arXiv subjects

Monika Raj

Publications and source records attributed to Monika Raj.

4 recordsLinked to original sources

arXiv2026

Imaging-anchored multiomics in cardiovascular disease: integrating cardiac imaging, bulk, single-cell, and spatial transcriptomics

Cardiovascular disease arises from interactions between inherited risk, molecular programmes, and tissue-scale remodelling that are observed clinically through imaging. Cardiac MRI (CMR), computed tomography (CT), and echocardiography are integral to routine cardiovascular care, while bulk RNA sequencing, single-cell RNA sequencing, and spatial transcriptomics are providing increasingly detailed molecular characterization of cardiac tissue. Yet, these imaging and molecular data are still analysed in largely separate pipelines. This review examines joint representations that link cardiac imaging phenotypes to transcriptomic and spatially resolved molecular states. An imaging-anchored perspective is adopted in which echocardiography, CMR, and CT define a spatial phenotype of the heart, and bulk, single-cell and spatial transcriptomics provide cell-type- and location-specific molecular context. We define the representation requirements of each modality, compare multimodal fusion strategies, and synthesize integrative pipelines for radiogenomics, spatial alignment, and image-based gene-expression prediction, together with their validation requirements, limitations, and failure modes. Spatial multiomic maps of human myocardium and atherosclerotic plaque, together with single-cell, spatial, and multimodal medical foundation models, are advancing imaging-anchored multiomics; however, cost, scalability, and tissue availability remain substantial barriers to large-scale cardiovascular translation.

q-bio.QM↗

arXiv2026

Navigating Route Latent Space for Synthesizable Molecular Design

Goal-directed molecular design has advanced rapidly, yet a substantial proportion of designed molecules remain difficult to synthesize in practice, limiting their real-world utility. Prior synthesizability-aware methods either project generated molecules back to synthesizable analogs that deviate from the intended target, or optimize directly in discrete synthesis spaces that lack a continuous landscape for efficient search. We argue that this limitation mainly comes from the search space rather than the optimizer. To address this, we propose RouteFlow, a framework that reformulates synthesizable molecular design as a search over a continuous route latent space, where each latent maps back to a complete synthesis route and synthesizability is inherently preserved. To navigate this space, we adopt reward-guided flow matching as an efficient sampler that steers toward high-property regions. Since reward optimization may push latents off the manifold of real synthesis routes, where decoding becomes unreliable, we further introduce a cycle-consistency mechanism to stabilize fine-tuning. Across 16 optimization tasks from Therapeutic Data Commons, RouteFlow achieves the best sample efficiency among synthesizability-aware baselines, with the best synthetic accessibility and the highest retrosynthesis success rate. Our results also confirm that the proposed cycle-consistency reliably keeps optimization on-manifold while improving target properties, supporting effective synthesizable molecular discovery.

cs.AI↗

arXiv2026

LLM-Guided Dynamic Action Spaces for Synthesizable Molecular Optimization

Synthesizable molecular optimization seeks to improve target properties while ensuring that molecular modifications follow feasible synthetic pathways. Existing synthesis-aware methods typically rely on exploring a large space of candidate transformations defined by reaction templates and purchasable building blocks. This search becomes even more challenging when property improvement requires multiple reaction steps, as the space expands further along the pathway. To address this challenge, we introduce MolReAct, which reformulates molecular optimization as search over compact reaction spaces proposed by a tool-augmented large language model (LLM). At each step, the LLM combines its prior chemical knowledge with cheminformatics tools to identify a molecule-specific set of compatible reactions, preserving synthesizability while making multi-step optimization feasible. Given this compact action space, we further leverage Group Relative Policy Optimization (GRPO) with the terminal oracle reward to improve long-term decision-making over multiple reaction steps. Across diverse molecular optimization tasks, MolReAct achieves the highest Top-10 score on 11 of 14 tasks and the best sample efficiency on 12 of 14 tasks, outperforming existing baselines under limited oracle budgets. Beyond these gains, MolReAct also provides each optimized molecule with a template-grounded synthetic pathway.

cs.LG↗

arXiv2026

Peeling Context from Cause for Molecular Property Prediction

Deep models are used for molecular property prediction, yet they are often difficult to interpret and may rely on spurious context rather than causal structure, which reduces reliability under distribution shift and harms predictive performance. We introduce CLaP (Causal Layerwise Peeling), a framework that separates causal signal from context in a layerwise manner and integrates diverse graph representations of molecules. At each layer, a causal block performs a soft split into causal and non-causal branches, fuses causal evidence across modalities, and progressively removes batch-coupled context to focus on label-relevant structure, thereby limiting shortcut signals and stabilizing layerwise refinement. Across four molecular benchmarks, CLaP consistently improves MAE, MSE, and $R^2$ over competitive baselines. The model also produces atom-level causal saliency maps that highlight substructures responsible for predictions, providing actionable guidance for targeted molecular edits. Case studies confirm the accuracy of these maps and their alignment with chemical intuition. By peeling context from cause at every layer, the model yields predictors that are both accurate and interpretable for molecular design.

cs.LG↗