arXiv subjects

Thomas Laurent

Publications and source records attributed to Thomas Laurent.

At least 37 records · Page 2Linked to original sources

arXiv2022

Benchmarking Graph Neural Networks

In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.

cs.LG↗

arXiv2022

Learning to Untangle Genome Assembly with Graph Convolutional Networks

A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered various tools and performed laborious manual inspection to achieve the first gapless genome sequence. However, such method can hardly be used as a general approach to assemble different genomes, especially when the assembly speed is critical given the large amount of data. In this work, we explore a different approach to the central part of the genome assembly task that consists of untangling a large assembly graph from which a genomic sequence needs to be reconstructed. Our main motivation is to reduce human-engineered heuristics and use deep learning to develop more generalizable reconstruction techniques. Precisely, we introduce a new learning framework to train a graph convolutional network to resolve assembly graphs by finding a correct path through them. The training is supervised with a dataset generated from the resolved CHM13 human sequence and tested on assembly graphs built using real human PacBio HiFi reads. Experimental results show that a model, trained on simulated graphs generated solely from a single chromosome, is able to remarkably resolve all other chromosomes. Moreover, the model outperforms hand-crafted heuristics from a state-of-the-art \textit{de novo} assembler on the same graphs. Reconstructed chromosomes with graph networks are more accurate on nucleotide level, report lower number of contigs, higher genome reconstructed fraction and NG50/NGA50 assessment metrics.

q-bio.GN↗

arXiv2022

Learning the Travelling Salesperson Problem Requires Rethinking Generalization

End-to-end training of neural network solvers for graph combinatorial optimization problems such as the Travelling Salesperson Problem (TSP) have seen a surge of interest recently, but remain intractable and inefficient beyond graphs with few hundreds of nodes. While state-of-the-art learning-driven approaches for TSP perform closely to classical solvers when trained on trivially small sizes, they are unable to generalize the learnt policy to larger instances at practical scales. This work presents an end-to-end neural combinatorial optimization pipeline that unifies several recent papers in order to identify the inductive biases, model architectures and learning algorithms that promote generalization to instances larger than those seen in training. Our controlled experiments provide the first principled investigation into such zero-shot generalization, revealing that extrapolating beyond training data requires rethinking the neural combinatorial optimization pipeline, from network layers and learning paradigms to evaluation protocols. Additionally, we analyze recent advances in deep learning for routing problems through the lens of our pipeline and provide new directions to stimulate future research.

cs.LG↗

arXiv2022

The Forgotten Margins of AI Ethics

How has recent AI Ethics literature addressed topics such as fairness and justice in the context of continued social and structural power asymmetries? We trace both the historical roots and current landmark work that have been shaping the field and categorize these works under three broad umbrellas: (i) those grounded in Western canonical philosophy, (ii) mathematical and statistical methods, and (iii) those emerging from critical data/algorithm/information studies. We also survey the field and explore emerging trends by examining the rapidly growing body of literature that falls under the broad umbrella of AI Ethics. To that end, we read and annotated peer-reviewed papers published over the past four years in two premier conferences: FAccT and AIES. We organize the literature based on an annotation scheme we developed according to three main dimensions: whether the paper deals with concrete applications, use-cases, and/or people's lived experience; to what extent it addresses harmed, threatened, or otherwise marginalized groups; and if so, whether it explicitly names such groups. We note that although the goals of the majority of FAccT and AIES papers were often commendable, their consideration of the negative impacts of AI on traditionally marginalized groups remained shallow. Taken together, our conceptual analysis and the data from annotated papers indicate that the field would benefit from an increased focus on ethical analysis grounded in concrete use-cases, people's experiences, and applications as well as from approaches that are sensitive to structural and historical power asymmetries.

cs.CY↗

arXiv2022

Combining Reinforcement Learning and Optimal Transport for the Traveling Salesman Problem

The traveling salesman problem is a fundamental combinatorial optimization problem with strong exact algorithms. However, as problems scale up, these exact algorithms fail to provide a solution in a reasonable time. To resolve this, current works look at utilizing deep learning to construct reasonable solutions. Such efforts have been very successful, but tend to be slow and compute intensive. This paper exemplifies the integration of entropic regularized optimal transport techniques as a layer in a deep reinforcement learning network. We show that we can construct a model capable of learning without supervision and inferences significantly faster than current autoregressive approaches. We also empirically evaluate the benefits of including optimal transport algorithms within deep learning models to enforce assignment constraints during end-to-end training.

cs.LG↗

arXiv2022

Graph Neural Networks with Learnable Structural and Positional Representations

Graph neural networks (GNNs) have become the standard learning architectures for graphs. GNNs have been applied to numerous domains ranging from quantum chemistry, recommender systems to knowledge graphs and natural language processing. A major issue with arbitrary graphs is the absence of canonical positional information of nodes, which decreases the representation power of GNNs to distinguish e.g. isomorphic nodes and other graph symmetries. An approach to tackle this issue is to introduce Positional Encoding (PE) of nodes, and inject it into the input layer, like in Transformers. Possible graph PE are Laplacian eigenvectors. In this work, we propose to decouple structural and positional representations to make easy for the network to learn these two essential properties. We introduce a novel generic architecture which we call LSPE (Learnable Structural and Positional Encodings). We investigate several sparse and fully-connected (Transformer-like) GNNs, and observe a performance increase for molecular datasets, from 1.79% up to 64.14% when considering learnable PE for both GNN classes.

