Scientific Discovery
CodeScientist: End-to-End Semi-Automated Scientific Discovery with Code-based Experimentation
Jansen, Peter, Tafjord, Oyvind, Radensky, Marissa, Siangliulue, Pao, Hope, Tom, Mishra, Bhavana Dalvi, Majumder, Bodhisattwa Prasad, Weld, Daniel S., Clark, Peter
Despite the surge of interest in autonomous scientific discovery (ASD) of software artifacts (e.g., improved ML algorithms), current ASD systems face two key limitations: (1) they largely explore variants of existing codebases or similarly constrained design spaces, and (2) they produce large volumes of research artifacts (such as automatically generated papers and code) that are typically evaluated using conference-style paper review with limited evaluation of code. In this work we introduce CodeScientist, a novel ASD system that frames ideation and experiment construction as a form of genetic search jointly over combinations of research articles and codeblocks defining common actions in a domain (like prompting a language model). We use this paradigm to conduct hundreds of automated experiments on machine-generated ideas broadly in the domain of agents and virtual environments, with the system returning 19 discoveries, 6 of which were judged as being both at least minimally sound and incrementally novel after a multi-faceted evaluation beyond that typically conducted in prior work, including external (conference-style) review, code review, and replication attempts. Moreover, the discoveries span new tasks, agents, metrics, and data, suggesting a qualitative shift from benchmark optimization to broader discoveries.
State Space Model Meets Transformer: A New Paradigm for 3D Object Detection
Wang, Chuxin, Yang, Wenfei, Liu, Xiang, Zhang, Tianzhu
DETR-based methods, which use multi-layer transformer decoders to refine object queries iteratively, have shown promising performance in 3D indoor object detection. However, the scene point features in the transformer decoder remain fixed, leading to minimal contributions from later decoder layers, thereby limiting performance improvement. Recently, State Space Models (SSM) have shown efficient context modeling ability with linear complexity through iterative interactions between system states and inputs. Inspired by SSMs, we propose a new 3D object DEtection paradigm with an interactive STate space model (DEST). In the interactive SSM, we design a novel state-dependent SSM parameterization method that enables system states to effectively serve as queries in 3D indoor detection tasks. In addition, we introduce four key designs tailored to the characteristics of point cloud and SSM: The serialization and bidirectional scanning strategies enable bidirectional feature interaction among scene points within the SSM. The inter-state attention mechanism models the relationships between state points, while the gated feed-forward network enhances inter-channel correlations. To the best of our knowledge, this is the first method to model queries as system states and scene points as system inputs, which can simultaneously update scene point features and query features with linear complexity. Extensive experiments on two challenging datasets demonstrate the effectiveness of our DEST-based method. Our method improves the GroupFree baseline in terms of AP50 on ScanNet V2 (+5.3) and SUN RGB-D (+3.2) datasets. Based on the VDETR baseline, Our method sets a new SOTA on the ScanNetV2 and SUN RGB-D datasets.
Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions
Gridach, Mourad, Nanavati, Jay, Abidine, Khaldoun Zine El, Mendes, Lenon, Mack, Christina
The integration of Agentic AI into scientific discovery marks a new frontier in research automation. These AI systems, capable of reasoning, planning, and autonomous decision-making, are transforming how scientists perform literature review, generate hypotheses, conduct experiments, and analyze results. This survey provides a comprehensive overview of Agentic AI for scientific discovery, categorizing existing systems and tools, and highlighting recent progress across fields such as chemistry, biology, and materials science. We discuss key evaluation metrics, implementation frameworks, and commonly used datasets to offer a detailed understanding of the current state of the field. Finally, we address critical challenges, such as literature review automation, system reliability, and ethical concerns, while outlining future research directions that emphasize human-AI collaboration and enhanced system calibration. The rapid advancements of Large Language Models (LLMs) (Touvron et al., 2023; Anil et al., 2023; Achiam et al., 2023) have opened a new era in scientific discovery, with Agentic AI systems (Kim et al., 2024; Guo et al., 2023; Wang et al., 2024; Abramovich et al., 2024) emerging as powerful tools for automating complex research workflows. Unlike traditional AI, Agentic AI systems are designed to operate with a high degree of autonomy, allowing them to independently perform tasks such as hypothesis generation, literature review, experimental design, and data analysis. These systems have the potential to significantly accelerate scientific research, reduce costs, and expand access to advanced tools across various fields, including chemistry, biology, and materials science. Recent efforts have demonstrated the potential of LLM-driven agents in supporting researchers with tasks such as literature reviews, experimentation, and report writing. Prominent frameworks, including LitSearch (Ajith et al., 2024), ResearchArena (Kang & Xiong, 2024), SciLitLLM (Li et al., 2024c), CiteME (Press et al., 2024), ResearchAgent (Baek et al., 2024) and Agent Laboratory (Schmidgall et al., 2025), have made strides in automating general research workflows, such as citation management, document discovery, and academic survey generation. However, these systems often lack the domain-specific focus and compliance-driven rigor essential for fields like biomedical domain, where the structured assessment of literature is critical for evidence synthesis.
A Unified View of Optimal Kernel Hypothesis Testing
This paper provides a unifying view of optimal kernel hypothesis testing across the MMD two-sample, HSIC independence, and KSD goodness-of-fit frameworks. Minimax optimal separation rates in the kernel and $L^2$ metrics are presented, with two adaptive kernel selection methods (kernel pooling and aggregation), and under various testing constraints: computational efficiency, differential privacy, and robustness to data corruption. Intuition behind the derivation of the power results is provided in a unified way accross the three frameworks, and open problems are highlighted.
Hypothesis Testing in Unsupervised Domain Adaptation with Applications in Alzheimer's Disease
We only observe their transformed versions h(\mathbf{x_s i}) and g(\mathbf{x_t i}), for some known function class h(\cdot) and g(\cdot) . Our goal is to perform a statistical test checking if P_{\rm source} P_{\rm target} while removing the distortions induced by the transformations. This problem is closely related to concepts underlying numerous domain adaptation algorithms, and in our case, is motivated by the need to combine clinical and imaging based biomarkers from multiple sites and/or batches, where this problem is fairly common and an impediment in the conduct of analyses with much larger sample sizes. We develop a framework that addresses this problem using ideas from hypothesis testing on the transformed measurements, where in the distortions need to be estimated {\it in tandem} with the testing. We derive a simple algorithm and study its convergence and consistency properties in detail, and we also provide lower-bound strategies based on recent work in continuous optimization.
NatureLM: Deciphering the Language of Nature for Scientific Discovery
Xia, Yingce, Jin, Peiran, Xie, Shufang, He, Liang, Cao, Chuan, Luo, Renqian, Liu, Guoqing, Wang, Yue, Liu, Zequn, Chen, Yuan-Jyue, Guo, Zekun, Bai, Yeqi, Deng, Pan, Min, Yaosen, Lu, Ziheng, Hao, Hongxia, Yang, Han, Li, Jielan, Liu, Chang, Zhang, Jia, Zhu, Jianwei, Wu, Kehan, Zhang, Wei, Gao, Kaiyuan, Pei, Qizhi, Wang, Qian, Liu, Xixian, Li, Yanting, Zhu, Houtian, Lu, Yeqing, Ma, Mingqian, Wang, Zun, Xie, Tian, Maziarz, Krzysztof, Segler, Marwin, Yang, Zhao, Chen, Zilong, Shi, Yu, Zheng, Shuxin, Wu, Lijun, Hu, Chen, Dai, Peggy, Liu, Tie-Yan, Liu, Haiguang, Qin, Tao
Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.
