Daily Papers

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Artificial intelligence systems are increasingly deployed in biomedical research. However, current evaluation frameworks may inadequately assess their effectiveness as research collaborators. This rapid review examines benchmarking practices for AI systems in preclinical biomedical research. Three major databases and two preprint servers were searched from January 1, 2018 to October 31, 2025, identifying 14 benchmarks that assess AI capabilities in literature understanding, experimental design, and hypothesis generation. The results revealed that all current benchmarks assess isolated component capabilities, including data analysis quality, hypothesis validity, and experimental protocol design. However, authentic research collaboration requires integrated workflows spanning multiple sessions, with contextual memory, adaptive dialogue, and constraint propagation. This gap implies that systems excelling on component benchmarks may fail as practical research co-pilots. A process-oriented evaluation framework is proposed that addresses four critical dimensions absent from current benchmarks: dialogue quality, workflow orchestration, session continuity, and researcher experience. These dimensions are essential for evaluating AI systems as research co-pilots rather than as isolated task executors.

There is a multitude of novel generative models for open-domain conversational systems; however, there is no systematic evaluation of different systems. Systematic comparisons require consistency in experimental design, evaluation sets, conversational systems and their outputs, and statistical analysis. We lay out a protocol for the evaluation of conversational models using head-to-head pairwise comparison. We analyze ten recent models that claim state-of-the-art performance using a paired head-to-head performance (win-loss-tie) on five evaluation datasets. Our findings show that DialoGPT and Blender are superior systems using Bradley-Terry model and TrueSkill ranking methods. These findings demonstrate the feasibility of our protocol to evaluate conversational agents and evaluation sets. Finally, we make all code and evaluations publicly available for researchers to compare their model to other state-of-the-art dialog models.

Keypoint detection & descriptors are foundational tech-nologies for computer vision tasks like image matching, 3D reconstruction and visual odometry. Hand-engineered methods like Harris corners, SIFT, and HOG descriptors have been used for decades; more recently, there has been a trend to introduce learning in an attempt to improve keypoint detectors. On inspection however, the results are difficult to interpret; recent learning-based methods employ a vast diversity of experimental setups and design choices: empirical results are often reported using different backbones, protocols, datasets, types of supervisions or tasks. Since these differences are often coupled together, it raises a natural question on what makes a good learned keypoint detector. In this work, we revisit the design of existing keypoint detectors by deconstructing their methodologies and identifying the key components. We re-design each component from first-principle and propose Simple Learned Keypoints (SiLK) that is fully-differentiable, lightweight, and flexible. Despite its simplicity, SiLK advances new state-of-the-art on Detection Repeatability and Homography Estimation tasks on HPatches and 3D Point-Cloud Registration task on ScanNet, and achieves competitive performance to state-of-the-art on camera pose estimation in 2022 Image Matching Challenge and ScanNet.

We evaluate existing foundation models video understanding capabilities using a carefully designed experiment protocol consisting of three hallmark tasks (action recognition, temporal localization, and spatiotemporal localization), eight datasets well received by the community, and four adaptation methods tailoring a foundation model (FM) for a downstream task. Moreover, we propose a scalar VideoGLUE score (VGS) to measure an FMs efficacy and efficiency when adapting to general video understanding tasks. Our main findings are as follows. First, task-specialized models significantly outperform the six FMs studied in this work, in sharp contrast to what FMs have achieved in natural language and image understanding. Second,video-native FMs, whose pretraining data contains the video modality, are generally better than image-native FMs in classifying motion-rich videos, localizing actions in time, and understanding a video of more than one action. Third, the video-native FMs can perform well on video tasks under light adaptations to downstream tasks(e.g., freezing the FM backbones), while image-native FMs win in full end-to-end finetuning. The first two observations reveal the need and tremendous opportunities to conduct research on video-focused FMs, and the last confirms that both tasks and adaptation methods matter when it comes to the evaluation of FMs.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

Understanding causality should be a core requirement of any attempt to build real impact through AI. Due to the inherent unobservability of counterfactuals, large randomised trials (RCTs) are the standard for causal inference. But large experiments are generically expensive, and randomisation carries its own costs, e.g. when suboptimal decisions are trialed. Recent work has proposed more sample-efficient alternatives to RCTs, but these are not adaptable to the downstream application for which the causal effect is sought. In this work, we develop a task-specific approach to experimental design and derive sampling strategies customised to particular downstream applications. Across a range of important tasks, real-world datasets, and sample sizes, our method outperforms other benchmarks, e.g. requiring an order-of-magnitude less data to match RCT performance on targeted marketing tasks.

