arXiv subjects

Evan Dramko

Publications and source records attributed to Evan Dramko.

5 recordsLinked to original sources

arXiv2026

Convergence Analysis of Two-Layer Neural Networks under Gaussian Input Masking

We investigate the convergence guarantee of two-layer neural network training with Gaussian randomly masked inputs. This scenario corresponds to Gaussian dropout at the input level, or noisy input training common in sensor networks, privacy-preserving training, and federated learning, where each user may have access to partial or corrupted features. Using a Neural Tangent Kernel (NTK) analysis, we demonstrate that training a two-layer ReLU network with Gaussian randomly masked inputs achieves linear convergence up to an error region proportional to the mask's variance. A key technical contribution is resolving the randomness within the non-linear activation, a problem of independent interest.

cs.LG↗

arXiv2025

On The Finetuning of MLIPs Through the Lens of Iterated Maps With BPTT

Accurate structural relaxation is critical for advanced materials design. Traditional approaches built on physics-derived first-principles calculations are computationally expensive, motivating the creation of machine-learning interatomic potentials (MLIPs), which strive to faithfully reproduce first-principles computed forces. We propose a fine-tuning method to be used on a pretrained MLIP in which we create a fully-differentiable end-to-end simulation loop that optimizes the predicted final structures directly. Trajectories are unrolled and gradients are tracked through the entire relaxation. We show that this method consistently improves performance across all evaluated pretrained models; resulting in an average of roughly 32% reduction in prediction error. Interestingly, we show the process is robust to substantial variation in the relaxation setup, achieving negligibly different results across varied hyperparameter and procedural modifications.

cond-mat.mtrl-sci↗

arXiv2025

Completion of partial structures using Patterson maps with the CrysFormer machine learning model

Protein structure determination has long been one of the primary challenges of structural biology, to which deep machine learning (ML)-based approaches have increasingly been applied. However, these ML models generally do not incorporate the experimental measurements directly, such as X-ray crystallographic diffraction data. To this end, we explore an approach that more tightly couples these traditional crystallographic and recent ML-based methods, by training a hybrid 3-d vision transformer and convolutional network on inputs from both domains. We make use of two distinct input constructs / Patterson maps, which are directly obtainable from crystallographic data, and ``partial structure'' template maps derived from predicted structures deposited in the AlphaFold Protein Structure Database with subsequently omitted residues. With these, we predict electron density maps that are then post-processed into atomic models through standard crystallographic refinement processes. Introducing an initial dataset of small protein fragments taken from Protein Data Bank entries and placing them in hypothetical crystal settings, we demonstrate that our method is effective at both improving the phases of the crystallographic structure factors and completing the regions missing from partial structure templates, as well as improving the agreement of the electron density maps with the ground truth atomic structures.

physics.bio-ph↗

arXiv2025

ADAPT: Lightweight, Long-Range Machine Learning Force Fields Without Graphs

Point defects play a central role in driving the properties of materials. First-principles methods are widely used to compute defect energetics and structures, including at scale for high-throughput defect databases. However, these methods are computationally expensive, making machine-learning force fields (MLFFs) an attractive alternative for accelerating structural relaxations. Most existing MLFFs are based on graph neural networks (GNNs), which can suffer from oversmoothing and poor representation of long-range interactions. Both of these issues are especially of concern when modeling point defects. To address these challenges, we introduce the Accelerated Deep Atomic Potential Transformer (ADAPT), an MLFF that replaces graph representations with a direct coordinates-in-space formulation and explicitly considers all pairwise atomic interactions. Atoms are treated as tokens, with a Transformer encoder modeling their interactions. Applied to a dataset of silicon point defects, ADAPT achieves a roughly 33 percent reduction in both force and energy prediction errors relative to a state-of-the-art GNN-based model, while requiring only a fraction of the computational cost.

cs.LG↗

arXiv2025

RecCrysFormer: Refined Protein Structural Prediction from 3D Patterson Maps via Recycling Training Runs

Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating experimental and ML approaches to protein structure determination from crystallographic data. $\texttt{RecCrysFormer}$ leverages Patterson maps and incorporates known standardized partial structures of amino acid residues to directly predict electron density maps, which are essential for constructing detailed atomic models through crystallographic refinement processes. $\texttt{RecCrysFormer}$ benefits from a ``recycling'' training regimen that iteratively incorporates results from crystallographic refinements and previous training runs as additional inputs in the form of template maps. Using a preliminary dataset of synthetic peptide fragments based on Protein Data Bank, $\texttt{RecCrysFormer}$ achieves good accuracy in structural predictions and shows robustness against variations in crystal parameters, such as unit cell dimensions and angles.

q-bio.QM↗