Author name cluster

Kilian Fatras

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

9 papers

2 author rows

TMLR Journal 2025 Journal Article

Slicing Unbalanced Optimal Transport

Clément Bonet
Kimia Nadjahi
Thibault Sejourne
Kilian Fatras
Nicolas Courty

Optimal transport (OT) is a powerful framework to compare probability measures, a fundamental task in many statistical and machine learning problems. Substantial advances have been made in designing OT variants which are either computationally and statistically more efficient or robust. Among them, sliced OT distances have been extensively used to mitigate optimal transport's cubic algorithmic complexity and curse of dimensionality. In parallel, unbalanced OT was designed to allow comparisons of more general positive measures, while being more robust to outliers. In this paper, we bridge the gap between those two concepts and develop a general framework for efficiently comparing positive measures. We notably formulate two different versions of sliced unbalanced OT, and study the associated topology and statistical properties. We then develop a GPU-friendly Frank-Wolfe like algorithm to compute the corresponding loss functions, and show that the resulting methodology is modular as it encompasses and extends prior related work. We finally conduct an empirical analysis of our loss functions and methodology on both synthetic and real datasets, to illustrate their computational efficiency, relevance and applicability to real-world scenarios including geophysical data.

PDF Details

TMLR Journal 2024 Journal Article

Improving and generalizing flow-based generative models with minibatch optimal transport

Alexander Tong
Kilian Fatras
Nikolay Malkin
Guillaume Huguet
Yanlei Zhang
Jarrid Rector-Brooks
Guy Wolf
Yoshua Bengio

Continuous normalizing flows (CNFs) are an attractive generative modeling technique, but they have been held back by limitations in their simulation-based maximum likelihood training. We introduce the generalized conditional flow matching (CFM) technique, a family of simulation-free training objectives for CNFs. CFM features a stable regression objective like that used to train the stochastic flow in diffusion models but enjoys the efficient inference of deterministic flow models. In contrast to both diffusion models and prior CNF training algorithms, CFM does not require the source distribution to be Gaussian or require evaluation of its density. A variant of our objective is optimal transport CFM (OT-CFM), which creates simpler flows that are more stable to train and lead to faster inference, as evaluated in our experiments. Furthermore, we show that when the true OT plan is available, our OT-CFM method approximates dynamic OT. Training CNFs with CFM improves results on a variety of conditional and unconditional generation tasks, such as inferring single cell dynamics, unsupervised image translation, and Schrödinger bridge inference. The Python code is available at https://github.com/atong01/conditional-flow-matching.

PDF Details

ICML Conference 2024 Conference Paper

No Wrong Turns: The Simple Geometry Of Neural Networks Optimization Paths

Charles Guille-Escuret
Hiroki Naganuma
Kilian Fatras
Ioannis Mitliagkas

Understanding the optimization dynamics of neural networks is necessary for closing the gap between theory and practice. Stochastic first-order optimization algorithms are known to efficiently locate favorable minima in deep neural networks. This efficiency, however, contrasts with the non-convex and seemingly complex structure of neural loss landscapes. In this study, we delve into the fundamental geometric properties of sampled gradients along optimization paths. We focus on two key quantities, the restricted secant inequality and error bound, as well as their ratio γ, which hold high significance for first-order optimization. Our analysis reveals that these quantities exhibit predictable, consistent behavior throughout training, despite the stochasticity induced by sampling minibatches. Our findings suggest that not only do optimization trajectories never encounter significant obstacles, but they also maintain stable dynamics during the majority of training. These observed properties are sufficiently expressive to theoretically guarantee linear convergence and prescribe learning rate schedules mirroring empirical practices. We conduct our experiments on image classification, semantic segmentation and language modeling across different batch sizes, network architectures, datasets, optimizers, and initialization seeds. We discuss the impact of each factor. Our work provides novel insights into the properties of neural network loss functions, and opens the door to theoretical frameworks more relevant to prevalent practice.

