Publications

GreenHyperSpectra: A multi-source hyperspectral dataset for global vegetation trait prediction
Eya Cherif
Arthur Ouaknine
Luke A. Brown
Phuong D. Dao
Kyle R. Kovach
Bing Lu
Daniel Mederer
Hannes Feilhauer
Teja Kattenborn
David Rolnick
Plant traits such as leaf carbon content and leaf mass are essential variables in the study of biodiversity and climate change. However, con… (see more)ventional field sampling cannot feasibly cover trait variation at ecologically meaningful spatial scales. Machine learning represents a valuable solution for plant trait prediction across ecosystems, leveraging hyperspectral data from remote sensing. Nevertheless, trait prediction from hyperspectral data is challenged by label scarcity and substantial domain shifts (\eg across sensors, ecological distributions), requiring robust cross-domain methods. Here, we present GreenHyperSpectra, a pretraining dataset encompassing real-world cross-sensor and cross-ecosystem samples designed to benchmark trait prediction with semi- and self-supervised methods. We adopt an evaluation framework encompassing in-distribution and out-of-distribution scenarios. We successfully leverage GreenHyperSpectra to pretrain label-efficient multi-output regression models that outperform the state-of-the-art supervised baseline. Our empirical analyses demonstrate substantial improvements in learning spectral representations for trait prediction, establishing a comprehensive methodological framework to catalyze research at the intersection of representation learning and plant functional traits assessment. All code and data are available at: https://github.com/echerif18/HyspectraSSL.
2025-09-17
NeurIPS.cc/2025/Datasets_and_Benchmarks_Track (poster)
doi.org
openreview.net
Learning to Solve Complex Problems via Dataset Decomposition
Wanru Zhao
Lucas Caccia
Zhengyan Shi
Minseon Kim
Weijia Xu
Xingdi Yuan
Alessandro Sordoni
Marc-Alexandre Côté
2025-09-17
NeurIPS.cc/2025/Conference (poster)
openreview.net
openreview.net
Mind the GAP! The Challenges of Scale in Pixel-based Deep Reinforcement Learning
Ghada Sokar
Pablo Samuel Castro
2025-09-17
NeurIPS.cc/2025/Conference (poster)
doi.org
openreview.net
POCO: Scalable Neural Forecasting through Population Conditioning
Yu Duan
Hamza Tahir Chaudhry
Misha B. Ahrens
Christopher D. Harvey
Matthew G. Perich
Karl Deisseroth
Kanaka Rajan
Predicting future neural activity is a core challenge in modeling brain dynamics, with applications ranging from scientific investigation to… (see more) closed-loop neurotechnology. While recent models of population activity emphasize interpretability and behavioral decoding, neural forecasting-particularly across multi-session, spontaneous recordings-remains underexplored. We introduce POCO, a unified forecasting model that combines a lightweight univariate forecaster with a population-level encoder to capture both neuron-specific and brain-wide dynamics. Trained across five calcium imaging datasets spanning zebrafish, mice, and C. elegans, POCO achieves state-of-the-art accuracy at cellular resolution in spontaneous behaviors. After pre-training, POCO rapidly adapts to new recordings with minimal fine-tuning. Notably, POCO's learned unit embeddings recover biologically meaningful structure-such as brain region clustering-without any anatomical labels. Our comprehensive analysis reveals several key factors influencing performance, including context length, session diversity, and preprocessing. Together, these results position POCO as a scalable and adaptable approach for cross-session neural forecasting and offer actionable insights for future model design. By enabling accurate, generalizable forecasting models of neural dynamics across individuals and species, POCO lays the groundwork for adaptive neurotechnologies and large-scale efforts for neural foundation models. Code is available at https://github.com/yuvenduan/POCO.
