Publications

Structure-Informed Protein Language Model
Zuobai Zhang
Jiarui Lu
Vijil Chenthamarakshan
Aurelie Lozano
Payel Das
Jian Tang
Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. Ho… (voir plus)wever, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights will be made available upon acceptance.
2024-03-04
ICLR.cc/2024/Workshop/GEM (poster)
openreview.net
openreview.net
Towards DNA-Encoded Library Generation with GFlowNets
Michał Koziarski
Mohammed Abukalam
Vedant Shah
Louis Vaillancourt
Doris Alexandra Schuetz
Moksh J. Jain
Almer M. van der Sloot
Mathieu Bourgey
Anne Marinier
Yoshua Bengio
2024-03-04
ICLR.cc/2024/Workshop/GEM (poster)
doi.org
openreview.net
Communicating Study Design Trade-offs in Software Engineering
Martin P. Robillard
Deeksha M. Arya
Neil Ernst
Jin Guo
Maxime Lamothe
Mathieu Nassif
Nicole Novielli
Alexander Serebrenik
Igor Steinmacher
Klaas-Jan Stol
2024-03-02
ACM Transactions on Software Engineering and Methodology (publié)
doi.org
A Compositional Typed Semantics for Universal Dependencies
Laurestine Bradford
Timothy John O'donnell
Siva Reddy
2024-03-02
ArXiv (prépublication)
doi.org
arxiv.org
Harmony in Diversity: Merging Neural Networks with Canonical Correlation Analysis
Stefan Horoi
Albert Manuel Orozco Camacho
Eugene Belilovsky
Guy Wolf
Ensembling multiple models enhances predictive performance by utilizing the varied learned features of the different models but incurs signi… (voir plus)ficant computational and storage costs. Model fusion, which combines parameters from multiple models into one, aims to mitigate these costs but faces practical challenges due to the complex, non-convex nature of neural network loss landscapes, where learned minima are often separated by high loss barriers. Recent works have explored using permutations to align network features, reducing the loss barrier in parameter space. However, permutations are restrictive since they assume a one-to-one mapping between the different models' neurons exists. We propose a new model merging algorithm, CCA Merge, which is based on Canonical Correlation Analysis and aims to maximize the correlations between linear combinations of the model features. We show that our method of aligning models leads to better performances than past methods when averaging models trained on the same, or differing data splits. We also extend this analysis into the harder many models setting where more than 2 models are merged, and we find that CCA Merge works significantly better in this setting than past methods.
2024-03-02
ICLR.cc/2024/Workshop/Re-Align (poster)
openreview.net
openreview.net
Latent Idiom Recognition for a Minimalist Functional Array Language Using Equality Saturation
Jonathan Van Der Cruysse
Christophe Dubach
Accelerating programs is typically done by recognizing code idioms matching high-performance libraries or hardware interfaces. However, reco… (voir plus)gnizing such idioms automatically is challenging. The idiom recognition machinery is difficult to write and requires expert knowledge. In addition, slight variations in the input program might hide the idiom and defeat the recognizer. This paper advocates for the use of a minimalist functional array language supporting a small, but expressive, set of operators. The minimalist design leads to a tiny sets of rewrite rules, which encode the language semantics. Crucially, the same minimalist language is also used to encode idioms. This removes the need for hand-crafted analysis passes, or for having to learn a complex domain-specific language to define the idioms. Coupled with equality saturation, this approach is able to match the core functions from the BLAS and PyTorch libraries on a set of computational kernels. Compared to reference C kernel implementations, the approach produces a geometric mean speedup of 1.46× for C programs using BLAS, when generating such programs from the high-level minimalist language.
2024-03-02
2024 IEEE/ACM International Symposium on Code Generation and Optimization (CGO) (publié)
doi.org
arxiv.org
Learning and Aligning Structured Random Feature Networks
Vivian White
Muawiz Sajjad Chaudhary
Guy Wolf
Guillaume Lajoie
Kameron Decker Harris
Artificial neural networks (ANNs) are considered ``black boxes'' due to the difficulty of interpreting their learned weights. While choosin… (voir plus)g the best features is not well understood, random feature networks (RFNs) and wavelet scattering ground some ANN learning mechanisms in function space with tractable mathematics. Meanwhile, the genetic code has evolved over millions of years, shaping the brain to devlop variable neural circuits with reliable structure that resemble RFNs. We explore a similar approach, embedding neuro-inspired, wavelet-like weights into multilayer RFNs. These can outperform scattering and have kernels that describe their function space at large width. We build learnable and deeper versions of these models where we can optimize separate spatial and channel covariances of the convolutional weight distributions. We find that these networks can perform comparatively with conventional ANNs while dramatically reducing the number of trainable parameters. Channel covariances are most influential, and both weight and activation alignment are needed for classification performance. Our work outlines how neuro-inspired configurations may lead to better performance in key cases and offers a potentially tractable reduced model for ANN learning.
