Publications

2025

1. Preprint

   MedMax: Mixed-Modal Instruction Tuning for Training Biomedical Assistants

   Hritik Bansal, Daniel Israel, Siyan Zhao, Shufan Li, Tung Nguyen, and Aditya Grover

   Under Review, 2025

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   Recent advancements in mixed-modal generative models have enabled flexible integration of information across image-text content. These models have opened new avenues for developing unified biomedical assistants capable of analyzing biomedical images, answering complex questions about them, and predicting the impact of medical procedures on a patient’s health. However, existing resources face challenges such as limited data availability, narrow domain coverage, and restricted sources (e.g., medical papers). To address these gaps, we present MedMax, the first large-scale multimodal biomedical instruction-tuning dataset for mixed-modal foundation models. With 1.47 million instances, MedMax encompasses a diverse range of tasks, including multimodal content generation (interleaved image-text data), biomedical image captioning and generation, visual chatting, and report understanding. These tasks span diverse medical domains such as radiology and histopathology. Subsequently, we fine-tune a mixed-modal foundation model on the MedMax dataset, achieving significant performance improvements: a 26% gain over the Chameleon model and an 18.3% improvement over GPT-4o across 12 downstream biomedical visual question-answering tasks. Additionally, we introduce a unified evaluation suite for biomedical tasks, providing a robust framework to guide the development of next-generation mixed-modal biomedical AI assistants.

2. Preprint

   Predicting from Strings: Language Model Embeddings for Bayesian Optimization

   Tung Nguyen, Qiuyi Zhang, Bangding Yang, Chansoo Lee, Jorg Bornschein, Yingjie Miao, Sagi Perel, Yutian Chen, and Xingyou Song

   Under Review, 2025

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   Bayesian Optimization is ubiquitous in the field of experimental design and blackbox optimization for improving search efficiency, but has been traditionally restricted to regression models which are only applicable to fixed search spaces and tabular input features. We propose Embed-then-Regress, a paradigm for applying in-context regression over string inputs, through the use of string embedding capabilities of pretrained language models. By expressing all inputs as strings, we are able to perform general-purpose regression for Bayesian Optimization over various domains including synthetic, combinatorial, and hyperparameter optimization, obtaining comparable results to state-of-the-art Gaussian Process-based algorithms. Code can be found at https://github.com/google-research/optformer/tree/main/optformer/embed_then_regress.

3. Preprint

   ClimDetect: A Benchmark Dataset for Climate Change Detection and Attribution

   Sungduk Yu, Brian L White, Anahita Bhiwandiwalla, Musashi Hinck, Matthew Lyle Olson, Tung Nguyen, and Vasudev Lal

   Under Review, 2025

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   Detecting and attributing temperature increases due to climate change is crucial for understanding global warming and guiding adaptation strategies. The complexity of distinguishing human-induced climate signals from natural variability has challenged traditional detection and attribution (D&A) approaches, which seek to identify specific "fingerprints" in climate response variables. Deep learning offers potential for discerning these complex patterns in expansive spatial datasets. However, lack of standard protocols has hindered consistent comparisons across studies. We introduce ClimDetect, a standardized dataset of over 816k daily climate snapshots, designed to enhance model accuracy in identifying climate change signals. ClimDetect integrates various input and target variables used in past research, ensuring comparability and consistency. We also explore the application of vision transformers (ViT) to climate data, a novel and modernizing approach in this context. Our open-access data and code serve as a benchmark for advancing climate science through improved model evaluations. ClimDetect is publicly accessible via Huggingface dataet respository at: https://huggingface.co/datasets/ClimDetect/ClimDetect.

