On Selecting Robust Approaches for Learning Predictive Biomarkers in Metabolomics Data Sets.
Thibaud Godon
Pier-Luc Plante
Jacques Corbeil
Pascal Germain
Alexandre Drouin
Metabolomics, the study of small molecules within biological systems, offers insights into metabolic processes and, consequently, holds grea… (see more)t promise for advancing health outcomes. Biomarker discovery in metabolomics represents a significant challenge, notably due to the high dimensionality of the data. Recent work has addressed this problem by analyzing the most important variables in machine learning models. Unfortunately, this approach relies on prior hypotheses about the structure of the data and may overlook simple patterns. To assess the true usefulness of machine learning methods, we evaluate them on a collection of 835 metabolomics data sets. This effort provides valuable insights for metabolomics researchers regarding where and when to use machine learning. It also establishes a benchmark for the evaluation of future methods. Nonetheless, the results emphasize the high diversity of data sets in metabolomics and the complexity of finding biologically relevant biomarkers. As a result, we propose a novel approach applicable across all data sets, offering guidance for future analyses. This method involves directly comparing univariate and multivariate models. We demonstrate through selected examples how this approach can guide data analysis across diverse data set structures, representative of the observed variability. Code and data are available for research purposes.
2025-06-12
Analytical Chemistry (published)
doi.org
Beyond Cosine Decay: On the effectiveness of Infinite Learning Rate Schedule for Continual Pre-training
Vaibhav Singh
Paul Janson
Paria Mehrbod
Adam Ibrahim
Irina Rish
Eugene Belilovsky
Benjamin Thérien
The ever-growing availability of unlabeled data presents both opportunities and challenges for training artificial intelligence systems. Whi… (see more)le self-supervised learning (SSL) has emerged as a powerful paradigm for extracting meaningful representations from vast amounts of unlabeled data, existing methods still struggle to adapt to the non-stationary, non-IID nature of real-world data streams without forgetting previously learned knowledge. Recent works have adopted a repeated cosine annealing schedule for large-scale continual pre-training; however, these schedules (1) inherently cause forgetting during the re-warming phase and (2) have not been systematically compared to existing continual SSL methods. In this work, we systematically compare the widely used cosine schedule with the recently proposed infinite learning rate schedule and empirically find the latter to be a more effective alternative. Our extensive empirical evaluation across diverse image and language datasets demonstrates that the infinite learning rate schedule consistently enhances continual pre-training performance compared to a repeated cosine decay without being restricted to a fixed iteration budget. For instance, in a small-scale MAE pre-training setup, it outperforms several strong baselines from the literature. We then scale up our experiments to larger MAE pre-training and autoregressive language model pre-training. Our results show that the infinite learning rate schedule remains effective at scale, surpassing repeated cosine decay for both MAE pre-training and zero-shot LM benchmarks.
2025-06-11
ICML.cc/2025/Workshop/ES-FoMo-III (published)
doi.org
openreview.net
Causal Climate Emulation with Bayesian Filtering
Sebastian H. M. Hickman
Ilija Trajkovic
Julia Kaltenborn
Francis Pelletier
Alex Archibald
Yaniv Gurwicz
Peer Nowack
David Rolnick
Julien Boussard
Traditional models of climate change use complex systems of coupled equations to simulate physical processes across the Earth system. These … (see more)simulations are highly computationally expensive, limiting our predictions of climate change and analyses of its causes and effects. Machine learning has the potential to quickly emulate data from climate models, but current approaches are not able to incorporate physics-informed causal relationships. Here, we develop an interpretable climate model emulator based on causal representation learning. We derive a physics-informed approach including a Bayesian filter for stable long-term autoregressive emulation. We demonstrate that our emulator learns accurate climate dynamics, and we show the importance of each one of its components on a realistic synthetic dataset and data from two widely deployed climate models.
2025-06-11
ArXiv (preprint)
doi.org
arxiv.org
Causal Climate Emulation with Bayesian Filtering
Sebastian H. M. Hickman
Ilija Trajkovic
Julia Kaltenborn
Francis Pelletier
Alex Archibald
Yaniv Gurwicz
Peer Nowack
David Rolnick
Julien Boussard
Traditional models of climate change use complex systems of coupled equations to simulate physical processes across the Earth system. These … (see more)simulations are highly computationally expensive, limiting our predictions of climate change and analyses of its causes and effects. Machine learning has the potential to quickly emulate data from climate models, but current approaches are not able to incorporate physics-informed causal relationships. Here, we develop an interpretable climate model emulator based on causal representation learning. We derive a physics-informed approach including a Bayesian filter for stable long-term autoregressive emulation. We demonstrate that our emulator learns accurate climate dynamics, and we show the importance of each one of its components on a realistic synthetic dataset and data from two widely deployed climate models.
