arXiv subjects

Farhad Ramezanghorbani

Publications and source records attributed to Farhad Ramezanghorbani.

3 recordsLinked to original sources

arXiv2026

Native Multi-Dimensional Subquadratic Operators via Input Dependent Long Convolutions

Subquadratic alternatives to attention require compromises when applied to multi-dimensional data: standard convolutions lack global receptive fields and input dependency, while recurrent models require rasterizing data such as images, volumes, and partial differential equation (PDE) into an ad-hoc $1\rm D$ scan order that violates their spatial structure. We introduce \textit{HyenaND}, a subquadratic, global, input-dependent operator that acts directly on the native geometry of multidimensional data through convolutions with implicitly parametrized global, input-dependent multi-dimensional convolutional kernels. Our CUDA implementation, \texttt{nSubQ}, fuses the FFT-convolution path to turn HyenaND's $\mathcal{O}(L \log L)$ scaling into wall-clock speedups. Across long-context genomics, computer vision, medical imaging, and PDE modeling, pure HyenaND stacks match the accuracy of strong attention baselines, while hybrid configurations that interleave HyenaND and attention layers outperform both pure attention and strong recurrence-based hybrids.

cs.LG↗

arXiv2025

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language models (pLM) training on hundreds of graphical processing units (GPUs). We introduce the BioNeMo Framework to facilitate the training of computational biology and chemistry AI models across hundreds of GPUs. Its modular design allows the integration of individual components, such as data loaders, into existing workflows and is open to community contributions. We detail technical features of the BioNeMo Framework through use cases such as pLM pre-training and fine-tuning. On 256 NVIDIA A100s, BioNeMo Framework trains a three billion parameter BERT-based pLM on over one trillion tokens in 4.2 days. The BioNeMo Framework is open-source and free for everyone to use.

cs.LG↗

arXiv2025

ToxBench: A Binding Affinity Prediction Benchmark with AB-FEP-Calculated Labels for Human Estrogen Receptor Alpha

Protein-ligand binding affinity prediction is essential for drug discovery and toxicity assessment. While machine learning (ML) promises fast and accurate predictions, its progress is constrained by the availability of reliable data. In contrast, physics-based methods such as absolute binding free energy perturbation (AB-FEP) deliver high accuracy but are computationally prohibitive for high-throughput applications. To bridge this gap, we introduce ToxBench, the first large-scale AB-FEP dataset designed for ML development and focused on a single pharmaceutically critical target, Human Estrogen Receptor Alpha (ER$α$). ToxBench contains 8,770 ER$α$-ligand complex structures with binding free energies computed via AB-FEP with a subset validated against experimental affinities at 1.75 kcal/mol RMSE, along with non-overlapping ligand splits to assess model generalizability. Using ToxBench, we further benchmark state-of-the-art ML methods, and notably, our proposed DualBind model, which employs a dual-loss framework to effectively learn the binding energy function. The benchmark results demonstrate the superior performance of DualBind and the potential of ML to approximate AB-FEP at a fraction of the computational cost.

cs.LG↗