Details

TMLR Journal 2024 Journal Article

PopulAtion Parameter Averaging (PAPA)

Alexia Jolicoeur-Martineau
Emy Gervais
Kilian Fatras
Yan Zhang
Simon Lacoste-Julien

Ensemble methods combine the predictions of multiple models to improve performance, but they require significantly higher computation costs at inference time. To avoid these costs, multiple neural networks can be combined into one by averaging their weights. However, this usually performs significantly worse than ensembling. Weight averaging is only beneficial when different enough to benefit from combining them, but similar enough to average well. Based on this idea, we propose PopulAtion Parameter Averaging (PAPA): a method that combines the generality of ensembling with the efficiency of weight averaging. PAPA leverages a population of diverse models (trained on different data orders, augmentations, and regularizations) while slowly pushing the weights of the networks toward the population average of the weights. We also propose PAPA variants (PAPA-all, and PAPA-2) that average weights rarely rather than continuously; all methods increase generalization, but PAPA tends to perform best. PAPA reduces the performance gap between averaging and ensembling, increasing the average accuracy of a population of models by up to 0.8% on CIFAR-10, 1.9% on CIFAR-100, and 1.6% on ImageNet when compared to training independent (non-averaged) models.

PDF Details

ICLR Conference 2024 Conference Paper

SE(3)-Stochastic Flow Matching for Protein Backbone Generation

Avishek Joey Bose
Tara Akhound-Sadegh
Guillaume Huguet
Kilian Fatras
Jarrid Rector-Brooks
Cheng-Hao Liu
Andrei Cristian Nica
Maksym Korablyov

The computational design of novel protein structures has the potential to impact numerous scientific disciplines greatly. Toward this goal, we introduce \foldflow, a series of novel generative models of increasing modeling power based on the flow-matching paradigm over $3\mathrm{D}$ rigid motions---i.e. the group $\mathrm{SE(3)}$---enabling accurate modeling of protein backbones. We first introduce $\text{FoldFlow-Base}$, a simulation-free approach to learning deterministic continuous-time dynamics and matching invariant target distributions on $\mathrm{SE(3)}$. We next accelerate training by incorporating Riemannian optimal transport to create $\text{FoldFlow-OT}$, leading to the construction of both more simple and stable flows. Finally, we design \foldflowsfm, coupling both Riemannian OT and simulation-free training to learn stochastic continuous-time dynamics over $\mathrm{SE(3)}$. Our family of $\text{FoldFlow}$, generative models offers several key advantages over previous approaches to the generative modeling of proteins: they are more stable and faster to train than diffusion-based approaches, and our models enjoy the ability to map any invariant source distribution to any invariant target distribution over $\mathrm{SE(3)}$. Empirically, we validate $\text{FoldFlow}$, on protein backbone generation of up to $300$ amino acids leading to high-quality designable, diverse, and novel samples.

Details

NeurIPS Conference 2024 Conference Paper

Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Generation

Guillaume Huguet
James Vuckovic
Kilian Fatras
Eric Thibodeau-Laufer
Pablo Lemos
Riashat Islam
Cheng-Hao Liu
Jarrid Rector-Brooks

Proteins are essential for almost all biological processes and derive their diverse functions from complex $3 \rm D$ structures, which are in turn determined by their amino acid sequences. In this paper, we exploit the rich biological inductive bias of amino acid sequences and introduce FoldFlow++, a novel sequence-conditioned $\text{SE}(3)$-equivariant flow matching model for protein structure generation. FoldFlow++ presents substantial new architectural features over the previous FoldFlow family of models including a protein large language model to encode sequence, a new multi-modal fusion trunk that combines structure and sequence representations, and a geometric transformer based decoder. To increase diversity and novelty of generated samples -- crucial for de-novo drug design -- wetrain FoldFlow++ at scale on a new dataset that is an order of magnitude larger than PDB datasets of prior works, containing both known proteins in PDB and high-quality synthetic structures achieved through filtering. We further demonstrate the ability to align FoldFlow++ to arbitrary rewards, e. g. increasing secondary structures diversity, by introducing a Reinforced Finetuning (ReFT) objective. We empirically observe that FoldFlow++ outperforms previous state-of-the-art protein structure-based generative models, improving over RFDiffusion in terms of unconditional generation across all metrics including designability, diversity, and novelty across all protein lengths, as well as exhibiting generalization on the task of equilibrium conformation sampling. Finally, we demonstrate that a fine-tuned FoldFlow++ makes progress on challenging conditional design tasks such as designing scaffolds for the VHH nanobody.

