Marcel Nassar

Kin Long Kelvin Lee, Carmelo Gonzales, Marcel Nassar et al. · deepmind

We propose MatSci ML, a novel benchmark for modeling MATerials SCIence using Machine Learning (MatSci ML) methods focused on solid-state materials with periodic crystal structures. Applying machine learning methods to solid-state materials is a nascent field with substantial fragmentation largely driven by the great variety of datasets used to develop machine learning models. This fragmentation makes comparing the performance and generalizability of different methods difficult, thereby hindering overall research progress in the field. Building on top of open-source datasets, including large-scale datasets like the OpenCatalyst, OQMD, NOMAD, the Carolina Materials Database, and Materials Project, the MatSci ML benchmark provides a diverse set of materials systems and properties data for model training and evaluation, including simulated energies, atomic forces, material bandgaps, as well as classification data for crystal symmetries via space groups. The diversity of properties in MatSci ML makes the implementation and evaluation of multi-task learning algorithms for solid-state materials possible, while the diversity of datasets facilitates the development of new, more generalized algorithms and methods across multiple datasets. In the multi-dataset learning setting, MatSci ML enables researchers to combine observations from multiple datasets to perform joint prediction of common properties, such as energy and forces. Using MatSci ML, we evaluate the performance of different graph neural networks and equivariant point cloud networks on several benchmark tasks spanning single task, multitask, and multi-data learning scenarios. Our open-source code is available at https://github.com/IntelLabs/matsciml.

Santiago Miret, Kin Long Kelvin Lee, Carmelo Gonzales et al.

We present the Open MatSci ML Toolkit: a flexible, self-contained, and scalable Python-based framework to apply deep learning models and methods on scientific data with a specific focus on materials science and the OpenCatalyst Dataset. Our toolkit provides: 1. A scalable machine learning workflow for materials science leveraging PyTorch Lightning, which enables seamless scaling across different computation capabilities (laptop, server, cluster) and hardware platforms (CPU, GPU, XPU). 2. Deep Graph Library (DGL) support for rapid graph neural network prototyping and development. By publishing and sharing this toolkit with the research community via open-source release, we hope to: 1. Lower the entry barrier for new machine learning researchers and practitioners that want to get started with the OpenCatalyst dataset, which presently comprises the largest computational materials science dataset. 2. Enable the scientific community to apply advanced machine learning tools to high-impact scientific challenges, such as modeling of materials behavior for clean energy applications. We demonstrate the capabilities of our framework by enabling three new equivariant neural network models for multiple OpenCatalyst tasks and arrive at promising results for compute scaling and model performance.

Yan Wu, Esther Wershof, Sebastian M Schmon et al.

We introduce a comprehensive framework for modeling single cell transcriptomic responses to perturbations, aimed at standardizing benchmarking in this rapidly evolving field. Our approach includes a modular and user-friendly model development and evaluation platform, a collection of diverse perturbational datasets, and a set of metrics designed to fairly compare models and dissect their performance. Through extensive evaluation of both published and baseline models across diverse datasets, we highlight the limitations of widely used models, such as mode collapse. We also demonstrate the importance of rank metrics which complement traditional model fit measures, such as RMSE, for validating model effectiveness. Notably, our results show that while no single model architecture clearly outperforms others, simpler architectures are generally competitive and scale well with larger datasets. Overall, this benchmarking exercise sets new standards for model evaluation, supports robust model development, and furthers the use of these models to simulate genetic and chemical screens for therapeutic discovery.

Zichao Yan, Yan Wu, Mica Xu Ji et al.