Indirect experiments provide a valuable framework for estimating treatment effects in situations where conducting randomized control trials (RCTs) is impractical or unethical. Unlike RCTs, indirect experiments estimate treatment effects by leveraging (conditional) instrumental variables, enabling estimation through encouragement and recommendation rather than strict treatment assignment. However, the sample efficiency of such estimators depends not only on the inherent variability in outcomes but also on the varying compliance levels of users with the instrumental variables and the choice of estimator being used, especially when dealing with numerous instrumental variables. While adaptive experiment design has a rich literature for direct experiments, in this paper we take the initial steps towards enhancing sample efficiency for indirect experiments by adaptively designing a data collection policy over instrumental variables. Our main contribution is a practical computational procedure that utilizes influence functions to search for an optimal data collection policy, minimizing the mean-squared error of the desired (non-linear) estimator. Through experiments conducted in various domains inspired by real-world applications, we showcase how our method can significantly improve the sample efficiency of indirect experiments.

The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution. All data, code, and models will be released publicly.

Quantum cryptography is arguably the fastest growing area in quantum information science. Novel theoretical protocols are designed on a regular basis, security proofs are constantly improving, and experiments are gradually moving from proof-of-principle lab demonstrations to in-field implementations and technological prototypes. In this review, we provide both a general introduction and a state of the art description of the recent advances in the field, both theoretically and experimentally. We start by reviewing protocols of quantum key distribution based on discrete variable systems. Next we consider aspects of device independence, satellite challenges, and high rate protocols based on continuous variable systems. We will then discuss the ultimate limits of point-to-point private communications and how quantum repeaters and networks may overcome these restrictions. Finally, we will discuss some aspects of quantum cryptography beyond standard quantum key distribution, including quantum data locking and quantum digital signatures.

Interference is ubiquitous when conducting causal experiments over networks. Except for certain network structures, causal inference on the network in the presence of interference is difficult due to the entanglement between the treatment assignments and the interference levels. In this article, we conduct causal inference under interference on an observed, sparse but connected network, and we propose a novel design of experiments based on an independent set. Compared to conventional designs, the independent-set design focuses on an independent subset of data and controls their interference exposures through the assignments to the rest (auxiliary set). We provide a lower bound on the size of the independent set from a greedy algorithm , and justify the theoretical performance of estimators under the proposed design. Our approach is capable of estimating both spillover effects and treatment effects. We justify its superiority over conventional methods and illustrate the empirical performance through simulations.

Biological protocols are fundamental to reproducible and safe life science research. While LLMs excel on general tasks, their systematic evaluation on these highly specialized, accuracy-critical, and inherently procedural texts remains limited. In this work, we present BioProBench, the first large-scale, integrated multi-task benchmark for biological protocol understanding and reasoning. While limited benchmarks have touched upon specific aspects like protocol QA, BioProBench provides a comprehensive suite of five core tasks: Protocol Question Answering, Step Ordering, Error Correction, Protocol Generation, and Protocol Reasoning, enabling a holistic evaluation of LLMs on procedural biological texts. Built upon 27K original protocols, it yields nearly 556K high-quality structured instances. We evaluate 12 mainstream open/closed-source LLMs on BioProBench. Experimental results reveal that while top models preform well on surface understanding tasks, struggle significantly with deep reasoning and structured generation tasks like ordering and generation. Furthermore, model comparisons reveal diverse performance: certain open-source models approach closed-source levels on some tasks, yet bio-specific small models lag behind general LLMs, indicating limitations on complex procedural content. Overall, our findings underscore that procedural reasoning within biological protocols represents a significant challenge for current LLMs. BioProBench serves as a standardized framework to diagnose these specific limitations and guide the development of AI systems better equipped for safely automating complex scientific procedures. The code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/GreatCaptainNemo/BioProBench.

Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited adaptability to dynamic lab conditions, inadequate error handling, and high operational complexity. Here we introduce BioMARS (Biological Multi-Agent Robotic System), an intelligent platform that integrates LLMs, VLMs, and modular robotics to autonomously design, plan, and execute biological experiments. BioMARS uses a hierarchical architecture: the Biologist Agent synthesizes protocols via retrieval-augmented generation; the Technician Agent translates them into executable robotic pseudo-code; and the Inspector Agent ensures procedural integrity through multimodal perception and anomaly detection. The system autonomously conducts cell passaging and culture tasks, matching or exceeding manual performance in viability, consistency, and morphological integrity. It also supports context-aware optimization, outperforming conventional strategies in differentiating retinal pigment epithelial cells. A web interface enables real-time human-AI collaboration, while a modular backend allows scalable integration with laboratory hardware. These results highlight the feasibility of generalizable, AI-driven laboratory automation and the transformative role of language-based reasoning in biological research.

Randomized controlled trials (RCTs) are the benchmark for causal inference, yet field implementation can deviate. We here present a remote audit - a design-based, preregistrable diagnostic that uses only pre-treatment satellite imagery to test whether assignment is independent of local conditions. The conditional randomization test of the remote audit evaluates whether treatment assignment is more predictable from pre-treatment satellite features than expected under the experiment's registered mechanism, providing a finite-sample valid, design-based diagnostic that requires no parametric assumptions. The procedure is finite-sample valid, honors blocks and clusters, and controls multiplicity across image models and resolutions via a max-statistic. We illustrate with two RCTs: Uganda's Youth Opportunities Program, where the audit corroborates randomization and flags selection and missing-data risks; and a school-based trial in Bangladesh, where assignment is highly predictable from pre-treatment features relative to the stated design, consistent with independent concerns about irregularities. Remote audits complement balance tests, lower early-stage costs, and enable rapid design checks when baseline surveys are expensive or infeasible.

We study experiment design for unique identification of the causal graph of a simple SCM, where the graph may contain cycles. The presence of cycles in the structure introduces major challenges for experiment design as, unlike acyclic graphs, learning the skeleton of causal graphs with cycles may not be possible from merely the observational distribution. Furthermore, intervening on a variable in such graphs does not necessarily lead to orienting all the edges incident to it. In this paper, we propose an experiment design approach that can learn both cyclic and acyclic graphs and hence, unifies the task of experiment design for both types of graphs. We provide a lower bound on the number of experiments required to guarantee the unique identification of the causal graph in the worst case, showing that the proposed approach is order-optimal in terms of the number of experiments up to an additive logarithmic term. Moreover, we extend our result to the setting where the size of each experiment is bounded by a constant. For this case, we show that our approach is optimal in terms of the size of the largest experiment required for uniquely identifying the causal graph in the worst case.

Recent advances in quantum information science enabled the development of quantum communication network prototypes and created an opportunity to study full-stack quantum network architectures. This work develops SeQUeNCe, a comprehensive, customizable quantum network simulator. Our simulator consists of five modules: Hardware models, Entanglement Management protocols, Resource Management, Network Management, and Application. This framework is suitable for simulation of quantum network prototypes that capture the breadth of current and future hardware technologies and protocols. We implement a comprehensive suite of network protocols and demonstrate the use of SeQUeNCe by simulating a photonic quantum network with nine routers equipped with quantum memories. The simulation capabilities are illustrated in three use cases. We show the dependence of quantum network throughput on several key hardware parameters and study the impact of classical control message latency. We also investigate quantum memory usage efficiency in routers and demonstrate that redistributing memory according to anticipated load increases network capacity by 69.1% and throughput by 6.8%. We design SeQUeNCe to enable comparisons of alternative quantum network technologies, experiment planning, and validation and to aid with new protocol design. We are releasing SeQUeNCe as an open source tool and aim to generate community interest in extending it.

We study the problem of designing mechanisms for information acquisition scenarios. This setting models strategic interactions between an uniformed receiver and a set of informed senders. In our model the senders receive information about the underlying state of nature and communicate their observation (either truthfully or not) to the receiver, which, based on this information, selects an action. Our goal is to design mechanisms maximizing the receiver's utility while incentivizing the senders to report truthfully their information. First, we provide an algorithm that efficiently computes an optimal incentive compatible (IC) mechanism. Then, we focus on the online problem in which the receiver sequentially interacts in an unknown game, with the objective of minimizing the cumulative regret w.r.t. the optimal IC mechanism, and the cumulative violation of the incentive compatibility constraints. We investigate two different online scenarios, i.e., the full and bandit feedback settings. For the full feedback problem, we propose an algorithm that guarantees mathcal O(sqrt T) regret and violation, while for the bandit feedback setting we present an algorithm that attains mathcal O(T^{alpha}) regret and mathcal O(T^{1-alpha/2}) violation for any alphain[1/2, 1]. Finally, we complement our results providing a tight lower bound.

