arXiv subjects

Mansoor Ahmed

Publications and source records attributed to Mansoor Ahmed.

10 recordsLinked to original sources

arXiv2026

ConTact: Contact-First Antibody CDR Design via Explicit Interface Reasoning

Computational antibody CDR design methods condition on antigen structure to generate binding loops. Yet, the existing architectures conflate two fundamentally distinct sub-problems: identifying which CDR positions will contact the antigen, and selecting amino acids at those positions. This forces models to learn contact reasoning implicitly through uniform message passing, diluting antigen signal across all positions equally. We introduce ConTact, a contact-then-act architecture that explicitly decomposes CDR design into three cascaded stages: learning surface complementarity fingerprints, predicting CDR-antigen contacts, and injecting contact-gated antigen features into the prediction head. A distance-biased cross-attention module encodes geometric priors favoring spatial neighbors, a contact-weighted cross-entropy loss concentrates gradient signal on binding-critical positions, and a standoff-aware contact-recovery loss places the designed loop against its native epitope. On the ChiMERa-Bench dataset, ConTact surpasses the baselines on the binding interface and structural metrics (backbone RMSD, fraction of native contacts, interface RMSD, DockQ, and epitope F1) on all three splits, improving native-contact recovery by 11 to 16%, while matching the best sequence recovery. The source code is available at: https://github.com/mansoor181/ConTact.git

cs.LG↗

arXiv2026

AgForce Enables Antigen-conditioned Generative Antibody Design

Antibody design methods condition on antigen structure to generate complementarity-determining regions (CDR), yet a systematic evaluation of baseline methods reveals that they largely ignore the antigen input. We identify three failure modes that explain this behavior. Antigen blindness arises because models derive predictions from antibody framework context rather than antigen information, producing nearly identical CDRs regardless of the target. Vocabulary collapse reduces predicted amino acids to three to five per position, far below the ground truth distribution in native sequences. The argmax bottleneck on the cross-entropy loss via greedy decoding acts as a null predictor that sees only position and loop length and recovers almost all the residues irrespective of the model architecture and the target antigen. We propose a novel encoder-decoder architecture called AgForce that uses a graph neural network (GNN) as the encoder and specialized decoders for sequence-structure co-design. Specifically, we apply framework dropout, gated bottlenecks, and hyperbolic cross attention that prevent the antibody shortcut path. In the decoder, a Mixture Density Network (MDN) sequence head with Potts-like pairwise coupling and annealed Multiple Choice Learning (aMCL) replaces the cross-entropy objective with a multi-component distribution. An antigen cycle consistency head routes gradients through the sequence decoder, forcing predicted distributions to encode antigen identity. On the ChiMERa-Bench dataset, AgForce leads the baselines on every interface metric on all three splits (fnat, iRMSD, DockQ, and epitope F1) together with structure and sequence, while achieving roughly a 2x larger effective vocabulary compared to the GNN baselines.

cs.LG↗

arXiv2026

Latent-Kernel Discrete Flow Maps for Few-Step Generation

Discrete diffusion and flow-matching models denoise a sequence over many steps, but to keep each step cheap, they factorize the transition across positions and decide every token independently. This makes few-step generation challenging for text when the target couples two positions, such as a subject and a verb that must agree. An independent update commits to them separately, and many function evaluations are spent repairing the mismatch. Existing few-step methods buy back the lost correlation by distilling or rectifying a slow teacher, and so inherit the teacher's quality ceiling. We ask instead whether a model can express correlated steps natively, and answer with Latent-Kernel Discrete Flow Maps (LKF), a from-scratch flow-map kernel that is a mixture of M factorized components tied by a single shared latent. Conditioned on the latent, each component is cheap, and the mixture is summed over the latent in closed form for small M. We show that a single step places mass on correlated completions with the same sampling time complexity as a factorized model, since one latent is drawn per sequence and reused across the entire denoising trajectory. We also show that the Masked Diffusion Language Model (MDLM) is a special case of our LKF model at M=1. The experiments for unconditional text generation on the One-Billion-Word (LM1B) and WikiText-103 benchmarks show that our LKF model learns strongly heterogeneous components and improves generative perplexity by 2.1x to 3.3x over the likelihood baselines without losing diversity. The gain grows with M, and at M=8, it surpasses distilled and rectified few-step samplers. The source code is available at: https://github.com/mansoor181/lkf.git