Predicting the effects of perturbations in-silico on cell state can identify drivers of cell behavior at scale and accelerate drug discovery. However, modeling challenges remain due to the inherent heterogeneity of single cell gene expression and the complex, latent gene dependencies. Here, we present PRiMeFlow, an end-to-end flow matching based approach to directly model the effects of genetic and small molecule perturbations in the gene expression space. The distribution-fitting approach taken by PRiMeFlow enables it to accurately approximate the empirical distribution of single-cell gene expression, which we demonstrate through extensive benchmarking inside PerturBench. Through ablation studies, we also validate important model design choices such as operating in gene expression space and parameterizing the velocity field with a U-Net architecture. The PRiMeFlow architecture was used as the basis for the model that won the Generalist Prize in the first ARC Virtual Cell Challenge.

Shengyu Feng, Subarna Tripathi, Hesham Mostafa et al.

Dynamic scene graph generation from a video is challenging due to the temporal dynamics of the scene and the inherent temporal fluctuations of predictions. We hypothesize that capturing long-term temporal dependencies is the key to effective generation of dynamic scene graphs. We propose to learn the long-term dependencies in a video by capturing the object-level consistency and inter-object relationship dynamics over object-level long-term tracklets using transformers. Experimental results demonstrate that our Dynamic Scene Graph Detection Transformer (DSG-DETR) outperforms state-of-the-art methods by a significant margin on the benchmark dataset Action Genome. Our ablation studies validate the effectiveness of each component of the proposed approach. The source code is available at https://github.com/Shengyu-Feng/DSG-DETR.

Sami Abu-El-Haija, Hesham Mostafa, Marcel Nassar et al.

Recent improvements in the performance of state-of-the-art (SOTA) methods for Graph Representational Learning (GRL) have come at the cost of significant computational resource requirements for training, e.g., for calculating gradients via backprop over many data epochs. Meanwhile, Singular Value Decomposition (SVD) can find closed-form solutions to convex problems, using merely a handful of epochs. In this paper, we make GRL more computationally tractable for those with modest hardware. We design a framework that computes SVD of \textit{implicitly} defined matrices, and apply this framework to several GRL tasks. For each task, we derive linear approximation of a SOTA model, where we design (expensive-to-store) matrix $\mathbf{M}$ and train the model, in closed-form, via SVD of $\mathbf{M}$, without calculating entries of $\mathbf{M}$. By converging to a unique point in one step, and without calculating gradients, our models show competitive empirical test performance over various graphs such as article citation and biological interaction networks. More importantly, SVD can initialize a deeper model, that is architected to be non-linear almost everywhere, though behaves linearly when its parameters reside on a hyperplane, onto which SVD initializes. The deeper model can then be fine-tuned within only a few epochs. Overall, our procedure trains hundreds of times faster than state-of-the-art methods, while competing on empirical test performance. We open-source our implementation at: https://github.com/samihaija/isvd

Kourosh Hakhamaneshi, Marcel Nassar, Mariano Phielipp et al.

Being able to predict the performance of circuits without running expensive simulations is a desired capability that can catalyze automated design. In this paper, we present a supervised pretraining approach to learn circuit representations that can be adapted to new circuit topologies or unseen prediction tasks. We hypothesize that if we train a neural network (NN) that can predict the output DC voltages of a wide range of circuit instances it will be forced to learn generalizable knowledge about the role of each circuit element and how they interact with each other. The dataset for this supervised learning objective can be easily collected at scale since the required DC simulation to get ground truth labels is relatively cheap. This representation would then be helpful for few-shot generalization to unseen circuit metrics that require more time consuming simulations for obtaining the ground-truth labels. To cope with the variable topological structure of different circuits we describe each circuit as a graph and use graph neural networks (GNNs) to learn node embeddings. We show that pretraining GNNs on prediction of output node voltages can encourage learning representations that can be adapted to new unseen topologies or prediction of new circuit level properties with up to 10x more sample efficiency compared to a randomly initialized model. We further show that we can improve sample efficiency of prior SoTA model-based optimization methods by 2x (almost as good as using an oracle model) via fintuning pretrained GNNs as the feature extractor of the learned models.