2025-06-11
ArXiv (preprint)
arxiv.org
arxiv.org
Fast Monte Carlo Tree Diffusion: 100x Speedup via Parallel Sparse Planning
Jaesik Yoon
Hyeonseo Cho
Yoshua Bengio
Sungjin Ahn
Diffusion models have recently emerged as a powerful approach for trajectory planning. However, their inherently non-sequential nature limit… (see more)s their effectiveness in long-horizon reasoning tasks at test time. The recently proposed Monte Carlo Tree Diffusion (MCTD) offers a promising solution by combining diffusion with tree-based search, achieving state-of-the-art performance on complex planning problems. Despite its strengths, our analysis shows that MCTD incurs substantial computational overhead due to the sequential nature of tree search and the cost of iterative denoising. To address this, we propose Fast-MCTD, a more efficient variant that preserves the strengths of MCTD while significantly improving its speed and scalability. Fast-MCTD integrates two techniques: Parallel MCTD, which enables parallel rollouts via delayed tree updates and redundancy-aware selection; and Sparse MCTD, which reduces rollout length through trajectory coarsening. Experiments show that Fast-MCTD achieves up to 100x speedup over standard MCTD while maintaining or improving planning performance. Remarkably, it even outperforms Diffuser in inference speed on some tasks, despite Diffuser requiring no search and yielding weaker solutions. These results position Fast-MCTD as a practical and scalable solution for diffusion-based inference-time reasoning.
2025-06-11
ArXiv (preprint)
arxiv.org
arxiv.org
Fast Monte Carlo Tree Diffusion: 100x Speedup via Parallel Sparse Planning
Jaesik Yoon
Hyeonseo Cho
Yoshua Bengio
Sungjin Ahn
Diffusion models have recently emerged as a powerful approach for trajectory planning. However, their inherently non-sequential nature limit… (see more)s their effectiveness in long-horizon reasoning tasks at test time. The recently proposed Monte Carlo Tree Diffusion (MCTD) offers a promising solution by combining diffusion with tree-based search, achieving state-of-the-art performance on complex planning problems. Despite its strengths, our analysis shows that MCTD incurs substantial computational overhead due to the sequential nature of tree search and the cost of iterative denoising. To address this, we propose Fast-MCTD, a more efficient variant that preserves the strengths of MCTD while significantly improving its speed and scalability. Fast-MCTD integrates two techniques: Parallel MCTD, which enables parallel rollouts via delayed tree updates and redundancy-aware selection; and Sparse MCTD, which reduces rollout length through trajectory coarsening. Experiments show that Fast-MCTD achieves up to 100x speedup over standard MCTD while maintaining or improving planning performance. Remarkably, it even outperforms Diffuser in inference speed on some tasks, despite Diffuser requiring no search and yielding weaker solutions. These results position Fast-MCTD as a practical and scalable solution for diffusion-based inference-time reasoning.
2025-06-11
ArXiv (preprint)
doi.org
arxiv.org
HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data
Hiren Madhu
João Felipe Rocha
Tinglin Huang
Siddharth Viswanath
Smita Krishnaswamy
Rex Ying
2025-06-11
ArXiv (preprint)
arxiv.org
arxiv.org
IntPhys 2: Benchmarking Intuitive Physics Understanding In Complex Synthetic Environments
Florian Bordes
Quentin Garrido
Justine T Kao
Adina Williams
Michael Rabbat
Emmanuel Dupoux
We present IntPhys 2, a video benchmark designed to evaluate the intuitive physics understanding of deep learning models. Building on the or… (see more)iginal IntPhys benchmark, IntPhys 2 focuses on four core principles related to macroscopic objects: Permanence, Immutability, Spatio-Temporal Continuity, and Solidity. These conditions are inspired by research into intuitive physical understanding emerging during early childhood. IntPhys 2 offers a comprehensive suite of tests, based on the violation of expectation framework, that challenge models to differentiate between possible and impossible events within controlled and diverse virtual environments. Alongside the benchmark, we provide performance evaluations of several state-of-the-art models. Our findings indicate that while these models demonstrate basic visual understanding, they face significant challenges in grasping intuitive physics across the four principles in complex scenes, with most models performing at chance levels (50%), in stark contrast to human performance, which achieves near-perfect accuracy. This underscores the gap between current models and human-like intuitive physics understanding, highlighting the need for advancements in model architectures and training methodologies.
