arXiv subjects

Aditya Malusare

Publications and source records attributed to Aditya Malusare.

7 recordsLinked to original sources

arXiv2025

GeneFlow: Translation of Single-cell Gene Expression to Histopathological Images via Rectified Flow

Spatial transcriptomics (ST) technologies can be used to align transcriptomes with histopathological morphology, presenting exciting new opportunities for biomolecular discovery. Using ST data, we construct a novel framework, GeneFlow, to map transcriptomics onto paired cellular images. By combining an attention-based RNA encoder with a conditional UNet guided by rectified flow, we generate high-resolution images with different staining methods (e.g. H&E, DAPI) to highlight various cellular/tissue structures. Rectified flow with high-order ODE solvers creates a continuous, bijective mapping between transcriptomics and image manifolds, addressing the many-to-one relationship inherent in this problem. Our method enables the generation of realistic cellular morphology features and spatially resolved intercellular interactions from observational gene expression profiles, provides potential to incorporate genetic/chemical perturbations, and enables disease diagnosis by revealing dysregulated patterns in imaging phenotypes. Our rectified flow-based method outperforms diffusion-based baseline method in all experiments. Code can be found at https://github.com/wangmengbo/GeneFlow.

q-bio.QM↗

arXiv2025

Augmenting generative models with biomedical knowledge graphs improves targeted drug discovery

Recent breakthroughs in generative modeling have demonstrated remarkable capabilities in molecular generation, yet the integration of comprehensive biomedical knowledge into these models has remained an untapped frontier. In this study, we introduce K-DREAM (Knowledge-Driven Embedding-Augmented Model), a novel framework that leverages knowledge graphs to augment diffusion-based generative models for drug discovery. By embedding structured information from large-scale knowledge graphs, K-DREAM directs molecular generation toward candidates with higher biological relevance and therapeutic suitability. This integration ensures that the generated molecules are aligned with specific therapeutic targets, moving beyond traditional heuristic-driven approaches. In targeted drug design tasks, K-DREAM generates drug candidates with improved binding affinities and predicted efficacy, surpassing current state-of-the-art generative models. It also demonstrates flexibility by producing molecules designed for multiple targets, enabling applications to complex disease mechanisms. These results highlight the utility of knowledge-enhanced generative models in rational drug design and their relevance to practical therapeutic development.

cs.LG↗

arXiv2025

Contrastive Cross-Modal Learning for Infusing Chest X-ray Knowledge into ECGs

Modern diagnostic workflows are increasingly multimodal, integrating diverse data sources such as medical images, structured records, and physiological time series. Among these, electrocardiograms (ECGs) and chest X-rays (CXRs) are two of the most widely used modalities for cardiac assessment. While CXRs provide rich diagnostic information, ECGs are more accessible and can support scalable early warning systems. In this work, we propose CroMoTEX, a novel contrastive learning-based framework that leverages chest X-rays during training to learn clinically informative ECG representations for multiple cardiac-related pathologies: cardiomegaly, pleural effusion, and edema. Our method aligns ECG and CXR representations using a novel supervised cross-modal contrastive objective with adaptive hard negative weighting, enabling robust and task-relevant feature learning. At test time, CroMoTEX relies solely on ECG input, allowing scalable deployment in real-world settings where CXRs may be unavailable. Evaluated on the large-scale MIMIC-IV-ECG and MIMIC-CXR datasets, CroMoTEX outperforms baselines across all three pathologies, achieving up to 78.31 AUROC on edema. Our code is available at github.com/vineetpmoorty/cromotex.