2024-03-02
ICLR.cc/2024/Workshop/Re-Align (poster)
openreview.net
openreview.net
Learning and Aligning Structured Random Feature Networks
Vivian White
Muawiz Sajjad Chaudhary
Guy Wolf
Guillaume Lajoie
Kameron Decker Harris
Artificial neural networks (ANNs) are considered "black boxes'' due to the difficulty of interpreting their learned weights. While choosing… (voir plus) the best features is not well understood, random feature networks (RFNs) and wavelet scattering ground some ANN learning mechanisms in function space with tractable mathematics. Meanwhile, the genetic code has evolved over millions of years, shaping the brain to develop variable neural circuits with reliable structure that resemble RFNs. We explore a similar approach, embedding neuro-inspired, wavelet-like weights into multilayer RFNs. These can outperform scattering and have kernels that describe their function space at large width. We build learnable and deeper versions of these models where we can optimize separate spatial and channel covariances of the convolutional weight distributions. We find that these networks can perform comparatively with conventional ANNs while dramatically reducing the number of trainable parameters. Channel covariances are most influential, and both weight and activation alignment are needed for classification performance. Our work outlines how neuro-inspired configurations may lead to better performance in key cases and offers a potentially tractable reduced model for ANN learning.
2024-03-02
ICLR.cc/2024/Workshop/Re-Align (poster)
openreview.net
openreview.net
Quality of Service-Constrained Online Routing in High Throughput Satellites
Olivier Bélanger
Olfa Ben Yahia
Stéphane Martel
Antoine Lesage-Landry
Gunes Karabulut Kurt
High throughput satellites (HTSs) outpace traditional satellites due to their multi-beam transmission. The rise of low Earth orbit mega cons… (voir plus)tellations amplifies HTS data rate demands to terabits/second with acceptable latency. This surge in data rate necessitates multiple modems, often exceeding single device capabilities. Consequently, satellites employ several processors, forming a complex packet-switch network. This can lead to potential internal congestion and challenges in adhering to strict quality of service (QoS) constraints. While significant research exists on constellation-level routing, a literature gap remains on the internal routing within a single HTS. The intricacy of this internal network architecture presents a significant challenge to achieve high data rates. This paper introduces an online optimal flow allocation and scheduling method for HTSs. The problem is presented as a multi-commodity flow instance with different priority data streams. An initial full time horizon model is proposed as a benchmark. We apply a model predictive control (MPC) approach to enable adaptive routing based on current information and the forecast within the prediction time horizon while allowing for deviation of the latter. Importantly, MPC is inherently suited to handle uncertainty in incoming flows. Our approach minimizes the packet loss by optimally and adaptively managing the priority queue schedulers and flow exchanges between satellite processing modules. Central to our method is a routing model focusing on optimal priority scheduling to enhance data rates and maintain QoS. The model's stages are critically evaluated, and results are compared to traditional methods via numerical simulations. Through simulations, our method demonstrates performance nearly on par with the hindsight optimum, showcasing its efficiency and adaptability in addressing satellite communication challenges.
2024-03-02
2024 IEEE Aerospace Conference (publié)
doi.org
arxiv.org
ADMM-Based Hierarchical Single-Loop Framework for EV Charging Scheduling Considering Power Flow Constraints
Sina Kiani
Keyhan Sheshyekani
Hanane Dagdougui
This article presents a three-layer hierarchical distributed framework for optimal electric vehicle charging scheduling (EVCS). The proposed… (voir plus) hierarchical EVCS structure includes a distribution system operator (DSO) at the top layer, electric vehicle aggregators (EVAs) at the middle layer, and electric vehicles (EVs) charging stations at the bottom layer. A single-loop iterative algorithm is developed to solve the EVCS problem by combining the alternating direction method of multipliers (ADMM) and the distribution line power flow model (DistFlow). Using the single-loop structure, the primal variables of all agents are updated simultaneously at every iteration resulting in a reduced number of iterations and faster convergence. The developed framework is employed to provide charging cost minimization at the EV charging stations level, peak load shaving at the EVAs level, and voltage regulation at the DSO level. In order to further improve the performance of the optimization framework, a neural network-based load forecasting model is implemented to include the uncertainties related to non-EV residential load demand. The efficiency and the optimality of the proposed EVCS framework are evaluated through numerical simulations, conducted for a modified IEEE 13 bus test feeder with different EV penetration levels.
