Chau Pham

selected publications

1. NeurIPS

   ChA-MAEViT: Unifying Channel-Aware Masked Autoencoders and Multi-Channel Vision Transformers for Improved Cross-Channel Learning

   Chau Pham, Juan C. Caicedo, and Bryan A. Plummer

   In Advances in Neural Information Processing Systems (NeurIPS) 2025

   Abstract PDF Bibtex Code

   Prior work using Masked Autoencoders (MAEs) typically relies on random patch masking based on the assumption that images have significant redundancies across different channels, allowing for the reconstruction of masked content using cross-channel correlations. However, this assumption does not hold in Multi-Channel Imaging (MCI), where channels may provide complementary information with minimal feature overlap. Thus, these MAEs primarily learn local structures within individual channels from patch reconstruction, failing to fully leverage cross-channel interactions and limiting their MCI effectiveness. In this paper, we present ChA-MAEViT, an MAE-based method that enhances feature learning across MCI channels via four key strategies: (1) dynamic channel-patch masking, which compels the model to reconstruct missing channels in addition to masked patches, thereby enhancing cross-channel dependencies and improving robustness to varying channel configurations; (2) memory tokens, which serve as long-term memory aids to promote information sharing across channels, addressing the challenges of reconstructing structurally diverse channels; (3) hybrid token fusion module, which merges fine-grained patch tokens with a global class token to capture richer representations; and (4) Channel-Aware Decoder, a lightweight decoder utilizes channel tokens to effectively reconstruct image patches. Experiments on satellite and microscopy datasets, CHAMMI, JUMP-CP, and So2Sat, show that ChA-MAEViT significantly outperforms state-of-the-art MCI-ViTs by 3.0-21.5%, highlighting the importance of cross-channel interactions in MCI. Our code is publicly available at https://github.com/chaudatascience/cha_mae_vit.

   @InProceedings{PhamChaMAE2025,
   author = {Chau Pham and Juan C. Caicedo and Bryan A. Plummer},
   title = {ChA-MAEViT: Unifying Channel-Aware Masked Autoencoders and Multi-Channel Vision Transformers for Improved Cross-Channel Learning},
   booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
   year = {2025}}
2. NeurIPS

   Enhancing Feature Diversity Boosts Channel-Adaptive Vision Transformers

   Chau Pham, and Bryan A. Plummer

   In Advances in Neural Information Processing Systems (NeurIPS) 2024

   Abstract PDF Bibtex Code

   Multi-Channel Imaging (MCI) contains an array of challenges for encoding useful feature representations not present in traditional images. For example, images from two different satellites may both contain RGB channels, but the remaining channels can be different for each imaging source. Thus, MCI models must support a variety of channel configurations at test time. Recent work has extended traditional visual encoders for MCI, such as Vision Transformers (ViT), by supplementing pixel information with an encoding representing the channel configuration. However, these methods treat each channel equally, i.e., they do not consider the unique properties of each channel type, which can result in needless and potentially harmful redundancies in the learned features. For example, if RGB channels are always present, the other channels can focus on extracting information that cannot be captured by the RGB channels. To this end, we propose DiChaViT, which aims to enhance the diversity in the learned features of MCI-ViT models. This is achieved through a novel channel sampling strategy that encourages the selection of more distinct channel sets for training. Additionally, we employ regularization and initialization techniques to increase the likelihood that new information is learned from each channel. Many of our improvements are architecture agnostic and can be incorporated into new architectures as they are developed. Experiments on both satellite and cell microscopy datasets, CHAMMI, JUMP-CP, and So2Sat, report DiChaViT yields a 1.5 - 5.0% gain over the state-of-the-art. Our code is publicly available at https://github.com/chaudatascience/diverse_channel_vit.

   @InProceedings{phamDiChaVit2024,
   author = {Chau Pham and Bryan A. Plummer},
   title = {Enhancing Feature Diversity Boosts Channel-Adaptive Vision Transformers},
   booktitle = {Advances in Neural Information Processing Systems (NeurIPS)},
   year = {2024}}
3. ICLR

   Let Models Speak Ciphers: Multiagent Debate through Embeddings

   Chau Pham*, Boyi Liu*, Yingxiang Yang, Zhengyu Chen, Tianyi Liu, Jianbo Yuan, Bryan A. Plummer, Zhaoran Wang, and Hongxia Yang

   In International Conference on Learning Representations (ICLR) 2024

   Abstract PDF Bibtex Code

   Discussion and debate among Large Language Models (LLMs) have gained considerable attention due to their potential to enhance the reasoning ability of LLMs. Although natural language is an obvious choice for communication due to LLM’s language understanding capability, the token sampling step needed when generating natural language poses a potential risk of information loss, as it uses only one token to represent the model’s belief across the entire vocabulary. In this paper, we introduce a communication regime named CIPHER (Communicative Inter-Model Protocol Through Embedding Representation) to address this issue. Specifically, we remove the token sampling step from LLMs and let them communicate their beliefs across the vocabulary through the expectation of the raw transformer output embeddings. Remarkably, by deviating from natural language, CIPHER offers an advantage of encoding a broader spectrum of information without any modification to the model weights, outperforming the state-of-the-art LLM debate methods using natural language by 0.5-5.0% across five reasoning tasks and multiple open-source LLMs of varying sizes. This showcases the superiority and robustness of embeddings as an alternative "language" for communication among LLMs. We anticipate that CIPHER will inspire further exploration for the design of interactions within LLM agent systems, offering a new direction that could significantly influence future developments in the field.

   @InProceedings{phamCIPHER2024,
   author={Chau Pham and Boyi Liu and Yingxiang Yang and Zhengyu Chen and Tianyi Liu and Jianbo Yuan and Bryan A. Plummer and Zhaoran Wang and Hongxia Yang},
   title={Let Models Speak Ciphers: Multiagent Debate through Embeddings},
   booktitle={International Conference on Learning Representations (ICLR)},
   year={2024}}
4. NeurIPS

   CHAMMI: A benchmark for channel-adaptive models in microscopy imaging

   Zitong Chen*, Chau Pham*, Siqi Wang, Michael Doron, Nikita Moshkov, Bryan A. Plummer, and Juan C. Caicedo

   In Advances in Neural Information Processing Systems (NeurIPS) 2023

   Abstract PDF Bibtex Code Data

   Most neural networks assume that input images have a fixed number of channels (three for RGB images). However, there are many settings where the number of channels may vary, such as microscopy images where the number of channels changes depending on instruments and experimental goals. Yet, there has not been a systemic attempt to create and evaluate neural networks that are invariant to the number and type of channels. As a result, trained models remain specific to individual studies and are hardly reusable for other microscopy settings. In this paper, we present a benchmark for investigating channel-adaptive models in microscopy imaging, which consists of 1) a dataset of varied-channel single-cell images, and 2) a biologically relevant evaluation framework. In addition, we adapted several existing techniques to create channel-adaptive models and compared their performance on this benchmark to fixed-channel, baseline models. We find that channel-adaptive models can generalize better to out-of-domain tasks and can be computationally efficient. We contribute a curated dataset and an evaluation API to facilitate objective comparisons in future research and applications.

   @InProceedings{ChenCHAMMI2023,
   author={Zitong Chen and Chau Pham and Siqi Wang and Michael Doron and Nikita Moshkov and Bryan A. Plummer and Juan C Caicedo},
   title={CHAMMI: A benchmark for channel-adaptive models in microscopy imaging},
   booktitle={Advances in Neural Information Processing Systems (NeurIPS) Track on Datasets and Benchmarks},
   year={2023}}