Mohammad Shahab Sepehri

Mohammad Shahab Sepehri, Zalan Fabian, Maryam Soltanolkotabi et al.

Multimodal Large Language Models (MLLMs) have tremendous potential to improve the accuracy, availability, and cost-effectiveness of healthcare by providing automated solutions or serving as aids to medical professionals. Despite promising first steps in developing medical MLLMs in the past few years, their capabilities and limitations are not well-understood. Recently, many benchmark datasets have been proposed that test the general medical knowledge of such models across a variety of medical areas. However, the systematic failure modes and vulnerabilities of such models are severely underexplored with most medical benchmarks failing to expose the shortcomings of existing models in this safety-critical domain. In this paper, we introduce MediConfusion, a challenging medical Visual Question Answering (VQA) benchmark dataset, that probes the failure modes of medical MLLMs from a vision perspective. We reveal that state-of-the-art models are easily confused by image pairs that are otherwise visually dissimilar and clearly distinct for medical experts. Strikingly, all available models (open-source or proprietary) achieve performance below random guessing on MediConfusion, raising serious concerns about the reliability of existing medical MLLMs for healthcare deployment. We also extract common patterns of model failure that may help the design of a new generation of more trustworthy and reliable MLLMs in healthcare.

Paula Arguello, Berk Tinaz, Mohammad Shahab Sepehri et al.

Deep learning underpins a wide range of applications in MRI, including reconstruction, artifact removal, and segmentation. However, progress has been driven largely by public datasets focused on brain and knee imaging, shaping how models are trained and evaluated. As a result, careful studies of the reliability of these models across diverse anatomical settings remain limited. In this work, we introduce MosaicMRI, a large and diverse collection of fully sampled raw musculoskeletal (MSK) MR measurements designed for training and evaluating machine-learning-based methods. MosaicMRI is the largest open-source raw MSK MRI dataset to date, comprising 2,671 volumes and 80,156 slices. The dataset offers substantial diversity in volume orientation (e.g., axial, sagittal), imaging contrasts (e.g., PD, T1, T2), anatomies (e.g., spine, knee, hip, ankle, and others), and numbers of acquisition coils. Using VarNet as a baseline for accelerated reconstruction task, we perform a comprehensive set of experiments to study scaling behavior with respect to both model capacity and dataset size. Interestingly, models trained on the combined anatomies significantly outperform anatomy-specific models in low-sample regimes, highlighting the benefits of anatomical diversity and the presence of exploitable cross-anatomical correlations. We further evaluate robustness and cross-anatomy generalization by training models on one anatomy (e.g., spine) and testing them on another (e.g., knee). Notably, we identify groups of body parts (e.g., foot and elbow) that generalize well with each other, and highlight that performance under domain shifts depends on both training set size, anatomy, and protocol-specific factors.

Mohammad Shahab Sepehri, Asal Mehradfar, Berk Tinaz et al.

Text-to-image diffusion models achieve high visual fidelity but surprisingly exhibit systematic failures in numerical control when prompts specify explicit object counts. To address this limitation, we introduce ATHENA, a model-agnostic, test-time adaptive steering framework that improves object count fidelity without modifying model architectures or requiring retraining. ATHENA leverages intermediate representations during sampling to estimate object counts and applies count-aware noise corrections early in the denoising process, steering the generation trajectory before structural errors become difficult to revise. We present three progressively more advanced variants of ATHENA that trade additional computation for improved numerical accuracy, ranging from static prompt-based steering to dynamically adjusted count-aware control. Experiments on established benchmarks and a new visually and semantically complex dataset show that ATHENA consistently improves count fidelity, particularly at higher target counts, while maintaining favorable accuracy-runtime trade-offs across multiple diffusion backbones.

Mohammad Shahab Sepehri, Zalan Fabian, Mahdi Soltanolkotabi

The landscape of computational building blocks of efficient image restoration architectures is dominated by a combination of convolutional processing and various attention mechanisms. However, convolutional filters, while efficient, are inherently local and therefore struggle with modeling long-range dependencies in images. In contrast, attention excels at capturing global interactions between arbitrary image regions, but suffers from a quadratic cost in image dimension. In this work, we propose Serpent, an efficient architecture for high-resolution image restoration that combines recent advances in state space models (SSMs) with multi-scale signal processing in its core computational block. SSMs, originally introduced for sequence modeling, can maintain a global receptive field with a favorable linear scaling in input size. We propose a novel hierarchical architecture inspired by traditional signal processing principles, that converts the input image into a collection of sequences and processes them in a multi-scale fashion. Our experimental results demonstrate that Serpent can achieve reconstruction quality on par with state-of-the-art techniques, while requiring orders of magnitude less compute (up to $150$ fold reduction in FLOPS) and a factor of up to $5\times$ less GPU memory while maintaining a compact model size. The efficiency gains achieved by Serpent are especially notable at high image resolutions.