2024-03-01
IEEE Transactions on Transportation Electrification (publié)
doi.org
Decoding face recognition abilities in the human brain
Simon Faghel-Soubeyrand
Meike Ramon
Eva Bamps
Matteo Zoia
Jessica Woodhams
Anne-Raphaelle Richoz
Roberto Caldara
Frédéric Gosselin
Ian Charest
Why are some individuals better at recognising faces? Uncovering the neural mechanisms supporting face recognition ability has proven elusiv… (voir plus)e. To tackle this challenge, we used a multi-modal data-driven approach combining neuroimaging, computational modelling, and behavioural tests. We recorded the high-density electroencephalographic brain activity of individuals with extraordinary face recognition abilities—super-recognisers—and typical recognisers in response to diverse visual stimuli. Using multivariate pattern analyses, we decoded face recognition abilities from 1 second of brain activity with up to 80% accuracy. To better understand the mechanisms subtending this decoding, we compared computations in the brains of our participants with those in artificial neural network models of vision and semantics, as well as with those involved in human judgments of shape and meaning similarity. Compared to typical recognisers, we found stronger associations between early brain computations of super-recognisers and mid-level computations of vision models as well as shape similarity judgments. Moreover, we found stronger associations between late brain representations of super-recognisers and computations of the artificial semantic model as well as meaning similarity judgments. Overall, these results indicate that important individual variations in brain processing, including neural computations extending beyond purely visual processes, support differences in face recognition abilities. They provide the first empirical evidence for an association between semantic computations and face recognition abilities. We believe that such multi-modal data-driven approaches will likely play a critical role in further revealing the complex nature of idiosyncratic face recognition in the human brain. Significance The ability to robustly recognise faces is crucial to our success as social beings. Yet, we still know little about the brain mechanisms allowing some individuals to excel at face recognition. This study builds on a sizeable neural dataset measuring the brain activity of individuals with extraordinary face recognition abilities—super-recognisers—to tackle this challenge. Using state-of-the-art computational methods, we show robust prediction of face recognition abilities in single individuals from a mere second of brain activity, and revealed specific brain computations supporting individual differences in face recognition ability. Doing so, we provide direct empirical evidence for an association between semantic computations and face recognition abilities in the human brain—a key component of prominent face recognition models.
2024-03-01
PNAS Nexus (publié)
doi.org
FedSwarm: An Adaptive Federated Learning Framework for Scalable AIoT
Haizhou Du
Chengdong Ni
Chaoqian Cheng
Qiao Xiang
Xi Chen
Xue (Steve) Liu
Federated learning (FL) is a key solution for datadriven the Artificial Intelligence of Things (AIoT). Although much progress has been made,… (voir plus) scalability remains a core challenge for real-world FL deployments. Existing solutions either suffer from accuracy loss or do not fully address the connectivity dynamicity of FL systems. In this article, we tackle the scalability issue with a novel, adaptive FL framework called FedSwarm, which improves system scalability for AIoT by deploying multiple collaborative edge servers. FedSwarm has two novel features: 1) adaptiveness on the number of local updates and 2) dynamicity of the synchronization between edge devices and edge servers. We formulate FedSwarm as a local update adaptation and perdevice dynamic server selection problem and prove FedSwarm‘s convergence bound. We further design a control mechanism consisting of a learning-based algorithm for collaboratively providing local update adaptation on the servers’ side and a bonus-based strategy for spurring dynamic per-device server selection on the devices’ side. Our extensive evaluation shows that FedSwarm significantly outperforms other studies with better scalability, lower energy consumption, and higher model accuracy.
2024-03-01
IEEE Internet of Things Journal (publié)
doi.org