cs.LG↗

arXiv2021

The Transformer Network for the Traveling Salesman Problem

The Traveling Salesman Problem (TSP) is the most popular and most studied combinatorial problem, starting with von Neumann in 1951. It has driven the discovery of several optimization techniques such as cutting planes, branch-and-bound, local search, Lagrangian relaxation, and simulated annealing. The last five years have seen the emergence of promising techniques where (graph) neural networks have been capable to learn new combinatorial algorithms. The main question is whether deep learning can learn better heuristics from data, i.e. replacing human-engineered heuristics? This is appealing because developing algorithms to tackle efficiently NP-hard problems may require years of research, and many industry problems are combinatorial by nature. In this work, we propose to adapt the recent successful Transformer architecture originally developed for natural language processing to the combinatorial TSP. Training is done by reinforcement learning, hence without TSP training solutions, and decoding uses beam search. We report improved performances over recent learned heuristics with an optimal gap of 0.004% for TSP50 and 0.39% for TSP100.

cs.LG↗

arXiv2019

On Learning Paradigms for the Travelling Salesman Problem

We explore the impact of learning paradigms on training deep neural networks for the Travelling Salesman Problem. We design controlled experiments to train supervised learning (SL) and reinforcement learning (RL) models on fixed graph sizes up to 100 nodes, and evaluate them on variable sized graphs up to 500 nodes. Beyond not needing labelled data, our results reveal favorable properties of RL over SL: RL training leads to better emergent generalization to variable graph sizes and is a key component for learning scale-invariant solvers for novel combinatorial problems.

cs.LG↗

arXiv2019

An Efficient Graph Convolutional Network Technique for the Travelling Salesman Problem

This paper introduces a new learning-based approach for approximately solving the Travelling Salesman Problem on 2D Euclidean graphs. We use deep Graph Convolutional Networks to build efficient TSP graph representations and output tours in a non-autoregressive manner via highly parallelized beam search. Our approach outperforms all recently proposed autoregressive deep learning techniques in terms of solution quality, inference speed and sample efficiency for problem instances of fixed graph sizes. In particular, we reduce the average optimality gap from 0.52% to 0.01% for 50 nodes, and from 2.26% to 1.39% for 100 nodes. Finally, despite improving upon other learning-based approaches for TSP, our approach falls short of standard Operations Research solvers.

cs.LG↗

arXiv2019

A Mutation-based Approach for Assessing Weight Coverage of a Path Planner

Autonomous cars are subjected to several different kind of inputs (other cars, road structure, etc.) and, therefore, testing the car under all possible conditions is impossible. To tackle this problem, scenario-based testing for automated driving defines categories of different scenarios that should be covered. Although this kind of coverage is a necessary condition, it still does not guarantee that any possible behaviour of the autonomous car is tested. In this paper, we consider the path planner of an autonomous car that decides, at each timestep, the short-term path to follow in the next few seconds; such decision is done by using a weighted cost function that considers different aspects (safety, comfort, etc.). In order to assess whether all the possible decisions that can be taken by the path planner are covered by a given test suite T, we propose a mutation-based approach that mutates the weights of the cost function and then checks if at least one scenario of T kills the mutant. Preliminary experiments on a manually designed test suite show that some weights are easier to cover as they consider aspects that more likely occur in a scenario, and that more complicated scenarios (that generate more complex paths) are those that allow to cover more weights.

cs.SE↗

arXiv2019

A Two-Step Graph Convolutional Decoder for Molecule Generation

We propose a simple auto-encoder framework for molecule generation. The molecular graph is first encoded into a continuous latent representation $z$, which is then decoded back to a molecule. The encoding process is easy, but the decoding process remains challenging. In this work, we introduce a simple two-step decoding process. In a first step, a fully connected neural network uses the latent vector $z$ to produce a molecular formula, for example CO$_2$ (one carbon and two oxygen atoms). In a second step, a graph convolutional neural network uses the same latent vector $z$ to place bonds between the atoms that were produced in the first step (for example a double bond will be placed between the carbon and each of the oxygens). This two-step process, in which a bag of atoms is first generated, and then assembled, provides a simple framework that allows us to develop an efficient molecule auto-encoder. Numerical experiments on basic tasks such as novelty, uniqueness, validity and optimized chemical property for the 250k ZINC molecules demonstrate the performances of the proposed system. Particularly, we achieve the highest reconstruction rate of 90.5\%, improving the previous rate of 76.7\%. We also report the best property improvement results when optimization is constrained by the molecular distance between the original and generated molecules.