PDF Details DOI

TMLR Journal 2023 Journal Article

A Reproducible and Realistic Evaluation of Partial Domain Adaptation Methods

Tiago Salvador
Kilian Fatras
Ioannis Mitliagkas
Adam M Oberman

Unsupervised Domain Adaptation (UDA) aims at classifying unlabeled target images leveraging source labeled ones. In the case of an extreme label shift scenario between the source and target domains, where we have extra source classes not present in the target domain, the UDA problem becomes a harder problem called Partial Domain Adaptation (PDA). While different methods have been developed to solve the PDA problem, most successful algorithms use model selection strategies that rely on target labels to find the best hyper-parameters and/or models along training. These strategies violate the main assumption in PDA: only unlabeled target domain samples are available. In addition, there are also experimental inconsistencies between developed methods - different architectures, hyper-parameter tuning, number of runs - yielding unfair comparisons. The main goal of this work is to provide a realistic evaluation of PDA methods under different model selection strategies and a consistent evaluation protocol. We evaluate 6 state-of-the-art PDA algorithms on 2 different real-world datasets using 7 different model selection strategies. Our two main findings are: (i) without target labels for model selection, the accuracy of the methods decreases up to 30 percentage points; (ii) only one method and model selection pair performs well on both datasets. Experiments were performed with our PyTorch framework, BenchmarkPDA, which we open source.

PDF Details

JMLR Journal 2021 Journal Article

POT: Python Optimal Transport

Rémi Flamary
Nicolas Courty
Alexandre Gramfort
Mokhtar Z. Alaya
Aurélie Boisbunon
Stanislas Chambon
Laetitia Chapel
Adrien Corenflos

Optimal transport has recently been reintroduced to the machine learning community thanks in part to novel efficient optimization procedures allowing for medium to large scale applications. We propose a Python toolbox that implements several key optimal transport ideas for the machine learning community. The toolbox contains implementations of a number of founding works of OT for machine learning such as Sinkhorn algorithm and Wasserstein barycenters, but also provides generic solvers that can be used for conducting novel fundamental research. This toolbox, named POT for Python Optimal Transport, is open source with an MIT license. [abs] [ pdf ][ bib ] [ code ] &copy JMLR 2021. ( edit, beta )

PDF Details

ICML Conference 2021 Conference Paper

Unbalanced minibatch Optimal Transport; applications to Domain Adaptation

Kilian Fatras
Thibault Séjourné
Rémi Flamary
Nicolas Courty

Optimal transport distances have found many applications in machine learning for their capacity to compare non-parametric probability distributions. Yet their algorithmic complexity generally prevents their direct use on large scale datasets. Among the possible strategies to alleviate this issue, practitioners can rely on computing estimates of these distances over subsets of data, i. e. minibatches. While computationally appealing, we highlight in this paper some limits of this strategy, arguing it can lead to undesirable smoothing effects. As an alternative, we suggest that the same minibatch strategy coupled with unbalanced optimal transport can yield more robust behaviors. We discuss the associated theoretical properties, such as unbiased estimators, existence of gradients and concentration bounds. Our experimental study shows that in challenging problems associated to domain adaptation, the use of unbalanced optimal transport leads to significantly better results, competing with or surpassing recent baselines.

Details