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Marcel Nassar

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5 papers

1 author row

NeurIPS Conference 2025 Conference Paper

PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis

Yan Wu
Esther Wershof
Sebastian Schmon
Marcel Nassar
Błażej Osiński
Ridvan Eksi
Zichao Yan
Rory Stark

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.

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NeurIPS Conference 2025 Conference Paper

scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling

Joel Dapello
Marcel Nassar
Ridvan Eksi
Ban Wang
Jules Gagnon-Marchand
Kenneth Gao
akram Baharlouei
Kyra Thrush

Understanding cellular responses to chemical interventions is critical to the discovery of effective therapeutics. Because individual biological techniques often measure only one axis of cellular response at a time, high-quality multimodal datasets are needed to unlock a holistic understanding of how cells respond to treatments and to advance computational methods that integrate modalities. However, many techniques destroy cells and thus preclude paired measurements, and attempts to match disparate unimodal datasets are often confounded by data being generated in incompatible experimental settings. Here we introduce scGeneScope, a multimodal single‑cell RNA sequencing (scRNA-seq) and Cell Painting microscopy image dataset conditionally paired by chemical treatment, designed to facilitate the development and benchmarking of unimodal, multimodal, and multiple profile machine learning methods for cellular profiling. 28 chemicals, each acting on distinct biological pathways or mechanisms of action (MoAs), were applied to U2-OS cells in two experimental data generation rounds, creating paired sets of replicates that were then profiled independently by scRNA‑seq or Cell Painting. Using scGeneScope, we derive a replicate- and experiment-split treatment identification benchmark simulating MoA discovery under realistic laboratory variability conditions and evaluate unimodal, multimodal, and multiprofile models ranging in complexity from linear approaches to recent foundation models. Multiprofile integration improved performance in both the unimodal and multimodal settings, with gains more consistent in the former. Evaluation of unimodal models for MoA identification demonstrated that recent scRNA-seq foundation models deployed zero-shot were consistently outperformed by classic fit-to-data methods, underscoring the need for careful, realistic benchmarking in machine learning for biology. We release the scGeneScope dataset and benchmarking code to support further research.

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TMLR Journal 2023 Journal Article

The Open MatSci ML Toolkit: A Flexible Framework for Machine Learning in Materials Science

Santiago Miret
Kin Long Kelvin Lee
Carmelo Gonzales
Marcel Nassar
Matthew Spellings

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. The code of the framework and experiments presented in this is paper are publicly available at https://github.com/IntelLabs/matsciml.

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NeurIPS Conference 2021 Conference Paper

Implicit SVD for Graph Representation Learning

Sami Abu-El-Haija
Hesham Mostafa
Marcel Nassar
Valentino Crespi
Greg Ver Steeg
Aram Galstyan

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 *implicitly* defined matrices, and apply this framework to several GRL tasks. For each task, we derive first-order 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 algorithm trains hundreds of times faster than state-of-the-art methods, while competing on test empirical performance. We open-source our implementation at: https: //github. com/samihaija/isvd

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NeurIPS Conference 2017 Conference Paper

Flexpoint: An Adaptive Numerical Format for Efficient Training of Deep Neural Networks

Urs Köster
Tristan Webb
Xin Wang
Marcel Nassar
Arjun Bansal
William Constable
Oguz Elibol
Scott Gray

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 \emph{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.

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