Mohammad Vali Sanian

Andrea Rubbi, Amir Akbarnejad, Mohammad Vali Sanian et al.

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.

Vidit Agrawal, John Peters, Tyler N. Thompson et al.

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), or because the target experimental conditions are out of distribution. 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.

Omid Ghahroodi, Marzia Nouri, Mohammad Vali Sanian et al.

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.