Generating entanglement between distant quantum systems is at the core of quantum networking. In recent years, numerous theoretical protocols for remote entanglement generation have been proposed, of which many have been experimentally realized. Here, we provide a modular theoretical framework to elucidate the general mechanisms of photon-mediated entanglement generation between single spins in atomic or solid-state systems. Our framework categorizes existing protocols at various levels of abstraction and allows for combining the elements of different schemes in new ways. These abstraction layers make it possible to readily compare protocols for different quantum hardware. To enable the practical evaluation of protocols tailored to specific experimental parameters, we have devised numerical simulations based on the framework with our codes available online.

Recently, Agentic AI has become an increasingly popular research field. However, we argue that current agent research practices lack standardization and scientific rigor, making it hard to conduct fair comparisons among methods. As a result, it is still unclear how different design choices in agent frameworks affect effectiveness, and measuring their progress remains challenging. In this work, we conduct a systematic empirical study on GAIA benchmark and BrowseComp to examine the impact of popular design choices in key agent components in a fair and rigorous manner. We find that the lack of a standard evaluation protocol makes previous works, even open-sourced ones, non-reproducible, with significant variance between random runs. Therefore, we introduce a more robust evaluation protocol to stabilize comparisons. Our study reveals which components and designs are crucial for effective agents, while others are redundant, despite seeming logical. Based on our findings, we build and open-source OAgents, a new foundation agent framework that achieves state-of-the-art performance among open-source projects. OAgents offers a modular design for various agent components, promoting future research in Agentic AI.

Recent text-to-video (T2V) technology advancements, as demonstrated by models such as Gen2, Pika, and Sora, have significantly broadened its applicability and popularity. Despite these strides, evaluating these models poses substantial challenges. Primarily, due to the limitations inherent in automatic metrics, manual evaluation is often considered a superior method for assessing T2V generation. However, existing manual evaluation protocols face reproducibility, reliability, and practicality issues. To address these challenges, this paper introduces the Text-to-Video Human Evaluation (T2VHE) protocol, a comprehensive and standardized protocol for T2V models. The T2VHE protocol includes well-defined metrics, thorough annotator training, and an effective dynamic evaluation module. Experimental results demonstrate that this protocol not only ensures high-quality annotations but can also reduce evaluation costs by nearly 50%. We will open-source the entire setup of the T2VHE protocol, including the complete protocol workflow, the dynamic evaluation component details, and the annotation interface code. This will help communities establish more sophisticated human assessment protocols.

The rapid development of large language models (LLMs) has led to the widespread deployment of LLM agents across diverse industries, including customer service, content generation, data analysis, and even healthcare. However, as more LLM agents are deployed, a major issue has emerged: there is no standard way for these agents to communicate with external tools or data sources. This lack of standardized protocols makes it difficult for agents to work together or scale effectively, and it limits their ability to tackle complex, real-world tasks. A unified communication protocol for LLM agents could change this. It would allow agents and tools to interact more smoothly, encourage collaboration, and triggering the formation of collective intelligence. In this paper, we provide the first comprehensive analysis of existing agent protocols, proposing a systematic two-dimensional classification that differentiates context-oriented versus inter-agent protocols and general-purpose versus domain-specific protocols. Additionally, we conduct a comparative performance analysis of these protocols across key dimensions such as security, scalability, and latency. Finally, we explore the future landscape of agent protocols by identifying critical research directions and characteristics necessary for next-generation protocols. These characteristics include adaptability, privacy preservation, and group-based interaction, as well as trends toward layered architectures and collective intelligence infrastructures. We expect this work to serve as a practical reference for both researchers and engineers seeking to design, evaluate, or integrate robust communication infrastructures for intelligent agents.