4. ICLR

   LICO: Large language models for in-context molecular optimization

   Tung Nguyen, and Aditya Grover

   International Conference on Learning Representations, 2025

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   Optimizing black-box functions is a fundamental problem in science and engineering. To solve this problem, many approaches learn a surrogate function that estimates the underlying objective from limited historical evaluations. Large Language Models (LLMs), with their strong pattern-matching capabilities via pretraining on vast amounts of data, stand out as a potential candidate for surrogate modeling. However, directly prompting a pretrained language model to produce predictions is not feasible in many scientific domains due to the scarcity of domain-specific data in the pretraining corpora and the challenges of articulating complex problems in natural language. In this work, we introduce LICO, a general-purpose model that extends arbitrary base LLMs for black-box optimization, with a particular application to the molecular domain. To achieve this, we equip the language model with a separate embedding layer and prediction layer, and train the model to perform in-context predictions on a diverse set of functions defined over the domain. Once trained, LICO can generalize to unseen molecule properties simply via in-context prompting. LICO achieves state-of-the-art performance on PMO, a challenging molecular optimization benchmark comprising over 20 objective functions.

2024

1. NeurIPS Best Paper

   Probing the Decision Boundaries of In-context Learning in Large Language Models

   Siyan Zhao, Tung Nguyen, and Aditya Grover

   Neural Information Processing Systems, 2024

   Best Paper Award, Foundation Model Interventions Workshop, NeurIPS 2024

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   Best Paper

   In-context learning is an emergent paradigm in large language models (LLMs) that enables them to generalize to new tasks and domains by simply prompting these models with a few exemplars without explicit parameter updates. Many attempts have been made to understand in-context learning in LLMs as a function of model scale, pretraining data, and other factors. In this work, we propose a new mechanism to probe and understand in-context learning from the lens of decision boundaries for in-context binary classification. Decision boundaries are straightforward to visualize and provide important information about the qualitative behavior of the inductive biases of standard classifiers. To our surprise, we find that the decision boundaries learned by current LLMs in simple binary classification tasks are often irregularly non-smooth, regardless of task linearity. This paper investigates the factors influencing these decision boundaries and explores methods to enhance their generalizability. We assess various approaches, including training-free and fine-tuning methods for LLMs, the impact of model architecture, and the effectiveness of active prompting techniques for smoothing decision boundaries in a data-efficient manner. Our findings provide a deeper understanding of in-context learning dynamics and offer practical improvements for enhancing robustness and generalizability of in-context learning.

2. NeurIPS Oral

   Chaosbench: A multi-channel, physics-based benchmark for subseasonal-to-seasonal climate prediction

   Juan Nathaniel, Yongquan Qu, Tung Nguyen, Sungduk Yu, Julius Busecke, Aditya Grover, and Pierre Gentine

   Neural Information Processing Systems Track on Datasets and Benchmarks, 2024

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   Oral

   Accurate prediction of climate in the subseasonal-to-seasonal scale is crucial for disaster preparedness and robust decision making amidst climate change. Yet, forecasting beyond the weather timescale is challenging because it deals with problems other than initial condition, including boundary interaction, butterfly effect, and our inherent lack of physical understanding. At present, existing benchmarks tend to have shorter forecasting range of up-to 15 days, do not include a wide range of operational baselines, and lack physics-based constraints for explainability. Thus, we propose ChaosBench, a challenging benchmark to extend the predictability range of data-driven weather emulators to S2S timescale. First, ChaosBench is comprised of variables beyond the typical surface-atmospheric ERA5 to also include ocean, ice, and land reanalysis products that span over 45 years to allow for full Earth system emulation that respects boundary conditions. We also propose physics-based, in addition to deterministic and probabilistic metrics, to ensure a physically-consistent ensemble that accounts for butterfly effect. Furthermore, we evaluate on a diverse set of physics-based forecasts from four national weather agencies as baselines to our data-driven counterpart such as ViT/ClimaX, PanguWeather, GraphCast, and FourCastNetV2. Overall, we find methods originally developed for weather-scale applications fail on S2S task: their performance simply collapse to an unskilled climatology. Nonetheless, we outline and demonstrate several strategies that can extend the predictability range of existing weather emulators, including the use of ensembles, robust control of error propagation, and the use of physics-informed models. Our benchmark, datasets, and instructions are available at https://leap-stc.github.io/ChaosBench.

