Aditya Malusare

Mengbo Wang, Shourya Verma, Aditya Malusare et al.

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.

Aditya Malusare, Harish Kothandaraman, Dipesh Tamboli et al.

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.

Long Phan, Alice Gatti, Ziwen Han et al. · amazon-science, apple-ml

Benchmarks are important tools for tracking the rapid advancements in large language model (LLM) capabilities. However, benchmarks are not keeping pace in difficulty: LLMs now achieve over 90\% accuracy on popular benchmarks like MMLU, limiting informed measurement of state-of-the-art LLM capabilities. In response, we introduce Humanity's Last Exam (HLE), a multi-modal benchmark at the frontier of human knowledge, designed to be the final closed-ended academic benchmark of its kind with broad subject coverage. HLE consists of 2,500 questions across dozens of subjects, including mathematics, humanities, and the natural sciences. HLE is developed globally by subject-matter experts and consists of multiple-choice and short-answer questions suitable for automated grading. Each question has a known solution that is unambiguous and easily verifiable, but cannot be quickly answered via internet retrieval. State-of-the-art LLMs demonstrate low accuracy and calibration on HLE, highlighting a significant gap between current LLM capabilities and the expert human frontier on closed-ended academic questions. To inform research and policymaking upon a clear understanding of model capabilities, we publicly release HLE at https://lastexam.ai.

Vineet Punyamoorty, Aditya Malusare, Vaneet Aggarwal

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.

Aditya Malusare, Vaneet Aggarwal

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.

Dipesh Tamboli, Souradip Chakraborty, Aditya Malusare et al.

Text-to-image (T2I) diffusion models have made remarkable advancements, yet aligning them with diverse preferences remains a persistent challenge. Current methods often optimize single metrics or depend on narrowly curated datasets, leading to overfitting and limited generalization across key visual quality metrics. We present BalancedDPO, a novel extension of Direct Preference Optimization (DPO) that addresses these limitations by simultaneously aligning T2I diffusion models with multiple metrics, including human preference, CLIP score, and aesthetic quality. Our key novelty lies in aggregating consensus labels from diverse metrics in the preference distribution space as compared to existing reward mixing approaches, enabling robust and scalable multi-metric alignment while maintaining the simplicity of the standard DPO pipeline that we refer to as BalancedDPO. Our evaluations on the Pick-a-Pic, PartiPrompt and HPD datasets show that BalancedDPO achieves state-of-the-art results, outperforming existing approaches across all major metrics. BalancedDPO improves the average win rates by 15%, 7.1%, and 10.3% on Pick-a-pic, PartiPrompt and HPD, respectively, from the DiffusionDPO.

Aditya Malusare, Vineet Punyamoorty, Vaneet Aggarwal

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.