cs.LG↗

arXiv2026

CHIMERA-Bench: A Benchmark Dataset for Epitope-Specific Antibody Design

Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development. These methods are evaluated on different SAbDab snapshots, non-overlapping test sets, and incompatible metrics, and the literature fragments the design problem into numerous sub-tasks with no common definition. We introduce CHIMERA-Bench: (CDR Modeling with Epitope-guided Redesign), a unified benchmark built around a single canonical task: epitope-conditioned CDR sequence-structure co-design. CHIMERA-Bench provides three components. The first is a curated, deduplicated dataset of 2,922 antibody-antigen complexes with epitope and paratope annotations. The second is a set of three biologically motivated splits that test generalization to unseen epitopes, unseen antigen folds, and prospective temporal targets. The third is a comprehensive evaluation protocol with five metric groups, including novel epitope-specificity measures. We benchmark eleven methods spanning six generative paradigms and report results across all splits. CHIMERA-Bench is the largest dataset of its kind for the antibody design problem, allowing the community to develop and test novel methods and evaluate their generalizability.

cs.LG↗

arXiv2026

EpiFormer: Learning Antigen-Antibody Interactions for Epitope Prediction via Geometric Deep Learning

Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes. Computational epitope prediction is critical for understanding immune recognition and guiding antibody engineering. However, existing methods face three fundamental challenges: antibody-aware models encode each chain independently and combine them only at a late stage, failing to capture co-dependent structural features that define binding interfaces, whereas severe class imbalance and scarcity of known antibody-antigen complexes render standard training objectives ineffective. We propose EpiFormer, a general encoder-decoder framework that addresses these challenges jointly. Our key design principle is interleaved cross-attention within GNN encoding layers, enabling bidirectional antigen-antibody information flow throughout representation learning rather than only at the output. This early-fusion principle is backbone-agnostic, providing consistent gains across GNN architectures from simple GCNs to equivariant models. We further show that sparsity-aware objectives are effective when paired with early-fusion architectures for the epitope prediction task. EpiFormer improves over the previous best method by over 40% in F1 score on standard benchmarks, demonstrating generalizability and cross-dataset transferability. Notably, EpiFormer discovers known biological principles as emergent behaviors of end-to-end training, where the learned cross-attention gates favor antigen-to-antibody information flow, consistent with the asymmetric roles of the two chains at the binding interface, and the model's preference for geometric over evolutionary features aligns with the established finding that epitope residues are not evolutionarily conserved. The source code is available at: https://github.com/mansoor181/epiformer.git

q-bio.QM↗

arXiv2026

EvoStruct: Bridging Evolutionary and Structural Priors for Antibody CDR Design via Protein Language Model Adaptation

Equivariant graph neural network (GNN) methods for antibody complementarity-determining region (CDR) design achieve the highest sequence recovery but suffer from severe vocabulary collapse. The current best GNN methods over-predict very few amino acids, such as tyrosine and glycine, while ignoring functionally important residues. We trace this failure to GNN encoders learning amino acid distributions de novo from limited structural data, discarding substitution patterns encoded in evolutionary databases. To resolve this, we propose EvoStruct, which bridges a frozen protein language model (PLM) with 3D structural context from an E(3)-equivariant GNN via a cross-attention adapter. Unlike prior PLM-structure adapters for general protein design, EvoStruct targets the vocabulary collapse problem specific to CDR design through progressive PLM unfreezing and R-Drop consistency regularization. On the CHIMERA-Bench dataset, EvoStruct achieves the highest amino acid recovery and lowest perplexity among several antibody design methods, improving sequence recovery by 16% and reducing perplexity by 43% relative to the best GNN baselines, while recovering 2.3x greater amino acid diversity and the highest binding-pair correlation with ground truth.