Hesham Mostafa, Marcel Nassar, Somdeb Majumdar

Many recent works have studied the performance of Graph Neural Networks (GNNs) in the context of graph homophily - a label-dependent measure of connectivity. Traditional GNNs generate node embeddings by aggregating information from a node's neighbors in the graph. Recent results in node classification tasks show that this local aggregation approach performs poorly in graphs with low homophily (heterophilic graphs). Several mechanisms have been proposed to improve the accuracy of GNNs on such graphs by increasing the aggregation range of a GNN layer, either through multi-hop aggregation, or through long-range aggregation from distant nodes. In this paper, we show that properly tuned classical GNNs and multi-layer perceptrons match or exceed the accuracy of recent long-range aggregation methods on heterophilic graphs. Thus, our results highlight the need for alternative datasets to benchmark long-range GNN aggregation mechanisms. We also show that homophily is a poor measure of the information in a node's local neighborhood and propose the Neighborhood Information Content(NIC) metric, which is a novel information-theoretic graph metric. We argue that NIC is more relevant for local aggregation methods as used by GNNs. We show that, empirically, it correlates better with GNN accuracy in node classification tasks than homophily.

Daniel Cummings, Marcel Nassar

Academic citation graphs represent citation relationships between publications across the full range of academic fields. Top cited papers typically reveal future trends in their corresponding domains which is of importance to both researchers and practitioners. Prior citation prediction methods often require initial citation trends to be established and do not take advantage of the recent advancements in graph neural networks (GNNs). We present GNN-based architecture that predicts the top set of papers at the time of publication. For experiments, we curate a set of academic citation graphs for a variety of conferences and show that the proposed model outperforms other classic machine learning models in terms of the F1-score.

Hesham Mostafa, Marcel Nassar

Graph convolutional networks (GCNs) update a node's feature vector by aggregating features from its neighbors in the graph. This ignores potentially useful contributions from distant nodes. Identifying such useful distant contributions is challenging due to scalability issues (too many nodes can potentially contribute) and oversmoothing (aggregating features from too many nodes risks swamping out relevant information and may result in nodes having different labels but indistinguishable features). We introduce a global attention mechanism where a node can selectively attend to, and aggregate features from, any other node in the graph. The attention coefficients depend on the Euclidean distance between learnable node embeddings, and we show that the resulting attention-based global aggregation scheme is analogous to high-dimensional Gaussian filtering. This makes it possible to use efficient approximate Gaussian filtering techniques to implement our attention-based global aggregation scheme. By employing an approximate filtering method based on the permutohedral lattice, the time complexity of our proposed global aggregation scheme only grows linearly with the number of nodes. The resulting GCNs, which we term permutohedral-GCNs, are differentiable and trained end-to-end, and they achieve state of the art performance on several node classification benchmarks.

Marcel Nassar, Xin Wang, Evren Tumer

We introduce a novel encoder-decoder architecture to embed functional processes into latent vector spaces. This embedding can then be decoded to sample the encoded functions over any arbitrary domain. This autoencoder generalizes the recently introduced Conditional Neural Process (CNP) model of random processes. Our architecture employs the latest advances in graph neural networks to process irregularly sampled functions. Thus, we refer to our model as Conditional Graph Neural Process (CGNP). Graph neural networks can effectively exploit `local' structures of the metric spaces over which the functions/processes are defined. The contributions of this paper are twofold: (i) a novel graph-based encoder-decoder architecture for functional and process embeddings, and (ii) a demonstration of the importance of using the structure of metric spaces for this type of representations.

Marcel Nassar

Recently, graph neural networks have been adopted in a wide variety of applications ranging from relational representations to modeling irregular data domains such as point clouds and social graphs. However, the space of graph neural network architectures remains highly fragmented impeding the development of optimized implementations similar to what is available for convolutional neural networks. In this work, we present BiGraphNet, a graph neural network architecture that generalizes many popular graph neural network models and enables new efficient operations similar to those supported by ConvNets. By explicitly separating the input and output nodes, BiGraphNet: (i) generalizes the graph convolution to support new efficient operations such as coarsened graph convolutions (similar to strided convolution in convnets), multiple input graphs convolution and graph expansions (unpooling) which can be used to implement various graph architectures such as graph autoencoders, and graph residual nets; and (ii) accelerates and scales the computations and memory requirements in hierarchical networks by performing computations only at specified output nodes.