Optimistic Interior Point Methods for Sequential Hypothesis Testing by Betting
The technique of "testing by betting" frames nonparametric sequential hypothesis testing as a multiple-round game, where a player bets on future observations that arrive in a streaming fashion, accumulates wealth that quantifies evidence against the null hypothesis, and rejects the null once the wealth exceeds a specified threshold while controlling the false positive error. Designing an online learning algorithm that achieves a small regret in the game can help rapidly accumulate the bettor's wealth, which in turn can shorten the time to reject the null hypothesis under the alternative $H_1$. However, many of the existing works employ the Online Newton Step (ONS) to update within a halved decision space to avoid a gradient explosion issue, which is potentially conservative for rapid wealth accumulation. In this paper, we introduce a novel strategy utilizing interior-point methods in optimization that allows updates across the entire interior of the decision space without the risk of gradient explosion. Our approach not only maintains strong statistical guarantees but also facilitates faster null hypothesis rejection in critical scenarios, overcoming the limitations of existing approaches.
CP-Guard+: A New Paradigm for Malicious Agent Detection and Defense in Collaborative Perception
Hu, Senkang, Tao, Yihang, Fang, Zihan, Xu, Guowen, Deng, Yiqin, Kwong, Sam, Fang, Yuguang
Collaborative perception (CP) is a promising method for safe connected and autonomous driving, which enables multiple vehicles to share sensing information to enhance perception performance. However, compared with single-vehicle perception, the openness of a CP system makes it more vulnerable to malicious attacks that can inject malicious information to mislead the perception of an ego vehicle, resulting in severe risks for safe driving. To mitigate such vulnerability, we first propose a new paradigm for malicious agent detection that effectively identifies malicious agents at the feature level without requiring verification of final perception results, significantly reducing computational overhead. Building on this paradigm, we introduce CP-GuardBench, the first comprehensive dataset provided to train and evaluate various malicious agent detection methods for CP systems. Furthermore, we develop a robust defense method called CP-Guard+, which enhances the margin between the representations of benign and malicious features through a carefully designed Dual-Centered Contrastive Loss (DCCLoss). Finally, we conduct extensive experiments on both CP-GuardBench and V2X-Sim, and demonstrate the superiority of CP-Guard+.
Transforming Science with Large Language Models: A Survey on AI-assisted Scientific Discovery, Experimentation, Content Generation, and Evaluation
Eger, Steffen, Cao, Yong, D'Souza, Jennifer, Geiger, Andreas, Greisinger, Christian, Gross, Stephanie, Hou, Yufang, Krenn, Brigitte, Lauscher, Anne, Li, Yizhi, Lin, Chenghua, Moosavi, Nafise Sadat, Zhao, Wei, Miller, Tristan
With the advent of large multimodal language models, science is now at a threshold of an AI-based technological transformation. Recently, a plethora of new AI models and tools has been proposed, promising to empower researchers and academics worldwide to conduct their research more effectively and efficiently. This includes all aspects of the research cycle, especially (1) searching for relevant literature; (2) generating research ideas and conducting experimentation; generating (3) text-based and (4) multimodal content (e.g., scientific figures and diagrams); and (5) AI-based automatic peer review. In this survey, we provide an in-depth overview over these exciting recent developments, which promise to fundamentally alter the scientific research process for good. Our survey covers the five aspects outlined above, indicating relevant datasets, methods and results (including evaluation) as well as limitations and scope for future research. Ethical concerns regarding shortcomings of these tools and potential for misuse (fake science, plagiarism, harms to research integrity) take a particularly prominent place in our discussion. We hope that our survey will not only become a reference guide for newcomers to the field but also a catalyst for new AI-based initiatives in the area of "AI4Science".
Reviews: Nonzero-sum Adversarial Hypothesis Testing Games
Summary of the model: A set of samples is either drawn from p or from some q chosen by an attacker from a set Q. The defended must look at the samples and decide which is the case. The attacker gets utility if the defender decides incorrectly, but pays some cost for drawing the samples that depends on the choice of q. Summary of results: Shows existence of a mixed-strategy Nash equilibrium. Leaves open existence of pure strategy, or natural conditions under which the equilibrium is pure (it seems to me this would be a very nice and likely result, given some strengthening of the assumptions). Shows that in equilibrium, error rates concentrate to zero as the number of samples n grows large.