arXiv subjects

Mohammad Vali Sanian

Publications and source records attributed to Mohammad Vali Sanian.

7 recordsLinked to original sources

arXiv2026

ORCA: Hunting Compositional Failures in Text-to-Image Diffusion

Text-to-image diffusion models fail predictably on compositional prompts: attributes bind to the wrong objects, spatial relations invert, and multi-object scenes lose count. Recent architectures already augment CLIP with a T5 encoder precisely because CLIP's contrastive embedding loses compositional structure, yet these failures persist. We argue the binding problem is therefore not one of missing information but of misaligned information: a text encoder preserves compositional structure, but in a representation space shaped by language modelling rather than vision, and the denoising objective does not directly reward aligning the two. We show this correspondence can be supplied as an explicit training signal, that the relevant cross-modal information is concentrated in a low-rank subspace of self-supervised visual features, and that supplying it can be folded into diffusion training as a single auxiliary loss. Our method, ORCA (Orthogonal Residual Compositional Alignment), aligns the latent of a diffusion transformer with a low-rank target derived from a frozen visual encoder, through a predictor whose orthogonal basis is parameterised by a learned residual between T5 and CLIP embeddings, which provides a prompt-dependent signal for selecting the visual readout subspace. We prove that the cross-modal information recoverable at a given rank is bounded by the spectral mass of the visual encoder's covariance in the top components. Across three diffusion-transformer backbones (DiT-B/2, DiT-L/2, U-ViT-L), ORCA improves FID and GenEval over both vanilla and REPA baselines at zero inference-time cost; on DiT-L/2 it reaches FID 16.65 and GenEval 0.291 at 200K steps, exceeding the strongest 400K baseline at half the training cost, with the largest gains concentrated on attribute binding, spatial relations, and multi-object prompts.

cs.CV↗

arXiv2026

CHAMMI-75: Pre-training multi-channel models with heterogeneous microscopy images

Quantifying cell morphology using images and machine learning has proven to be a powerful tool to study the response of cells to treatments. However, models used to quantify cellular morphology are typically trained with a single microscopy imaging type. This results in specialized models that cannot be reused across biological studies because the technical specifications do not match (e.g., different number of channels). Here, we present CHAMMI-75, an open access dataset of heterogeneous, multi-channel microscopy images from 75 diverse biological studies. We curated this resource from publicly available sources to investigate cellular morphology models that are channel-adaptive and can process any microscopy image type. Our experiments show that training with CHAMMI-75 can improve performance in multi-channel bioimaging tasks primarily because of its high diversity in microscopy modalities. This work paves the way to create the next generation of cellular morphology models for biological studies.

cs.CV↗

arXiv2026

Shortest-Path Flow Matching with Mixture-Conditioned Bases for OOD Generalization to Unseen Conditions

Robust generalization under distribution shift remains a key challenge for conditional generative modeling: conditional flow-based methods often fit the training conditions well but fail to extrapolate to unseen ones. We introduce SP-FM, a shortest-path flow-matching framework that improves out-of-distribution (OOD) generalization by conditioning both the base distribution and the flow field on the condition. Specifically, SP-FM learns a condition-dependent base distribution parameterized as a flexible, learnable mixture, together with a condition-dependent vector field trained via shortest-path flow matching. Conditioning the base allows the model to adapt its starting distribution across conditions, enabling smooth interpolation and more reliable extrapolation beyond the observed training range. We provide theoretical insights into the resulting conditional transport and show how mixture-conditioned bases enhance robustness under shift. Empirically, SP-FM is effective across heterogeneous domains, including predicting responses to unseen perturbations in single-cell transcriptomics and modeling treatment effects in high-content microscopy--based drug screening. Overall, SP-FM provides a simple yet effective plug-in strategy for improving conditional generative modeling and OOD generalization across diverse domains.

cs.LG↗

arXiv2025

SIGMMA: Hierarchical Graph-Based Multi-Scale Multi-modal Contrastive Alignment of Histopathology Image and Spatial Transcriptome

Recent advances in computational pathology have leveraged vision-language models to learn joint representations of Hematoxylin and Eosin (HE) images with spatial transcriptomic (ST) profiles. However, existing approaches typically align HE tiles with their corresponding ST profiles at a single scale, overlooking fine-grained cellular structures and their spatial organization. To address this, we propose Sigmma, a multi-modal contrastive alignment framework for learning hierarchical representations of HE images and spatial transcriptome profiles across multiple scales. Sigmma introduces multi-scale contrastive alignment, ensuring that representations learned at different scales remain coherent across modalities. Furthermore, by representing cell interactions as a graph and integrating inter- and intra-subgraph relationships, our approach effectively captures cell-cell interactions, ranging from fine to coarse, within the tissue microenvironment. We demonstrate that Sigmm learns representations that better capture cross-modal correspondences, leading to an improvement of avg. 9.78\% in the gene-expression prediction task and avg. 26.93\% in the cross-modal retrieval task across datasets. We further show that it learns meaningful multi-tissue organization in downstream analyses.