2025-06-11
ArXiv (preprint)
arxiv.org
arxiv.org
IntPhys 2: Benchmarking Intuitive Physics Understanding In Complex Synthetic Environments
Florian Bordes
Quentin Garrido
Justine T Kao
Adina Williams
Michael Rabbat
Emmanuel Dupoux
We present IntPhys 2, a video benchmark designed to evaluate the intuitive physics understanding of deep learning models. Building on the or… (see more)iginal IntPhys benchmark, IntPhys 2 focuses on four core principles related to macroscopic objects: Permanence, Immutability, Spatio-Temporal Continuity, and Solidity. These conditions are inspired by research into intuitive physical understanding emerging during early childhood. IntPhys 2 offers a comprehensive suite of tests, based on the violation of expectation framework, that challenge models to differentiate between possible and impossible events within controlled and diverse virtual environments. Alongside the benchmark, we provide performance evaluations of several state-of-the-art models. Our findings indicate that while these models demonstrate basic visual understanding, they face significant challenges in grasping intuitive physics across the four principles in complex scenes, with most models performing at chance levels (50%), in stark contrast to human performance, which achieves near-perfect accuracy. This underscores the gap between current models and human-like intuitive physics understanding, highlighting the need for advancements in model architectures and training methodologies.
2025-06-11
ArXiv (preprint)
doi.org
arxiv.org
Learning What Matters: Prioritized Concept Learning via Relative Error-driven Sample Selection
Shivam Chandhok
Qian Yang
Oscar Mañas
Kanishk Jain
Leonid Sigal
Aishwarya Agrawal
Instruction tuning has been central to the success of recent vision-language models (VLMs), but it remains expensive-requiring large-scale d… (see more)atasets, high-quality annotations, and large compute budgets. We propose PRioritized cOncept learninG via Relative Error-driven Sample Selection (PROGRESS), a data- and compute-efficient framework that enables VLMs to dynamically select what to learn next based on their evolving needs during training. At each stage, the model tracks its learning progress across skills and selects the most informative samples-those it has not already mastered and that are not too difficult to learn at the current stage of training. This strategy effectively controls skill acquisition and the order in which skills are learned. Specifically, we sample from skills showing the highest learning progress, prioritizing those with the most rapid improvement. Unlike prior methods, PROGRESS requires no upfront answer annotations, queries answers only on a need basis, avoids reliance on additional supervision from auxiliary VLMs, and does not require compute-heavy gradient computations for data selection. Experiments across multiple instruction-tuning datasets of varying scales demonstrate that PROGRESS consistently outperforms state-of-the-art baselines with much less data and supervision. Additionally, we show strong cross-architecture generalization and transferability to larger models, validating PROGRESS as a scalable solution for efficient learning.
2025-06-11
ICML.cc/2025/Workshop/ES-FoMo-III (published)
doi.org
openreview.net
Mapping Delayed Canopy Loss and Durable Fire Refugia for the 2020 Wildfires in Washington State Using Multiple Sensors
Anika M. Anderson
Meg A. Krawchuk
Flavie Pelletier
Jeff Cardille
2025-06-11
Fire (published)
doi.org
Mixture-of-Recursions: Learning Dynamic Recursive Depths for Adaptive Token-Level Thinking
Sangmin Bae
Yujin Kim
Reza Bayat
Sungnyun Kim
Jiyoun Ha
Tal Schuster
Adam Fisch
Hrayr Harutyunyan
Ziwei Ji
Aaron Courville
Se-Young Yun
Scaling language models unlocks impressive capabilities, but the accompanying computational and memory demands make both training and deploy… (see more)ment expensive. Existing efficiency efforts typically target either parameter sharing or adaptive computation, leaving open the question of how to attain both simultaneously. We introduce Mixture-of-Recursions (MoR), a unified framework that combines the two axes of efficiency inside a single Recursive Transformer. MoR reuses a shared stack of layers across recursion steps to achieve parameter efficiency, while lightweight routers enable adaptive token-level thinking by dynamically assign recursion depth to tokens, thereby focusing quadratic attention computation only where it is most useful. Further enhancing its efficiency, MoR incorporates a recursion-wise key-value caching mechanism that eliminates redundant memory access across recursion steps by selectively storing only the key-value caches for designated tokens. Across pretraining runs at model scales ranging from 135M to 1.7B parameters, MoR forms a new Pareto frontier: at equal training FLOPs and smaller model sizes, it significantly lowers validation perplexity and improves few-shot accuracy, while delivering higher throughput compared with vanilla and existing recursive baselines. These gains demonstrate that MoR is an effective path towards large-model quality without incurring large-model cost.
2025-06-11
ICML.cc/2025/Workshop/ES-FoMo-III (published)
openreview.net
openreview.net