2025-09-17
NeurIPS.cc/2025/Conference (poster)
doi.org
openreview.net
Risks of AI scientists: prioritizing safeguarding over autonomy
Xiangru Tang
Qiao Jin
Kunlun Zhu
Tongxin Yuan
Yichi Zhang
Wangchunshu Zhou
Meng Qu
Yilun Zhao
Jian Tang
Zhuosheng Zhang
Arman Cohan
Dov Greenbaum
Zhiyong Lu
Mark Gerstein
AI scientists powered by large language models have demonstrated substantial promise in autonomously conducting experiments and facilitating… (see more) scientific discoveries across various disciplines. While their capabilities are promising, these agents also introduce novel vulnerabilities that require careful consideration for safety. However, there has been limited comprehensive exploration of these vulnerabilities. This perspective examines vulnerabilities in AI scientists, shedding light on potential risks associated with their misuse, and emphasizing the need for safety measures. We begin by providing an overview of the potential risks inherent to AI scientists, taking into account user intent, the specific scientific domain, and their potential impact on the external environment. Then, we explore the underlying causes of these vulnerabilities and provide a scoping review of the limited existing works. Based on our analysis, we propose a triadic framework involving human regulation, agent alignment, and an understanding of environmental feedback (agent regulation) to mitigate these identified risks. Furthermore, we highlight the limitations and challenges associated with safeguarding AI scientists and advocate for the development of improved models, robust benchmarks, and comprehensive regulations.
2025-09-17
Nature Communications (published)
doi.org
SEEA-R1: Tree-Structured Reinforcement Fine-Tuning for Self-Evolving Embodied Agents
Wanxin Tian
Shijie Zhang
Kevin Zhang
Xiaowei Chi
Chun-Kai Fan
Junyu Lu
Yulin Luo
Qiang Zhou
Yiming Zhao
Ning Liu
Siyu Lin
Zhiyuan Qin
Xiaozhu Ju
Shanghang Zhang
Jian Tang
2025-09-17
NeurIPS.cc/2025/Conference (poster)
openreview.net
openreview.net
State Entropy Regularization for Robust Reinforcement Learning
Yonatan Ashlag
Uri Koren
Mirco Mutti
Esther Derman
Pierre-Luc Bacon
Shie Mannor
State entropy regularization has empirically shown better exploration and sample complexity in reinforcement learning (RL). However, its the… (see more)oretical guarantees have not been studied. In this paper, we show that state entropy regularization improves robustness to structured and spatially correlated perturbations. These types of variation are common in transfer learning but often overlooked by standard robust RL methods, which typically focus on small, uncorrelated changes. We provide a comprehensive characterization of these robustness properties, including formal guarantees under reward and transition uncertainty, as well as settings where the method performs poorly. Much of our analysis contrasts state entropy with the widely used policy entropy regularization, highlighting their different benefits. Finally, from a practical standpoint, we illustrate that compared with policy entropy, the robustness advantages of state entropy are more sensitive to the number of rollouts used for policy evaluation.
2025-09-17
NeurIPS.cc/2025/Conference (oral)
doi.org
openreview.net
THUNDER: Tile-level Histopathology image UNDERstanding benchmark
Pierre Marza
Leo Fillioux
Sofiène Boutaj
KUNAL MAHATHA
Christian Desrosiers
Pablo Piantanida
Jose Dolz
Stergios Christodoulidis
Maria Vakalopoulou
Progress in a research field can be hard to assess, in particular when many concurrent methods are proposed in a short period of time. This … (see more)is the case in digital pathology, where many foundation models have been released recently to serve as feature extractors for tile-level images, being used in a variety of downstream tasks, both for tile- and slide-level problems. Benchmarking available methods then becomes paramount to get a clearer view of the research landscape. In particular, in critical domains such as healthcare, a benchmark should not only focus on evaluating downstream performance, but also provide insights about the main differences between methods, and importantly, further consider uncertainty and robustness to ensure a reliable usage of proposed models. For these reasons, we introduce THUNDER, a tile-level benchmark for digital pathology foundation models, allowing for efficient comparison of many models on diverse datasets with a series of downstream tasks, studying their feature spaces and assessing the robustness and uncertainty of predictions informed by their embeddings. THUNDER is a fast, easy-to-use, dynamic benchmark that can already support a large variety of state-of-the-art foundation, as well as local user-defined models for direct tile-based comparison. In this paper, we provide a comprehensive comparison of 23 foundation models on 16 different datasets covering diverse tasks, feature analysis, and robustness. The code for THUNDER is publicly available at https://github.com/MICS-Lab/thunder.