cs.LG↗

arXiv2025

BalancedDPO: Adaptive Multi-Metric Alignment

Diffusion models have achieved remarkable progress in text-to-image generation, yet aligning them with human preference remains challenging due to the presence of multiple, sometimes conflicting, evaluation metrics (e.g., semantic consistency, aesthetics, and human preference scores). Existing alignment methods typically optimize for a single metric or rely on scalarized reward aggregation, which can bias the model toward specific evaluation criteria. To address this challenge, we propose BalancedDPO, a framework that achieves multi-metric preference alignment within the Direct Preference Optimization (DPO) paradigm. Unlike prior DPO variants that rely on a single metric, BalancedDPO introduces a majority-vote consensus over multiple preference scorers and integrates it directly into the DPO training loop with dynamic reference model updates. This consensus-based formulation avoids reward-scale conflicts and ensures more stable gradient directions across heterogeneous metrics. Experiments on Pick-a-Pic, PartiPrompt, and HPD datasets demonstrate that BalancedDPO consistently improves preference win rates over the baselines across Stable Diffusion 1.5, Stable Diffusion 2.1 and SDXL backbones. Comprehensive ablations further validate the benefits of majority-vote aggregation and dynamic reference updating, highlighting the method's robustness and generalizability across diverse alignment settings.

cs.CV↗

arXiv2024

Improving Molecule Generation and Drug Discovery with a Knowledge-enhanced Generative Model

Recent advancements in generative models have established state-of-the-art benchmarks in the generation of molecules and novel drug candidates. Despite these successes, a significant gap persists between generative models and the utilization of extensive biomedical knowledge, often systematized within knowledge graphs, whose potential to inform and enhance generative processes has not been realized. In this paper, we present a novel approach that bridges this divide by developing a framework for knowledge-enhanced generative models called KARL. We develop a scalable methodology to extend the functionality of knowledge graphs while preserving semantic integrity, and incorporate this contextual information into a generative framework to guide a diffusion-based model. The integration of knowledge graph embeddings with our generative model furnishes a robust mechanism for producing novel drug candidates possessing specific characteristics while ensuring validity and synthesizability. KARL outperforms state-of-the-art generative models on both unconditional and targeted generation tasks.

cs.LG↗

arXiv2024

Understanding the Natural Language of DNA using Encoder-Decoder Foundation Models with Byte-level Precision

This paper presents the Ensemble Nucleotide Byte-level Encoder-Decoder (ENBED) foundation model, analyzing DNA sequences at byte-level precision with an encoder-decoder Transformer architecture. ENBED uses a sub-quadratic implementation of attention to develop an efficient model capable of sequence-to-sequence transformations, generalizing previous genomic models with encoder-only or decoder-only architectures. We use Masked Language Modeling to pre-train the foundation model using reference genome sequences and apply it in the following downstream tasks: (1) identification of enhancers, promotors and splice sites, (2) recognition of sequences containing base call mismatches and insertion/deletion errors, an advantage over tokenization schemes involving multiple base pairs, which lose the ability to analyze with byte-level precision, (3) identification of biological function annotations of genomic sequences, and (4) generating mutations of the Influenza virus using the encoder-decoder architecture and validating them against real-world observations. In each of these tasks, we demonstrate significant improvement as compared to the existing state-of-the-art results.

cs.LG↗

arXiv2021

Size Dependence in Flux-Flow Hall Effect using Time-Dependent Ginzburg-Landau Equations

We study the Hall effect in square, planar type-II superconductors using numerical simulations of time dependent Ginzburg-Landau (TDGL) equations. The Hall field in some type-II superconductors displays sign-change behavior at some magnetic fields due to the induced field of vortex flow, when its contribution is strong enough to reverse the field direction. In this work, we use modified TDGL equations which couple an externally applied current, and also incorporate normal-state and flux-flow Hall effects. We obtain the profile of Hall angle as a function of applied magnetic field for four different sizes (l\times l) of the superconductor: l/ ξbelongs to {3, 5, 15, 20}. We obtain vastly different profiles for each size, proving that size is an important parameter that determines Hall behavior. We find that electric field dynamics provides an insight into several anomalous features including signchange of Hall angle, and leads us to the precise transient behavior of order parameter responsible for them.

cond-mat.supr-con↗