cs.LG↗

arXiv2023

Robust Brain Age Estimation via Regression Models and MRI-derived Features

The determination of biological brain age is a crucial biomarker in the assessment of neurological disorders and understanding of the morphological changes that occur during aging. Various machine learning models have been proposed for estimating brain age through Magnetic Resonance Imaging (MRI) of healthy controls. However, developing a robust brain age estimation (BAE) framework has been challenging due to the selection of appropriate MRI-derived features and the high cost of MRI acquisition. In this study, we present a novel BAE framework using the Open Big Healthy Brain (OpenBHB) dataset, which is a new multi-site and publicly available benchmark dataset that includes region-wise feature metrics derived from T1-weighted (T1-w) brain MRI scans of 3965 healthy controls aged between 6 to 86 years. Our approach integrates three different MRI-derived region-wise features and different regression models, resulting in a highly accurate brain age estimation with a Mean Absolute Error (MAE) of 3.25 years, demonstrating the framework's robustness. We also analyze our model's regression-based performance on gender-wise (male and female) healthy test groups. The proposed BAE framework provides a new approach for estimating brain age, which has important implications for the understanding of neurological disorders and age-related brain changes.

eess.IV↗

arXiv2023

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.

astro-ph.IM↗

arXiv2020

MobChain: Three-Way Collusion Resistance in Witness-Oriented Location Proof Systems Using Distributed Consensus

Smart devices have accentuated the importance of geolocation information. Geolocation identification using smart devices has paved the path for incentive-based location-based services (LBS). A location proof is a digital certificate of the geographical location of a user, which can be used to access various LBS. However, a user full control over a device allows the tampering of location proof. Initially, to resist false proofs, two-party trusted centralized location proof systems (LPS) were introduced to aid the users in generating secure location proofs mutually. However, two-party protocols suffered from the collusion attacks by the participants of the protocol. Consequently, many witness-oriented LPS have emerged to mitigate collusion attacks in two-party protocols. However, witness-oriented LPS presented the possibility of three-way collusion attacks (involving the user, location authority, and the witness). The three-way collusion attacks are inevitable in all existing witness-oriented schemes. To mitigate the inability to resist three-way collusion of existing schemes, in this paper, we introduce a decentralized consensus protocol called as MobChain, where the selection of a witness and location authority is achieved through a distributed consensus of nodes in an underlying P2P network of a private blockchain. The persistent provenance data over the blockchain provides strong security guarantees, as a result, the forging and manipulation become impractical. MobChain provides secure location provenance architecture, relying on decentralized decision making for the selection of participants of the protocol to resist three-way collusion problem. Our prototype implementation and comparison with the state-of-the-art solutions show that MobChain is computationally efficient, highly available while improving the security of LPS.

cs.CR↗

arXiv2019

An artificial neural network framework for reduced order modeling of transient flows

This paper proposes a supervised machine learning framework for the non-intrusive model order reduction of unsteady fluid flows to provide accurate predictions of non-stationary state variables when the control parameter values vary. Our approach utilizes a training process from full-order scale direct numerical simulation data projected on proper orthogonal decomposition (POD) modes to achieve an artificial neural network (ANN) model with reduced memory requirements. This data-driven ANN framework allows for a nonlinear time evolution of the modal coefficients without performing a Galerkin projection. Our POD-ANN framework can thus be considered an equation-free approach for latent space dynamics evolution of nonlinear transient systems and can be applied to a wide range of physical and engineering applications. Within this framework we introduce two architectures, namely sequential network (SN) and residual network (RN), to train the trajectory of modal coefficients. We perform a systematic analysis of the performance of the proposed reduced order modeling approaches on prediction of a nonlinear wave-propagation problem governed by the viscous Burgers equation, a simplified prototype setting for transient flows. We find that the POD-ANN-RN yields stable and accurate results for test problems assessed both within inside and outside of the database range and performs significantly better than the standard intrusive Galerkin projection model. Our results show that the proposed framework provides a non-intrusive alternative to the evolution of transient physics in a POD basis spanned space, and can be used as a robust predictive model order reduction tool for nonlinear dynamical systems.

physics.flu-dyn↗