3. NeurIPS Best Paper

   Scaling transformer neural networks for skillful and reliable medium-range weather forecasting

   Tung Nguyen, Rohan Shah, Hritik Bansal, Troy Arcomano, Romit Maulik, Rao Kotamarthi, Ian Foster, Sandeep Madireddy, and Aditya Grover

   Neural Information Processing Systems, 2024

   Best Paper Award, Tackling Climate Change with Machine Learning Workshop, ICLR 2024

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   Best Paper

   Weather forecasting is a fundamental problem for anticipating and mitigating the impacts of climate change. Recently, data-driven approaches for weather forecasting based on deep learning have shown great promise, achieving accuracies that are competitive with operational systems. However, those methods often employ complex, customized architectures without sufficient ablation analysis, making it difficult to understand what truly contributes to their success. Here we introduce Stormer, a simple transformer model that achieves state-of-the art performance on weather forecasting with minimal changes to the standard transformer backbone. We identify the key components of Stormer through careful empirical analyses, including weather-specific embedding, randomized dynamics forecast, and pressure-weighted loss. At the core of Stormer is a randomized forecasting objective that trains the model to forecast the weather dynamics over varying time intervals. During inference, this allows us to produce multiple forecasts for a target lead time and combine them to obtain better forecast accuracy. On WeatherBench 2, Stormer performs competitively at short to medium-range forecasts and outperforms current methods beyond 7 days, while requiring orders-of-magnitude less training data and compute. Additionally, we demonstrate Stormer’s favorable scaling properties, showing consistent improvements in forecast accuracy with increases in model size and training tokens. Code and checkpoints are available at https://github.com/tung-nd/stormer.

2023

1. NeurIPS

   ExPT: Synthetic Pretraining for Few-Shot Experimental Design

   Tung Nguyen, Sudhanshu Agrawal, and Aditya Grover

   Neural Information Processing Systems, 2023

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   Experimental design is a fundamental problem in many science and engineering fields. In this problem, sample efficiency is crucial due to the time, money, and safety costs of real-world design evaluations. Existing approaches either rely on active data collection or access to large, labeled datasets of past experiments, making them impractical in many real-world scenarios. In this work, we address the more challenging yet realistic setting of few-shot experimental design, where only a few labeled data points of input designs and their corresponding values are available. We approach this problem as a conditional generation task, where a model conditions on a few labeled examples and the desired output to generate an optimal input design. To this end, we introduce Experiment Pretrained Transformers (ExPT), a foundation model for few-shot experimental design that employs a novel combination of synthetic pretraining with in-context learning. In ExPT, we only assume knowledge of a finite collection of unlabelled data points from the input domain and pretrain a transformer neural network to optimize diverse synthetic functions defined over this domain. Unsupervised pretraining allows ExPT to adapt to any design task at test time in an in-context fashion by conditioning on a few labeled data points from the target task and generating the candidate optima. We evaluate ExPT on few-shot experimental design in challenging domains and demonstrate its superior generality and performance compared to existing methods. The source code is available at https://github.com/tung-nd/ExPT.

2. NeurIPS

   ClimateLearn: Benchmarking Machine Learning for Weather and Climate Modeling

   Tung Nguyen^*, Jason Jewik^*, Hritik Bansal, Prakhar Sharma, and Aditya Grover

   Neural Information Processing Systems Track on Datasets and Benchmarks, 2023

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   Modeling weather and climate is an essential endeavor to understand the near- and long-term impacts of climate change, as well as inform technology and policymaking for adaptation and mitigation efforts. In recent years, there has been a surging interest in applying data-driven methods based on machine learning for solving core problems such as weather forecasting and climate downscaling. Despite promising results, much of this progress has been impaired due to the lack of large-scale, open-source efforts for reproducibility, resulting in the use of inconsistent or underspecified datasets, training setups, and evaluations by both domain scientists and artificial intelligence researchers. We introduce ClimateLearn, an open-source PyTorch library that vastly simplifies the training and evaluation of machine learning models for data-driven climate science. ClimateLearn consists of holistic pipelines for dataset processing (e.g., ERA5, CMIP6, PRISM), implementation of state-of-the-art deep learning models (e.g., Transformers, ResNets), and quantitative and qualitative evaluation for standard weather and climate modeling tasks. We supplement these functionalities with extensive documentation, contribution guides, and quickstart tutorials to expand access and promote community growth. We have also performed comprehensive forecasting and downscaling experiments to showcase the capabilities and key features of our library. To our knowledge, ClimateLearn is the first large-scale, open-source effort for bridging research in weather and climate modeling with modern machine learning systems. Our library is available publicly at https://github.com/aditya-grover/climate-learn.

