifications for Neural Network Verification
Chuqin Geng
Zhaoyue Wang
Haolin Ye
Saifei Liao
Xujie Si
Specifications play a crucial role in neural network verification. They define the precise input regions we aim to verify, typically represe… (see more)nted as L-infinity norm balls. While recent research suggests using neural activation patterns (NAPs) as specifications for verifying unseen test set data, it focuses on computing the most refined NAPs, often limited to very small regions in the input space. In this paper, we study the following problem: Given a neural network, find a minimal (coarsest) NAP that is sufficient for formal verification of the network's robustness. Finding the minimal NAP specification not only expands verifiable bounds but also provides insights into which neurons contribute to the model's robustness. To address this problem, we propose several exact and approximate approaches. Our exact approaches leverage the verification tool to find minimal NAP specifications in either a deterministic or statistical manner. Whereas the approximate methods efficiently estimate minimal NAPs using adversarial examples and local gradients, without making calls to the verification tool. This allows us to inspect potential causal links between neurons and the robustness of state-of-the-art neural networks, a task for which existing verification frameworks fail to scale. Our experimental results suggest that minimal NAP specifications require much smaller fractions of neurons compared to the most refined NAP specifications, yet they can significantly expand the verifiable boundaries to several orders of magnitude larger.
2024-04-06
ArXiv (preprint)
doi.org
arxiv.org
SAT-DIFF: A Tree Diffing Framework Using SAT Solving
Chuqin Geng
Haolin Ye
Yihan Zhang
Brigitte Pientka
Xujie Si
Computing differences between tree-structured data is a critical but challenging problem in software analysis. In this paper, we propose a n… (see more)ovel tree diffing approach called SatDiff, which reformulates the structural diffing problem into a MaxSAT problem. By encoding the necessary transformations from the source tree to the target tree, SatDiff generates correct, minimal, and type safe low-level edit scripts with formal guarantees. We then synthesize concise high-level edit scripts by effectively merging low-level edits in the appropriate topological order. Our empirical results demonstrate that SatDiff outperforms existing heuristic-based approaches by a significant margin in terms of conciseness while maintaining a reasonable runtime.
2024-04-06
ArXiv (preprint)
doi.org
arxiv.org