Urs Köster, Tristan J. Webb, Xin Wang et al.

Deep neural networks are commonly developed and trained in 32-bit floating point format. Significant gains in performance and energy efficiency could be realized by training and inference in numerical formats optimized for deep learning. Despite advances in limited precision inference in recent years, training of neural networks in low bit-width remains a challenging problem. Here we present the Flexpoint data format, aiming at a complete replacement of 32-bit floating point format training and inference, designed to support modern deep network topologies without modifications. Flexpoint tensors have a shared exponent that is dynamically adjusted to minimize overflows and maximize available dynamic range. We validate Flexpoint by training AlexNet, a deep residual network and a generative adversarial network, using a simulator implemented with the neon deep learning framework. We demonstrate that 16-bit Flexpoint closely matches 32-bit floating point in training all three models, without any need for tuning of model hyperparameters. Our results suggest Flexpoint as a promising numerical format for future hardware for training and inference.

Marcel Nassar, Philip Schniter, Brian L. Evans

We propose a novel receiver for orthogonal frequency division multiplexing (OFDM) transmissions in impulsive noise environments. Impulsive noise arises in many modern wireless and wireline communication systems, such as Wi-Fi and powerline communications, due to uncoordinated interference that is much stronger than thermal noise. We first show that the bit-error-rate optimal receiver jointly estimates the propagation channel coefficients, the noise impulses, the finite-alphabet symbols, and the unknown bits. We then propose a near-optimal yet computationally tractable approach to this joint estimation problem using loopy belief propagation. In particular, we merge the recently proposed "generalized approximate message passing" (GAMP) algorithm with the forward-backward algorithm and soft-input soft-output decoding using a "turbo" approach. Numerical results indicate that the proposed receiver drastically outperforms existing receivers under impulsive noise and comes within 1 dB of the matched-filter bound. Meanwhile, with N tones, the proposed factor-graph-based receiver has only O(N log N) complexity, and it can be parallelized.

Jing Lin, Marcel Nassar, Brian L. Evans

Additive asynchronous and cyclostationary impulsive noise limits communication performance in OFDM powerline communication (PLC) systems. Conventional OFDM receivers assume additive white Gaussian noise and hence experience degradation in communication performance in impulsive noise. Alternate designs assume a parametric statistical model of impulsive noise and use the model parameters in mitigating impulsive noise. These receivers require overhead in training and parameter estimation, and degrade due to model and parameter mismatch, especially in highly dynamic environments. In this paper, we model impulsive noise as a sparse vector in the time domain without any other assumptions, and apply sparse Bayesian learning methods for estimation and mitigation without training. We propose three iterative algorithms with different complexity vs. performance trade-offs: (1) we utilize the noise projection onto null and pilot tones to estimate and subtract the noise impulses; (2) we add the information in the data tones to perform joint noise estimation and OFDM detection; (3) we embed our algorithm into a decision feedback structure to further enhance the performance of coded systems. When compared to conventional OFDM PLC receivers, the proposed receivers achieve SNR gains of up to 9 dB in coded and 10 dB in uncoded systems in the presence of impulsive noise.

Il Memming Park, Marcel Nassar, Mijung Park

The ultimate goal of optimization is to find the minimizer of a target function.However, typical criteria for active optimization often ignore the uncertainty about the minimizer. We propose a novel criterion for global optimization and an associated sequential active learning strategy using Gaussian processes.Our criterion is the reduction of uncertainty in the posterior distribution of the function minimizer. It can also flexibly incorporate multiple global minimizers. We implement a tractable approximation of the criterion and demonstrate that it obtains the global minimizer accurately compared to conventional Bayesian optimization criteria.