Mohammad Shahab Sepehri, Asal Mehradfar, Mahdi Soltanolkotabi et al.

Predicting Bitcoin price remains a challenging problem due to the high volatility and complex non-linear dynamics of cryptocurrency markets. Traditional time-series models, such as ARIMA and GARCH, and recurrent neural networks, like LSTMs, have been widely applied to this task but struggle to capture the regime shifts and long-range dependencies inherent in the data. In this work, we propose CryptoMamba, a novel Mamba-based State Space Model (SSM) architecture designed to effectively capture long-range dependencies in financial time-series data. Our experiments show that CryptoMamba not only provides more accurate predictions but also offers enhanced generalizability across different market conditions, surpassing the limitations of previous models. Coupled with trading algorithms for real-world scenarios, CryptoMamba demonstrates its practical utility by translating accurate forecasts into financial outcomes. Our findings signal a huge advantage for SSMs in stock and cryptocurrency price forecasting tasks.

Mohammad Shahab Sepehri, Berk Tinaz, Zalan Fabian et al.

Mental visualization, the ability to construct and manipulate visual representations internally, is a core component of human cognition and plays a vital role in tasks involving reasoning, prediction, and abstraction. Despite the rapid progress of Multimodal Large Language Models (MLLMs), current benchmarks primarily assess passive visual perception, offering limited insight into the more active capability of internally constructing visual patterns to support problem solving. Yet mental visualization is a critical cognitive skill in humans, supporting abilities such as spatial navigation, predicting physical trajectories, and solving complex visual problems through imaginative simulation. To bridge this gap, we introduce Hyperphantasia, a synthetic benchmark designed to evaluate the mental visualization abilities of MLLMs through four carefully constructed puzzles. Each task is procedurally generated and presented at three difficulty levels, enabling controlled analysis of model performance across increasing complexity. Our comprehensive evaluation of state-of-the-art models reveals a substantial gap between the performance of humans and MLLMs. Additionally, we explore the potential of reinforcement learning to improve visual simulation capabilities. Our findings suggest that while some models exhibit partial competence in recognizing visual patterns, robust mental visualization remains an open challenge for current MLLMs.

Haosheng Gan, Berk Tinaz, Mohammad Shahab Sepehri et al.

Current text-to-image (T2I) benchmarks evaluate models on rigid prompts, potentially underestimating true generative capabilities due to prompt sensitivity and creating biases that favor certain models while disadvantaging others. We introduce ConceptMix++, a framework that disentangles prompt phrasing from visual generation capabilities by applying iterative prompt optimization. Building on ConceptMix, our approach incorporates a multimodal optimization pipeline that leverages vision-language model feedback to refine prompts systematically. Through extensive experiments across multiple diffusion models, we show that optimized prompts significantly improve compositional generation performance, revealing previously hidden model capabilities and enabling fairer comparisons across T2I models. Our analysis reveals that certain visual concepts -- such as spatial relationships and shapes -- benefit more from optimization than others, suggesting that existing benchmarks systematically underestimate model performance in these categories. Additionally, we find strong cross-model transferability of optimized prompts, indicating shared preferences for effective prompt phrasing across models. These findings demonstrate that rigid benchmarking approaches may significantly underrepresent true model capabilities, while our framework provides more accurate assessment and insights for future development.

Asal Mehradfar, Mohammad Shahab Sepehri, Jose Miguel Hernandez-Lobato et al.

The discovery of new ionizable lipids for efficient lipid nanoparticle (LNP)-mediated RNA delivery remains a critical bottleneck for RNA-based therapeutics development. Recent advances have highlighted the potential of machine learning (ML) to predict transfection efficiency from molecular structure, enabling high-throughput virtual screening and accelerating lead identification. However, existing approaches are hindered by inadequate data quality, ineffective feature representations, low predictive accuracy, and poor generalizability. Here, we present LANTERN (Lipid nANoparticle Transfection Efficiency pRedictioN), a robust ML framework for predicting transfection efficiency based on ionizable lipid representation. We benchmarked a diverse set of ML models against AGILE, a previously published model developed for transfection prediction. Our results show that combining simpler models with chemically informative features, particularly count-based Morgan fingerprints, outperforms more complex models that rely on internally learned embeddings, such as AGILE. We also show that a multi-layer perceptron trained on a combination of Morgan fingerprints and Expert descriptors achieved the highest performance ($\text{R}^2$ = 0.8161, r = 0.9053), significantly exceeding AGILE ($\text{R}^2$ = 0.2655, r = 0.5488). We show that the models in LANTERN consistently have strong performance across multiple evaluation metrics. Thus, LANTERN offers a robust benchmarking framework for LNP transfection prediction and serves as a valuable tool for accelerating lipid-based RNA delivery systems design.