Publications

E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking
Yang Zhang
Huiyu Cai
Chence Shi
Bozitao Zhong
In silico prediction of the ligand binding pose to a given protein target is a crucial but challenging task in drug discovery. This work foc… (see more)uses on blind flexible self-docking, where we aim to predict the positions, orientations and conformations of docked molecules. Traditional physics-based methods usually suffer from inaccurate scoring functions and high inference cost. Recently, data-driven methods based on deep learning techniques are attracting growing interest thanks to their efficiency during inference and promising performance. These methods usually either adopt a two-stage approach by first predicting the distances between proteins and ligands and then generating the final coordinates based on the predicted distances, or directly predicting the global roto-translation of ligands. In this paper, we take a different route. Inspired by the resounding success of AlphaFold2 for protein structure prediction, we propose E3Bind, an end-to-end equivariant network that iteratively updates the ligand pose. E3Bind models the protein-ligand interaction through careful consideration of the geometric constraints in docking and the local context of the binding site. Experiments on standard benchmark datasets demonstrate the superior performance of our end-to-end trainable model compared to traditional and recently-proposed deep learning methods.
Fooling SHAP with Stealthily Biased Sampling
gabriel laberge
Satoshi Hara
Mario Marchand
SHAP explanations aim at identifying which features contribute the most to the difference in model prediction at a specific input versus a … (see more)background distribution. Recent studies have shown that they can be manipulated by malicious adversaries to produce arbitrary desired explanations. However, existing attacks focus solely on altering the black-box model itself. In this paper, we propose a complementary family of attacks that leave the model intact and manipulate SHAP explanations using stealthily biased sampling of the data points used to approximate expectations w.r.t the background distribution. In the context of fairness audit, we show that our attack can reduce the importance of a sensitive feature when explaining the difference in outcomes between groups, while remaining undetected. These results highlight the manipulability of SHAP explanations and encourage auditors to treat post-hoc explanations with skepticism.
Game theoretical analysis of Kidney Exchange Programs
A General Framework For Proving The Equivariant Strong Lottery Ticket Hypothesis
Damien Ferbach
Christos Tsirigotis
Avishek Joey Bose
Joey Bose
The Strong Lottery Ticket Hypothesis (SLTH) stipulates the existence of a subnetwork within a sufficiently overparameterized (dense) neural … (see more)network that -- when initialized randomly and without any training -- achieves the accuracy of a fully trained target network. Recent works by Da Cunha et. al 2022; Burkholz 2022 demonstrate that the SLTH can be extended to translation equivariant networks -- i.e. CNNs -- with the same level of overparametrization as needed for the SLTs in dense networks. However, modern neural networks are capable of incorporating more than just translation symmetry, and developing general equivariant architectures such as rotation and permutation has been a powerful design principle. In this paper, we generalize the SLTH to functions that preserve the action of the group
Generative Augmented Flow Networks
Ling Pan
Dinghuai Zhang
Longbo Huang
The Generative Flow Network is a probabilistic framework where an agent learns a stochastic policy for object generation, such that the prob… (see more)ability of generating an object is proportional to a given reward function. Its effectiveness has been shown in discovering high-quality and diverse solutions, compared to reward-maximizing reinforcement learning-based methods. Nonetheless, GFlowNets only learn from rewards of the terminal states, which can limit its applicability. Indeed, intermediate rewards play a critical role in learning, for example from intrinsic motivation to provide intermediate feedback even in particularly challenging sparse reward tasks. Inspired by this, we propose Generative Augmented Flow Networks (GAFlowNets), a novel learning framework to incorporate intermediate rewards into GFlowNets. We specify intermediate rewards by intrinsic motivation to tackle the exploration problem in sparse reward environments. GAFlowNets can leverage edge-based and state-based intrinsic rewards in a joint way to improve exploration. Based on extensive experiments on the GridWorld task, we demonstrate the effectiveness and efficiency of GAFlowNet in terms of convergence, performance, and diversity of solutions. We further show that GAFlowNet is scalable to a more complex and large-scale molecule generation domain, where it achieves consistent and significant performance improvement.