Large language model (LLM)-powered agents are increasingly used to plan and execute scientific workflows, yet most research cyberinfrastructure (CI) exposes heterogeneous APIs and implements security models that present barriers for use by agents. We report on our experience using the Model Context Protocol (MCP) as a unifying interface that makes research capabilities discoverable, invokable, and composable. Our approach is pragmatic: we implement thin MCP servers over mature services, including Globus Transfer, Compute, and Search; status APIs exposed by computing facilities; Octopus event fabric; and domain-specific tools such as Garden and Galaxy. We use case studies in computational chemistry, bioinformatics, quantum chemistry, and filesystem monitoring to illustrate how this MCP-oriented architecture can be used in practice. We distill lessons learned and outline open challenges in evaluation and trust for agent-led science.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

We consider in this paper the problem of optimal experiment design where a decision maker can choose which points to sample to obtain an estimate hatβ of the hidden parameter β^{star} of an underlying linear model. The key challenge of this work lies in the heteroscedasticity assumption that we make, meaning that each covariate has a different and unknown variance. The goal of the decision maker is then to figure out on the fly the optimal way to allocate the total budget of T samples between covariates, as sampling several times a specific one will reduce the variance of the estimated model around it (but at the cost of a possible higher variance elsewhere). By trying to minimize the ell^2-loss E [lVerthatβ-β^{star}rVert^2] the decision maker is actually minimizing the trace of the covariance matrix of the problem, which corresponds then to online A-optimal design. Combining techniques from bandit and convex optimization we propose a new active sampling algorithm and we compare it with existing ones. We provide theoretical guarantees of this algorithm in different settings, including a O(T^{-2}) regret bound in the case where the covariates form a basis of the feature space, generalizing and improving existing results. Numerical experiments validate our theoretical findings.

As large language models (LLMs) become more powerful and are deployed more autonomously, it will be increasingly important to prevent them from causing harmful outcomes. Researchers have investigated a variety of safety techniques for this purpose, e.g. using models to review the outputs of other models, or red-teaming techniques to surface subtle failure modes. However, researchers have not evaluated whether such techniques still ensure safety if the model is itself intentionally trying to subvert them. In this paper, we develop and evaluate pipelines of safety techniques ("protocols") that are robust to intentional subversion. We investigate a scenario in which we want to solve a sequence of programming problems, using access to a powerful but untrusted model (in our case, GPT-4), access to a less powerful trusted model (in our case, GPT-3.5), and limited access to high-quality trusted labor. We investigate protocols that aim to never submit solutions containing backdoors, which we operationalize here as logical errors that are not caught by test cases. We investigate a range of protocols and test each against strategies that the untrusted model could use to subvert them. One protocol is what we call trusted editing. This protocol first asks GPT-4 to write code, and then asks GPT-3.5 to rate the suspiciousness of that code. If the code is below some suspiciousness threshold, it is submitted. Otherwise, GPT-3.5 edits the solution to remove parts that seem suspicious and then submits the edited code. Another protocol is untrusted monitoring. This protocol asks GPT-4 to write code, and then asks another instance of GPT-4 whether the code is backdoored, using various techniques to prevent the GPT-4 instances from colluding. These protocols improve substantially on simple baselines.

The Multi-armed bandit offer the advantage to learn and exploit the already learnt knowledge at the same time. This capability allows this approach to be applied in different domains, going from clinical trials where the goal is investigating the effects of different experimental treatments while minimizing patient losses, to adaptive routing where the goal is to minimize the delays in a network. This article provides a review of the recent results on applying bandit to real-life scenario and summarize the state of the art for each of these fields. Different techniques has been proposed to solve this problem setting, like epsilon-greedy, Upper confident bound (UCB) and Thompson Sampling (TS). We are showing here how this algorithms were adapted to solve the different problems of exploration exploitation.

We introduce a gradient-based approach for the problem of Bayesian optimal experimental design to learn causal models in a batch setting -- a critical component for causal discovery from finite data where interventions can be costly or risky. Existing methods rely on greedy approximations to construct a batch of experiments while using black-box methods to optimize over a single target-state pair to intervene with. In this work, we completely dispose of the black-box optimization techniques and greedy heuristics and instead propose a conceptually simple end-to-end gradient-based optimization procedure to acquire a set of optimal intervention target-state pairs. Such a procedure enables parameterization of the design space to efficiently optimize over a batch of multi-target-state interventions, a setting which has hitherto not been explored due to its complexity. We demonstrate that our proposed method outperforms baselines and existing acquisition strategies in both single-target and multi-target settings across a number of synthetic datasets.