cs.LG↗

arXiv2019

GraphTSNE: A Visualization Technique for Graph-Structured Data

We present GraphTSNE, a novel visualization technique for graph-structured data based on t-SNE. The growing interest in graph-structured data increases the importance of gaining human insight into such datasets by means of visualization. Among the most popular visualization techniques, classical t-SNE is not suitable on such datasets because it has no mechanism to make use of information from the graph structure. On the other hand, visualization techniques which operate on graphs, such as Laplacian Eigenmaps and tsNET, have no mechanism to make use of information from node features. Our proposed method GraphTSNE produces visualizations which account for both graph structure and node features. It is based on scalable and unsupervised training of a graph convolutional network on a modified t-SNE loss. By assembling a suite of evaluation metrics, we demonstrate that our method produces desirable visualizations on three benchmark datasets.

cs.LG↗

arXiv2018

Deep linear neural networks with arbitrary loss: All local minima are global

We consider deep linear networks with arbitrary convex differentiable loss. We provide a short and elementary proof of the fact that all local minima are global minima if the hidden layers are either 1) at least as wide as the input layer, or 2) at least as wide as the output layer. This result is the strongest possible in the following sense: If the loss is convex and Lipschitz but not differentiable then deep linear networks can have sub-optimal local minima.

cs.LG↗

arXiv2018

The Multilinear Structure of ReLU Networks

We study the loss surface of neural networks equipped with a hinge loss criterion and ReLU or leaky ReLU nonlinearities. Any such network defines a piecewise multilinear form in parameter space. By appealing to harmonic analysis we show that all local minima of such network are non-differentiable, except for those minima that occur in a region of parameter space where the loss surface is perfectly flat. Non-differentiable minima are therefore not technicalities or pathologies; they are heart of the problem when investigating the loss of ReLU networks. As a consequence, we must employ techniques from nonsmooth analysis to study these loss surfaces. We show how to apply these techniques in some illustrative cases.

cs.LG↗

arXiv2018

Residual Gated Graph ConvNets

Graph-structured data such as social networks, functional brain networks, gene regulatory networks, communications networks have brought the interest in generalizing deep learning techniques to graph domains. In this paper, we are interested to design neural networks for graphs with variable length in order to solve learning problems such as vertex classification, graph classification, graph regression, and graph generative tasks. Most existing works have focused on recurrent neural networks (RNNs) to learn meaningful representations of graphs, and more recently new convolutional neural networks (ConvNets) have been introduced. In this work, we want to compare rigorously these two fundamental families of architectures to solve graph learning tasks. We review existing graph RNN and ConvNet architectures, and propose natural extension of LSTM and ConvNet to graphs with arbitrary size. Then, we design a set of analytically controlled experiments on two basic graph problems, i.e. subgraph matching and graph clustering, to test the different architectures. Numerical results show that the proposed graph ConvNets are 3-17% more accurate and 1.5-4x faster than graph RNNs. Graph ConvNets are also 36% more accurate than variational (non-learning) techniques. Finally, the most effective graph ConvNet architecture uses gated edges and residuality. Residuality plays an essential role to learn multi-layer architectures as they provide a 10% gain of performance.

cs.LG↗

arXiv2016

A recurrent neural network without chaos

We introduce an exceptionally simple gated recurrent neural network (RNN) that achieves performance comparable to well-known gated architectures, such as LSTMs and GRUs, on the word-level language modeling task. We prove that our model has simple, predicable and non-chaotic dynamics. This stands in stark contrast to more standard gated architectures, whose underlying dynamical systems exhibit chaotic behavior.

cs.NE↗

arXiv2016

The regularity of the boundary of a multidimensional aggregation patch

Let $d \geq 2$ and let $N(y)$ be the fundamental solution of the Laplace equation in $R^d$ We consider the aggregation equation $$ \frac{\partial ρ}{\partial t} + \operatorname{div}(ρv) =0, v = -\nabla N * ρ$$ with initial data $ρ(x,0) = χ_{D_0}$, where $χ_{D_0}$ is the indicator function of a bounded domain $D_0 \subset R^d.$ We now fix $0 < γ< 1$ and take $D_0$ to be a bounded $C^{1+γ}$ domain (a domain with smooth boundary of class $C^{1+γ}$). Then we have Theorem: If $D_0$ is a $C^{1 + γ}$ domain, then the initial value problem above has a solution given by $$ρ(x,t) = \frac{1}{1 -t} χ_{D_t}(x), \quad x \in R^d, \quad 0 \le t < 1$$ where $D_t$ is a $C^{1 + γ}$ domain for all $0 \leq t < 1$.

math.AP↗

arXiv2016

Assessing and Improving the Mutation Testing Practice of PIT

Mutation testing is used extensively to support the experimentation of software engineering studies. Its application to real-world projects is possible thanks to modern tools that automate the whole mutation analysis process. However, popular mutation testing tools use a restrictive set of mutants which do not conform to the community standards as supported by the mutation testing literature. This can be problematic since the effectiveness of mutation depends on its mutants. We therefore examine how effective are the mutants of a popular mutation testing tool, named PIT, compared to comprehensive ones, as drawn from the literature and personal experience. We show that comprehensive mutants are harder to kill and encode faults not captured by the mutants of PIT for a range of 11% to 62% of the Java classes of the considered projects.

cs.SE↗