GFlowNets and variational inference
Nikolay Malkin
Salem Lahlou
Tristan Deleu
Xu Ji
Edward J Hu
Katie E Everett
Dinghuai Zhang
This paper builds bridges between two families of probabilistic algorithms: (hierarchical) variational inference (VI), which is typically us… (see more)ed to model distributions over continuous spaces, and generative flow networks (GFlowNets), which have been used for distributions over discrete structures such as graphs. We demonstrate that, in certain cases, VI algorithms are equivalent to special cases of GFlowNets in the sense of equality of expected gradients of their learning objectives. We then point out the differences between the two families and show how these differences emerge experimentally. Notably, GFlowNets, which borrow ideas from reinforcement learning, are more amenable than VI to off-policy training without the cost of high gradient variance induced by importance sampling. We argue that this property of GFlowNets can provide advantages for capturing diversity in multimodal target distributions.
How gradient estimator variance and bias impact learning in neural networks
Arna Ghosh
Yuhan Helena Liu
Konrad Paul Kording
There is growing interest in understanding how real brains may approximate gradients and how gradients can be used to train neuromorphic chi… (see more)ps. However, neither real brains nor neuromorphic chips can perfectly follow the loss gradient, so parameter updates would necessarily use gradient estimators that have some variance and/or bias. Therefore, there is a need to understand better how variance and bias in gradient estimators impact learning dependent on network and task properties. Here, we show that variance and bias can impair learning on the training data, but some degree of variance and bias in a gradient estimator can be beneficial for generalization. We find that the ideal amount of variance and bias in a gradient estimator are dependent on several properties of the network and task: the size and activity sparsity of the network, the norm of the gradient, and the curvature of the loss landscape. As such, whether considering biologically-plausible learning algorithms or algorithms for training neuromorphic chips, researchers can analyze these properties to determine whether their approximation to gradient descent will be effective for learning given their network and task properties.
ImageNet-X: Understanding Model Mistakes with Factor of Variation Annotations
Badr Youbi Idrissi
Diane Bouchacourt
Randall Balestriero
Ivan Evtimov
Caner Hazirbas
Nicolas Ballas
Michal Drozdzal
David Lopez-Paz
Mark Ibrahim
Deep learning vision systems are widely deployed across applications where reliability is critical. However, even today's best models can fa… (see more)il to recognize an object when its pose, lighting, or background varies. While existing benchmarks surface examples challenging for models, they do not explain why such mistakes arise. To address this need, we introduce ImageNet-X—a set of sixteen human annotations of factors such as pose, background, or lighting the entire ImageNet-1k validation set as well as a random subset of 12k training images. Equipped with ImageNet-X, we investigate 2,200 current recognition models and study the types of mistakes as a function of model’s (1) architecture, e.g. transformer vs. convolutional, (2) learning paradigm, e.g. supervised vs. self-supervised, and (3) training procedures, e.g., data augmentation. Regardless of these choices, we find models have consistent failure modes across ImageNet-X categories. We also find that while data augmentation can improve robustness to certain factors, they induce spill-over effects to other factors. For example, color-jitter augmentation improves robustness to color and brightness, but surprisingly hurts robustness to pose. Together, these insights suggest to advance the robustness of modern vision models, future research should focus on collecting additional data and understanding data augmentation schemes. Along with these insights, we release a toolkit based on ImageNet-X to spur further study into the mistakes image recognition systems make.
Latent Bottlenecked Attentive Neural Processes
Leo Feng
Hossein Hajimirsadeghi
Mohamed Osama Ahmed
Neural Processes (NPs) are popular methods in meta-learning that can estimate predictive uncertainty on target datapoints by conditioning on… (see more) a context dataset. Previous state-of-the-art method Transformer Neural Processes (TNPs) achieve strong performance but require quadratic computation with respect to the number of context datapoints, significantly limiting its scalability. Conversely, existing sub-quadratic NP variants perform significantly worse than that of TNPs. Tackling this issue, we propose Latent Bottlenecked Attentive Neural Processes (LBANPs), a new computationally efficient sub-quadratic NP variant, that has a querying computational complexity independent of the number of context datapoints. The model encodes the context dataset into a constant number of latent vectors on which self-attention is performed. When making predictions, the model retrieves higher-order information from the context dataset via multiple cross-attention mechanisms on the latent vectors. We empirically show that LBANPs achieve results competitive with the state-of-the-art on meta-regression, image completion, and contextual multi-armed bandits. We demonstrate that LBANPs can trade-off the computational cost and performance according to the number of latent vectors. Finally, we show LBANPs can scale beyond existing attention-based NP variants to larger dataset settings.