2025-09-17
NeurIPS.cc/2025/Datasets_and_Benchmarks_Track (spotlight)
openreview.net
openreview.net
On Traceability in $\ell_p$ Stochastic Convex Optimization
Sasha Voitovych
MAHDI HAGHIFAM
Idan Attias
Gintare Karolina Dziugaite
Roi Livni
Daniel M. Roy
In this paper, we investigate the necessity of traceability for accurate learning in stochastic convex optimization (SCO) under …
2025-09-17
NeurIPS.cc/2025/Conference (spotlight)
doi.org
openreview.net
Transforming Generic Coder LLMs to Effective Binary Code Embedding Models for Similarity Detection
Litao Li
Leo Song
Steven Ding
Benjamin C. M. Fung
Philippe Charland
Cybersecurity and software research have crossed paths with modern deep learning research for a few years. The power of large language model… (see more)s (LLMs) in particular has intrigued us to apply them to understanding binary code. In this paper, we investigate some of the many ways LLMs can be applied to binary code similarity detection, as it is a significantly more difficult task compared to source code similarity detection due to the sparsity of information and less meaningful syntax. It also has great practical implications, such as vulnerability and malware detection. We find that pretrained LLMs are mostly capable of detecting similar binary code, even with a zero-shot setting. Our main contributions and findings are to provide several supervised fine-tuning methods that, when combined, significantly surpass zero-shot LLMs and state-of-the-art binary code similarity detection methods. Specifically, we up-train the model through data augmentation, translation-style causal learning, LLM2Vec, and cumulative GTE loss. With a complete ablation study, we show that our training method can transform a generic language model into a powerful binary similarity expert, and is also robust and general enough for cross-optimization, cross-architecture, and cross-obfuscation detection.
2025-09-17
NeurIPS.cc/2025/Conference (poster)
openreview.net
openreview.net
CellSexID: Sex-Based Computational Tracking of Cellular Origins in Chimeric Models
Huilin Tai
Qian Li
Jingtao Wang
Jiahui Tan
Bowen Zhao
Ryann Lang
Basil J. Petrof
Jun Ding
Cell tracking in chimeric models is essential yet challenging, particularly in developmental biology, regenerative medicine, and transplanta… (see more)tion studies. Existing methods, such as fluorescent labeling and genetic barcoding, are technically demanding, costly, and often impractical for dynamic, heterogeneous tissues. To address these limitations, we propose a computational framework that leverages sex as a surrogate marker for cell tracking. Our approach uses a machine learning model trained on single-cell transcriptomic data to predict cell sex with high accuracy, enabling clear distinction between donor (male) and recipient (female) cells in sex-mismatched chimeric models. The model identifies specific genes critical for sex prediction and has been validated using public datasets and experimental flow sorting, confirming the biological relevance of the identified cell populations. Applied to skeletal muscle macrophages, our method revealed distinct transcriptional profiles associated with cellular origins. This pipeline offers a robust, cost-effective solution for cell tracking in chimeric models, advancing research in regenerative medicine and immunology by providing precise insights into cellular origins and therapeutic outcomes.
2025-09-16
Cell Reports Methods (published)
doi.org
Combining cortical and spinal stimulation maximizes improvement of gait after spinal cord injury
Roxanne Drainville
Marco Bonizzato
Davide Burchielli
Rose Guay-Hottin
Alexandre Sheasby
Marina Martinez
Most spinal cord injuries (SCI) spare descending motor pathways and sublesional networks, which can be activated through motor cortex and sp… (see more)inal cord stimulation to mitigate locomotor deficits. However, the potential synergy between cortical and spinal stimulation as a neuroprosthetic intervention remains unknown. Here, we first investigated phase-locked electrical stimulation of the motor cortex and lumbar spinal cord at 40 Hz in a rat model of unilateral SCI. Combining cortical and lumbar stimulation around the anticipated lift synergistically enhanced leg movements. When integrated into rehabilitation training, cortical stimulation proved essential for recovery of skilled locomotion. As a further refinement, we next investigated the effects of high-frequency (330 Hz) lumbar and sacral stimulation combined with cortical stimulation. Timely integration during the swing phase showed that cortical and rostral lumbar stimulations enhance the initial and mid-swing phases, while sacral stimulation improves extension velocity in the late swing. These findings indicate that supraspinal and sublesional neuromodulation offer complementary neuroprosthetic effects in targeted SCI gait rehabilitation. Cortical and spinal stimulations summate motor outputs via distinct pathways. Each improves gait post-SCI, but combined stimulation maximizes gait improvement. Integrating cortico-spinal stimulation into rehabilitation promotes lasting recovery. EES capabilities extended using high-frequency lumbosacral protocols.
2025-09-16
iScience (published)
doi.org