Assessing Y-Axis Influence: Bias in Multimodal Language Models on Chart-to-Table Translation

Chart-to-table translation converts chart images into structured tabular data. Accurate translation is crucial for Multimodal Language Model (MLM) to answer complex queries. We observe imbalances in the number of images across different aspects of the y-axis information in public chart datasets. Such imbalances can introduce unintended biases, causing uneven MLM performance. Previous works have not systematically examined these biases. To address this gap, we propose a new framework, FairChart2Table, for analyzing y-axis-related bias on five state-of-the-art models. Key Findings: (1) There are significant y-axis biases related to the digit length of the major tick values, the number of major ticks, the range of values, and the tick value format (e.g., abbreviation or scientific format). (2) The number of legends/entities in chart images impacts MLM performance. (3) Prompting MLM with y-axis information can significantly enhance the performance for some MLMs.

Beyond Single Plots: A Benchmark for Question Answering on Multi-Charts

Charts are widely used to present complex information. Deriving meaningful insights in real-world contexts often requires interpreting multiple related charts together. Research on understanding multi-chart images has not been extensively explored. We introduce PolyChartQA, a mid-scale dataset specifically designed for question answering over multi-chart images. PolyChartQA comprises 534 multi-chart images (with a total of 2,297 sub-charts) sourced from peer-reviewed computer science research publications and 2,694 QA pairs. We evaluate the performance of nine state-of-the-art Multimodal Language Models (MLMs) on PolyChartQA across question type, difficulty, question source, and key structural characteristics of multi-charts. Our results show a 27.4% LLM-based accuracy (L-Accuracy) drop on human-authored questions compared to MLM-generated questions, and a 5.39% L-accuracy gain with our proposed prompting method.

Reducing Domain Gap with Diffusion-Based Domain Adaptation for Cell Counting

Generating realistic synthetic microscopy images is critical for training deep learning models in label-scarce environments, such as cell counting with many cells per image. However, traditional domain adaptation methods often struggle to bridge the domain gap when synthetic images lack the complex textures and visual patterns of real samples. In this work, we adapt the Inversion-Based Style Transfer (InST) framework originally designed for artistic style transfer to biomedical microscopy images. Our method combines latent-space Adaptive Instance Normalization with stochastic inversion in a diffusion model to transfer the style from real fluorescence microscopy images to synthetic ones, while weakly preserving content structure. We evaluate the effectiveness of our InST-based synthetic dataset for downstream cell counting by pre-training and fine-tuning EfficientNet-B0 models on various data sources, including real data, hard-coded synthetic data, and the public Cell200-s dataset. Models trained with our InST-synthesized images achieve up to 37\% lower Mean Absolute Error (MAE) compared to models trained on hard-coded synthetic data, and a 52\% reduction in MAE compared to models trained on Cell200-s (from 53.70 to 25.95 MAE). Notably, our approach also outperforms models trained on real data alone (25.95 vs. 27.74 MAE). Further improvements are achieved when combining InST-synthesized data with lightweight domain adaptation techniques such as DACS with CutMix. These findings demonstrate that InST-based style transfer most effectively reduces the domain gap between synthetic and real microscopy data. Our approach offers a scalable path for enhancing cell counting performance while minimizing manual labeling effort. The source code and resources are publicly available at: https://github.com/MohammadDehghan/InST-Microscopy.

IDCIA: Immunocytochemistry Dataset for Cellular Image Analysis

We present a new annotated microscopic cellular image dataset to improve the effectiveness of machine learning methods for cellular image analysis. Cell counting is an important step in cell analysis. Typically, domain experts manually count cells in a microscopic image. Automated cell counting can potentially eliminate this tedious, time-consuming process. However, a good, labeled dataset is required for training an accurate machine learning model. Our dataset includes microscopic images of cells, and for each image, the cell count and the location of individual cells. The data were collected as part of an ongoing study investigating the potential of electrical stimulation to modulate stem cell differentiation and possible applications for neural repair. Compared to existing publicly available datasets, our dataset has more images of cells stained with more variety of antibodies (protein components of immune responses against invaders) typically used for cell analysis. The experimental results on this dataset indicate that none of the five existing models under this study are able to achieve sufficiently accurate count to replace the manual methods. The dataset is available at https://figshare.com/articles/dataset/Dataset/21970604.