3. ICML Best Paper

   ClimaX: A foundation model for weather and climate

   Tung Nguyen, Johannes Brandstetter, Ashish Kapoor , Jayesh K Gupta, and Aditya Grover

   International Conference on Machine Learning, 2023

   Best Paper Award, Synergy of Scientific and Machine Learning Modeling Workshop, ICML 2023

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   Best Paper

   Most state-of-the-art approaches for weather and climate modeling are based on physics-informed numerical models of the atmosphere. These approaches aim to model the non-linear dynamics and complex interactions between multiple variables, which are challenging to approximate. Additionally, many such numerical models are computationally intensive, especially when modeling the atmospheric phenomenon at a fine-grained spatial and temporal resolution. Recent data-driven approaches based on machine learning instead aim to directly solve a downstream forecasting or projection task by learning a data-driven functional mapping using deep neural networks. However, these networks are trained using curated and homogeneous climate datasets for specific spatiotemporal tasks, and thus lack the generality of numerical models. We develop and demonstrate ClimaX, a flexible and generalizable deep learning model for weather and climate science that can be trained using heterogeneous datasets spanning different variables, spatio-temporal coverage, and physical groundings. ClimaX extends the Transformer architecture with novel encoding and aggregation blocks that allow effective use of available compute while maintaining general utility. ClimaX is pre-trained with a self-supervised learning objective on climate datasets derived from CMIP6. The pre-trained ClimaX can then be fine-tuned to address a breadth of climate and weather tasks, including those that involve atmospheric variables and spatio-temporal scales unseen during pretraining. Compared to existing data-driven baselines, we show that this generality in ClimaX results in superior performance on benchmarks for weather forecasting and climate projections, even when pretrained at lower resolutions and compute budgets. The source code is available at https://github.com/microsoft/ClimaX.

2022

1. ICML

   Transformer Neural Processes: Uncertainty-Aware Meta Learning Via Sequence Modeling

   Tung Nguyen, and Aditya Grover

   International Conference on Machine Learning, 2022

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   Neural Processes (NPs) are a popular class of approaches for meta-learning. Similar to Gaussian Processes (GPs), NPs define distributions over functions and can estimate uncertainty in their predictions. However, unlike GPs, NPs and their variants suffer from underfitting and often have intractable likelihoods, which limit their applications in sequential decision making. We propose Transformer Neural Processes (TNPs), a new member of the NP family that casts uncertainty-aware meta learning as a sequence modeling problem. We learn TNPs via an autoregressive likelihood-based objective and instantiate it with a novel transformer-based architecture. The model architecture respects the inductive biases inherent to the problem structure, such as invariance to the observed data points and equivariance to the unobserved points. We further investigate knobs within the TNP framework that tradeoff expressivity of the decoding distribution with extra computation. Empirically, we show that TNPs achieve state-of-the-art performance on various benchmark problems, outperforming all previous NP variants on meta regression, image completion, contextual multi-armed bandits, and Bayesian optimization.

