Instrumental variable based estimation of a causal effect has emerged as a standard approach to mitigate confounding bias in the social sciences and epidemiology, where conducting randomized experiments can be too costly or impossible. However, justifying the validity of the instrument often poses a significant challenge. In this work, we highlight a problem generally neglected in arguments for instrumental variable validity: the presence of an ''aggregate treatment variable'', where the treatment (e.g., education, GDP, caloric intake) is composed of finer-grained components that each may have a different effect on the outcome. We show that the causal effect of an aggregate treatment is generally ambiguous, as it depends on how interventions on the aggregate are instantiated at the component level, formalized through the aggregate-constrained component intervention distribution. We then characterize conditions on the interventional distribution and the aggregate setting under which standard instrumental variable estimators identify the aggregate effect. The contrived nature of these conditions implies major limitations on the interpretation of instrumental variable estimates based on aggregate treatments and highlights the need for a broader justificatory base for the exclusion restriction in such settings.

Researchers risk fire, explosion or poisoning by allowing AI to design experiments, warn scientists. The use of AI models in scientific laboratories risks enabling dangerous experiments that could cause fires or explosions, researchers have warned. Such models offer a convincing illusion of understanding but are susceptible to missing basic and vital safety precautions. In tests of 19 cutting-edge AI models, every single one made potentially deadly mistakes. Serious accidents in university labs are rare but certainly not unheard of.

Large Language Models (LLMs) have shown growing potential in molecular sciences, but they often produce chemically inaccurate descriptions and struggle to recognize or justify potential errors. This raises important concerns about their robustness and reliability in scientific applications. To support more rigorous evaluation of LLMs in chemical reasoning, we present the MolErr2Fix benchmark, designed to assess LLMs on error detection and correction in molecular descriptions. Unlike existing benchmarks focused on molecule-to-text generation or property prediction, MolErr2Fix emphasizes fine-grained chemical understanding. It tasks LLMs with identifying, localizing, explaining, and revising potential structural and semantic errors in molecular descriptions. Specifically, MolErr2Fix consists of 1,193 fine-grained annotated error instances. Each instance contains quadruple annotations, i.e,. (error type, span location, the explanation, and the correction). These tasks are intended to reflect the types of reasoning and verification required in real-world chemical communication. Evaluations of current state-of-the-art LLMs reveal notable performance gaps, underscoring the need for more robust chemical reasoning capabilities. MolErr2Fix provides a focused benchmark for evaluating such capabilities and aims to support progress toward more reliable and chemically informed language models. All annotations and an accompanying evaluation API will be publicly released to facilitate future research.

A large language model (LLM) with knowledge in both scientific and general tasks is the foundation of science general intelligence. However, directly continued pretraining an LLM using science data usually leads to catastrophic forgetting, which indicates severe degradation in general ability. In this report, we present Innovator, which solves this problem by upcycling a pre-trained dense LLM into a fine-grained Mixtures-of-Experts model during continued pretraining, where different experts are expected to learn science knowledge in different disciplines, and a shared expert is utilized for general tasks. Innovator introduces a four-stage upcycle training paradigm: (1) Scientific Expert Induction on discipline-specific data, (2) Fine-grained Expert Splitting via FFN dimension decomposition, (3) Science-Aware Routing warmup, and (4) Generalist-Scientist Integration training on hybrid datasets. Such a paradigm enables knowledge in the general domain, and different scientific disciplines can be decoupled, avoiding the negative influence among knowledge in different domains. With 53.3B total parameters and 13.3B activated, Innovator extends Qwen2.5-7B using a shared general expert and 64 specialized scientific experts with 8 activated. Trained on 300B tokens with tri-level quality-controlled data, Innovator achieves 25% average improvement across 30 scientific tasks with a win rate as 70%, while retaining 99% performance in general tasks. Furthermore, Innovator-Reason, which is post-trained from Innovator for reasoning boosting, exhibits excellent reasoning performance in solving complex scientific problems with improvements over 30%.

Effectively integrating molecular graph structures with Large Language Models (LLMs) is a key challenge in drug discovery. Most existing multi-modal alignment methods typically process these structures by fine-tuning the LLM or adding a static adapter simultaneously. However, these approaches have two main limitations: (1) it optimizes a shared parameter space across all molecular inputs, limiting the model's ability to capture instance-specific structural features; and (2) fine-tuning the LLM for molecular tasks can lead to catastrophic forgetting, undermining its general reasoning capabilities. In this paper, instead of static task-oriented adaptation, we propose an instance-specific parameter space alignment approach for each molecule on-the-fly. To this end, we introduce Molecule-aware Low-Rank Adaptation (MoRA) that produces a unique set of low-rank adaptation weights for each input molecular graph. These weights are then dynamically injected into a frozen LLM, allowing the model to adapt its reasoning to the structure of each molecular input, while preserving the LLM's core knowledge. Extensive experiments demonstrate that on key molecular tasks, such as chemical reaction prediction and molecular captioning, MoRA's instance-specific dynamic adaptation outperforms statically adapted baselines, including a 14.1% relative improvement in reaction prediction exact match and a 22% reduction in error for quantum property prediction. The code is available at https://github.com/jk-sounds/MoRA.