cs.CV↗

arXiv2025

3D-Guided Scalable Flow Matching for Generating Volumetric Tissue Spatial Transcriptomics from Serial Histology

A scalable and robust 3D tissue transcriptomics profile can enable a holistic understanding of tissue organization and provide deeper insights into human biology and disease. Most predictive algorithms that infer ST directly from histology treat each section independently and ignore 3D structure, while existing 3D-aware approaches are not generative and do not scale well. We present Holographic Tissue Expression Inpainting and Analysis (HoloTea), a 3D-aware flow-matching framework that imputes spot-level gene expression from H&E while explicitly using information from adjacent sections. Our key idea is to retrieve morphologically corresponding spots on neighboring slides in a shared feature space and fuse this cross section context into a lightweight ControlNet, allowing conditioning to follow anatomical continuity. To better capture the count nature of the data, we introduce a 3D-consistent prior for flow matching that combines a learned zero-inflated negative binomial (ZINB) prior with a spatial-empirical prior constructed from neighboring sections. A global attention block introduces 3D H&E scaling linearly with the number of spots in the slide, enabling training and inference on large 3D ST datasets. Across three spatial transcriptomics datasets spanning different tissue types and resolutions, HoloTea consistently improves 3D expression accuracy and generalization compared to 2D and 3D baselines. We envision HoloTea advancing the creation of accurate 3D virtual tissues, ultimately accelerating biomarker discovery and deepening our understanding of disease.

cs.CV↗

arXiv2025

MEENA (PersianMMMU): Multimodal-Multilingual Educational Exams for N-level Assessment

Recent advancements in large vision-language models (VLMs) have primarily focused on English, with limited attention given to other languages. To address this gap, we introduce MEENA (also known as PersianMMMU), the first dataset designed to evaluate Persian VLMs across scientific, reasoning, and human-level understanding tasks. Our dataset comprises approximately 7,500 Persian and 3,000 English questions, covering a wide range of topics such as reasoning, mathematics, physics, diagrams, charts, and Persian art and literature. Key features of MEENA include: (1) diverse subject coverage spanning various educational levels, from primary to upper secondary school, (2) rich metadata, including difficulty levels and descriptive answers, (3) original Persian data that preserves cultural nuances, (4) a bilingual structure to assess cross-linguistic performance, and (5) a series of diverse experiments assessing various capabilities, including overall performance, the model's ability to attend to images, and its tendency to generate hallucinations. We hope this benchmark contributes to enhancing VLM capabilities beyond English.

cs.AI↗

arXiv2024

Khayyam Challenge (PersianMMLU): Is Your LLM Truly Wise to The Persian Language?

Evaluating Large Language Models (LLMs) is challenging due to their generative nature, necessitating precise evaluation methodologies. Additionally, non-English LLM evaluation lags behind English, resulting in the absence or weakness of LLMs for many languages. In response to this necessity, we introduce Khayyam Challenge (also known as PersianMMLU), a meticulously curated collection comprising 20,192 four-choice questions sourced from 38 diverse tasks extracted from Persian examinations, spanning a wide spectrum of subjects, complexities, and ages. The primary objective of the Khayyam Challenge is to facilitate the rigorous evaluation of LLMs that support the Persian language. Distinctive features of the Khayyam Challenge are (i) its comprehensive coverage of various topics, including literary comprehension, mathematics, sciences, logic, intelligence testing, etc., aimed at assessing different facets of LLMs such as language comprehension, reasoning, and information retrieval across various educational stages, from lower primary school to upper secondary school (ii) its inclusion of rich metadata such as human response rates, difficulty levels, and descriptive answers (iii) its utilization of new data to avoid data contamination issues prevalent in existing frameworks (iv) its use of original, non-translated data tailored for Persian speakers, ensuring the framework is free from translation challenges and errors while encompassing cultural nuances (v) its inherent scalability for future data updates and evaluations without requiring special human effort. Previous works lacked an evaluation framework that combined all of these features into a single comprehensive benchmark. Furthermore, we evaluate a wide range of existing LLMs that support the Persian language, with statistical analyses and interpretations of their outputs.

cs.CL↗