Latent State Marginalization as a Low-cost Approach for Improving Exploration
Dinghuai Zhang
Qinqing Zheng
Amy Zhang
Ricky T. Q. Chen
Learning From FM Communications: Toward Accurate, Efficient, All-Terrain Vehicle Localization
Xi Chen
Qiao Xiang
Linghe Kong
Huisan Xu
Vehicle localization service is a fundamental component of intelligent transportation systems. The widely used satellite navigation systems … (see more)perform poorly in urban areas because the lines of sight to satellites are blocked by complex terrain characteristics, e.g., buildings, elevated streets and interchanges. In this paper, we design RadioLoc, a novel system achieving accurate, efficient, all-terrain vehicle localization with two key design points. First, RadioLoc harvests the frequency modulation (FM) signal, which has higher availability than satellite signal in complex terrains, as the signal source for localization. Second, RadioLoc integrates modern machine learning techniques into the processing of FM signals to efficiently learn the accurate vehicle localization in all-terrain environments. We validate the feasibility of FM-based vehicle localization and corresponding challenges and practical issues via field tests (e.g., signal distortion, signal inconsistency and limited in- vehicle radio bandwidth), and develop a series of advanced techniques in RadioLoc to address them, including adaptive batching, frequency sweeping, a novel multipath delay spread filter, a reconstructive PCA denoiser and a tailored FM feature extractor. We then develop a generic, modular localization module in RadioLoc, and design different learning-based 3D position identification algorithms for this module. We implement a prototype of RadioLoc and perform extensive field experiments to evaluate its efficiency and efficacy. Results show that (1) RadioLoc achieves a real-time localization latency of less than 100 milliseconds; (2) RadioLoc achieves a worst-case localization accuracy of 99.6% even in an underground parking lot, and (3) the horizontal error of RadioLoc is only one sixth of a dedicated GPS device even when the vehicle is moving at a high-speed (i.e., 80 km/h) in a complex highway scenario.
Learning From FM Communications: Toward Accurate, Efficient, All-Terrain Vehicle Localization
X. Chen
Qiao Xiang
L. Kong
Huisan Xu
Xuemei Liu
Vehicle localization service is a fundamental component of intelligent transportation systems. The widely used satellite navigation systems … (see more)perform poorly in urban areas because the lines of sight to satellites are blocked by complex terrain characteristics, e.g., buildings, elevated streets and interchanges. In this paper, we design RadioLoc, a novel system achieving accurate, efficient, all-terrain vehicle localization with two key design points. First, RadioLoc harvests the frequency modulation (FM) signal, which has higher availability than satellite signal in complex terrains, as the signal source for localization. Second, RadioLoc integrates modern machine learning techniques into the processing of FM signals to efficiently learn the accurate vehicle localization in all-terrain environments. We validate the feasibility of FM-based vehicle localization and corresponding challenges and practical issues via field tests (e.g., signal distortion, signal inconsistency and limited in- vehicle radio bandwidth), and develop a series of advanced techniques in RadioLoc to address them, including adaptive batching, frequency sweeping, a novel multipath delay spread filter, a reconstructive PCA denoiser and a tailored FM feature extractor. We then develop a generic, modular localization module in RadioLoc, and design different learning-based 3D position identification algorithms for this module. We implement a prototype of RadioLoc and perform extensive field experiments to evaluate its efficiency and efficacy. Results show that (1) RadioLoc achieves a real-time localization latency of less than 100 milliseconds; (2) RadioLoc achieves a worst-case localization accuracy of 99.6% even in an underground parking lot, and (3) the horizontal error of RadioLoc is only one sixth of a dedicated GPS device even when the vehicle is moving at a high-speed (i.e., 80 km/h) in a complex highway scenario.