The automation of chemical research through self-driving laboratories (SDLs) promises to accelerate scientific discovery, yet the reliability and granular performance of the underlying AI agents remain critical, under-examined challenges. In this work, we introduce AutoLabs, a self-correcting, multi-agent architecture designed to autonomously translate natural-language instructions into executable protocols for a high-throughput liquid handler. The system engages users in dialogue, decomposes experimental goals into discrete tasks for specialized agents, performs tool-assisted stoichiometric calculations, and iteratively self-corrects its output before generating a hardware-ready file. We present a comprehensive evaluation framework featuring five benchmark experiments of increasing complexity, from simple sample preparation to multi-plate timed syntheses. Through a systematic ablation study of 20 agent configurations, we assess the impact of reasoning capacity, architectural design (single- vs. multi-agent), tool use, and self-correction mechanisms. Our results demonstrate that agent reasoning capacity is the most critical factor for success, reducing quantitative errors in chemical amounts (nRMSE) by over 85% in complex tasks. When combined with a multi-agent architecture and iterative self-correction, AutoLabs achieves near-expert procedural accuracy (F1-score > 0.89) on challenging multi-step syntheses. These findings establish a clear blueprint for developing robust and trustworthy AI partners for autonomous laboratories, highlighting the synergistic effects of modular design, advanced reasoning, and self-correction to ensure both performance and reliability in high-stakes scientific applications. Code: https://github.com/pnnl/autolabs

Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness, restricting the training of generalizable multimodal models. We present MolTextNet, a dataset of 2.5 million high-quality molecule-text pairs designed to overcome these limitations. To construct it, we propose a synthetic text generation pipeline that integrates structural features, computed properties, bioactivity data, and synthetic complexity. Using GPT-4o-mini, we create structured descriptions for 2.5 million molecules from ChEMBL35, with text over 10 times longer than prior datasets. MolTextNet supports diverse downstream tasks, including property prediction and structure retrieval. Pretraining CLIP-style models with Graph Neural Networks and ModernBERT on MolTextNet yields improved performance, highlighting its potential for advancing foundational multimodal modeling in molecular science. Our dataset is available at https://huggingface.co/datasets/liuganghuggingface/moltextnet.

Test-time scaling improves large language model performance by adding extra compute during decoding. Best-of-N (BoN) sampling serves as a common scaling technique, broadening the search space for finding better solutions from the model distribution. However, traditional BoN requires N full generations, leading to high GPU memory overhead and time latency. Moreover, some methods depend on reward models, adding computational cost and limiting domain generalization. In this paper, we propose Self-Truncation Best-of-N (ST-BoN), a novel decoding method that avoids fully generating all samplings and eliminates the need for reward models. ST-BoN introduces early sampling consistency to estimate the most promising sample, truncating suboptimal ones to free memory and accelerate inference. This pushes the sampling-efficient test-time scaling. Compared to traditional BoN, ST-BoN can reduce dynamic GPU memory overhead by over 90% and time latency by 50%, while achieving comparable or even better performance across reasoning and open-ended domains.

Testing for the conditional independence structure in data is a fundamental and critical task in statistics and machine learning, which finds natural applications in causal discovery-a highly relevant problem to many scientific disciplines. Existing methods seek to design explicit test statistics that quantify the degree of conditional dependence, which is highly challenging yet cannot capture nor utilize prior knowledge in a data-driven manner. In this study, an entirely new approach is introduced, where we instead propose to amortize conditional independence testing and devise ACID ( Amortized C onditional In D ependence test)- a novel transformer-based neural network architecture that learns to test for conditional independence . ACID can be trained on synthetic data in a supervised learning fashion, and the learned model can then be applied to any dataset of similar natures or adapted to new domains by fine-tuning with a negligible computational cost. Our extensive empirical evaluations on both synthetic and real data reveal that ACID consistently achieves state-of-the-art performance against existing baselines under multiple metrics, and is able to generalize robustly to unseen sample sizes, dimensionalities, as well as non-linearities with a remarkably low inference time.

There are many examples in which the statistical units of interest are samples of a continuous time categorical random process, that is to say a continuous time stochastic process taking values in a finite state space. Without loosing any information, we associate to each state a binary random function, taking values in $\{0,1\}$, and turn the problem of statistical modeling of a categorical process into a multivariate functional data analysis issue. The (multivariate) covariance operator has nice interpretations in terms of departure from independence of the joint probabilities and the multivariate functional principal components are simple to interpret. Under the weak hypothesis assuming only continuity in probability of the $0-1$ trajectories, it is simple to build consistent estimators of the covariance kernel and perform multivariate functional principal components analysis. The sample paths being piecewise constant, with a finite number of jumps, this a rare case in functional data analysis in which the trajectories can be observed exhaustively. The approach is illustrated on a data set of sensory perceptions, considering different gustometer-controlled stimuli experiments. We show how it can be easily extended to analyze experiments, such as temporal check-all-that-apply, in which two states or more can be observed at the same time.