2. Workshop

   Reliable conditioning of behavioral cloning for offline reinforcement learning

   Tung Nguyen, Qinqing Zheng, and Aditya Grover

   NeurIPS 2022 Foundation Models for Decision Making Workshop, 2022

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   Behavioral cloning (BC) provides a straightforward solution to offline RL by mimicking offline trajectories via supervised learning. Recent advances (Chen et al., 2021; Janner et al., 2021; Emmons et al., 2021) have shown that by conditioning on desired future returns, BC can perform competitively to their value-based counterparts, while enjoying much more simplicity and training stability. While promising, we show that these methods can be unreliable, as their performance may degrade significantly when conditioned on high, out-of-distribution (ood) returns. This is crucial in practice, as we often expect the policy to perform better than the offline dataset by conditioning on an ood value. We show that this unreliability arises from both the suboptimality of training data and model architectures. We propose ConserWeightive Behavioral Cloning (CWBC), a simple and effective method for improving the reliability of conditional BC with two key components: trajectory weighting and conservative regularization. Trajectory weighting upweights the high-return trajectories to reduce the train-test gap for BC methods, while conservative regularizer encourages the policy to stay close to the data distribution for ood conditioning. We study CWBC in the context of RvS (Emmons et al., 2021) and Decision Transformers (Chen et al., 2021), and show that CWBC significantly boosts their performance on various benchmarks.

2021

1. ICML

   Temporal predictive coding for model-based planning in latent space

   Tung Nguyen^*, Rui Shu^*, Tuan Pham^*, Hung Bui, and Stefano Ermon

   International Conference on Machine Learning, 2021

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   High-dimensional observations are a major challenge in the application of model-based reinforcement learning (MBRL) to real-world environments. To handle high-dimensional sensory inputs, existing approaches use representation learning to map high-dimensional observations into a lower-dimensional latent space that is more amenable to dynamics estimation and planning. In this work, we present an information-theoretic approach that employs temporal predictive coding to encode elements in the environment that can be predicted across time. Since this approach focuses on encoding temporally-predictable information, we implicitly prioritize the encoding of task-relevant components over nuisance information within the environment that are provably task-irrelevant. By learning this representation in conjunction with a recurrent state space model, we can then perform planning in latent space. We evaluate our model on a challenging modification of standard DMControl tasks where the background is replaced with natural videos that contain complex but irrelevant information to the planning task. Our experiments show that our model is superior to existing methods in the challenging complex-background setting while remaining competitive with current state-of-the-art models in the standard setting.

2020

1. ICML

   Predictive coding for locally-linear control

   Rui Shu, Tung Nguyen^*, Yinlam Chow, Tuan Pham, Khoat Than, Mohammad Ghavamzadeh, Stefano Ermon, and Hung Bui

   International Conference on Machine Learning, 2020

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   High-dimensional observations and unknown dynamics are major challenges when applying optimal control to many real-world decision making tasks. The Learning Controllable Embedding (LCE) framework addresses these challenges by embedding the observations into a lower dimensional latent space, estimating the latent dynamics, and then performing control directly in the latent space. To ensure the learned latent dynamics are predictive of next-observations, all existing LCE approaches decode back into the observation space and explicitly perform next-observation prediction—a challenging high-dimensional task that furthermore introduces a large number of nuisance parameters (ie, the decoder) which are discarded during control. In this paper, we propose a novel information-theoretic LCE approach and show theoretically that explicit next-observation prediction can be replaced with predictive coding. We then use predictive coding to develop a decoder-free LCE model whose latent dynamics are amenable to locally-linear control. Extensive experiments on benchmark tasks show that our model reliably learns a controllable latent space that leads to superior performance when compared with state-of-the-art LCE baselines.

2019

1. IEEE Big Data

   Infinite dropout for training bayesian models from data streams

   Van-Son Nguyen, Tung Nguyen, Linh Ngo Van, and Khoat Than

   IEEE International Conference on Big Data, 2019

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   The ability to continuously train Bayesian models in streaming environments is highly important in the era of big data. However, it has to face the famous stability-plasticity dilemma and the problem of noisy and sparse data. We propose a novel and easy-to-implement framework, called Infinite Dropout (iDropout), to address these challenges. iDropout has an easy mechanism to balance between old and new information, which allows models to trade off stability against plasticity. Thanks to the ability to reduce overfitting and the ensemble property of Dropout, our framework obtains better generalization, thus effectively handles undesirable effects of noise and sparsity. Further, iDropout is able to adapt quickly to abnormal changes in data streams. We theoretically analyze the equivalence of Dropout in iDropout to a regularizer, well applied to a much larger context than what was known before. Extensive experiments show that iDropout significantly outperforms the state-of-the-art baselines.