The diffusion MRI Neurite Exchange Imaging model offers a promising framework for probing gray matter microstructure by estimating parameters such as compartment sizes, diffusivities, and inter-compartmental water exchange time. However, existing protocols require long scan times. This study proposes a reduced acquisition scheme for the Connectome 2.0 scanner that preserves model accuracy while substantially shortening scan duration. We developed a data-driven framework using explainable artificial intelligence with a guided recursive feature elimination strategy to identify an optimal 8-feature subset from a 15-feature protocol. The performance of this optimized protocol was validated in vivo and benchmarked against the full acquisition and alternative reduction strategies. Parameter accuracy, preservation of anatomical contrast, and test-retest reproducibility were assessed. The reduced protocol yielded parameter estimates and cortical maps comparable to the full protocol, with low estimation errors in synthetic data and minimal impact on test-retest variability. Compared to theory-driven and heuristic reduction schemes, the optimized protocol demonstrated superior robustness, reducing the deviation in water exchange time estimates by over two-fold. In conclusion, this hybrid optimization framework enables viable imaging of neurite exchange in 14 minutes without loss of parameter fidelity. This approach supports the broader application of exchange-sensitive diffusion magnetic resonance imaging in neuroscience and clinical research, and offers a generalizable method for designing efficient acquisition protocols in biophysical parameter mapping.

Access to the right evidence does not guarantee that large language models (LLMs) will reason with it correctly. This gap between retrieval and reasoning is especially concerning in clinical settings, where outputs must align with structured protocols. We study this gap using Written Exposure Therapy (WET) guidelines as a testbed. In evaluating model responses to curated clinician-vetted questions, we find that errors persist even when authoritative passages are provided. To address this, we propose an evaluation framework that measures accuracy, consistency, and fidelity of reasoning. Our results highlight both the potential and the risks: retrieval-augmented generation (RAG) can constrain outputs, but safe deployment requires assessing reasoning as rigorously as retrieval.

Evaluations are critical for understanding the capabilities of large language models (LLMs). Fundamentally, evaluations are experiments; but the literature on evaluations has largely ignored the literature from other sciences on experiment analysis and planning. This article shows researchers with some training in statistics how to think about and analyze data from language model evaluations. Conceptualizing evaluation questions as having been drawn from an unseen super-population, we present formulas for analyzing evaluation data, measuring differences between two models, and planning an evaluation experiment. We make a number of specific recommendations for running language model evaluations and reporting experiment results in a way that minimizes statistical noise and maximizes informativeness.

We consider the task of evaluating policies of algorithmic resource allocation through randomized controlled trials (RCTs). Such policies are tasked with optimizing the utilization of limited intervention resources, with the goal of maximizing the benefits derived. Evaluation of such allocation policies through RCTs proves difficult, notwithstanding the scale of the trial, because the individuals' outcomes are inextricably interlinked through resource constraints controlling the policy decisions. Our key contribution is to present a new estimator leveraging our proposed novel concept, that involves retrospective reshuffling of participants across experimental arms at the end of an RCT. We identify conditions under which such reassignments are permissible and can be leveraged to construct counterfactual trials, whose outcomes can be accurately ascertained, for free. We prove theoretically that such an estimator is more accurate than common estimators based on sample means -- we show that it returns an unbiased estimate and simultaneously reduces variance. We demonstrate the value of our approach through empirical experiments on synthetic, semi-synthetic as well as real case study data and show improved estimation accuracy across the board.

As large language models (LLMs) become increasingly capable, it is prudent to assess whether safety measures remain effective even if LLMs intentionally try to bypass them. Previous work introduced control evaluations, an adversarial framework for testing deployment strategies of untrusted models (i.e., models which might be trying to bypass safety measures). While prior work treats a single failure as unacceptable, we perform control evaluations in a "distributed threat setting" -- a setting where no single action is catastrophic and no single action provides overwhelming evidence of misalignment. We approach this problem with a two-level deployment framework that uses an adaptive macro-protocol to choose between micro-protocols. Micro-protocols operate on a single task, using a less capable, but extensively tested (trusted) model to harness and monitor the untrusted model. Meanwhile, the macro-protocol maintains an adaptive credence on the untrusted model's alignment based on its past actions, using it to pick between safer and riskier micro-protocols. We evaluate our method in a code generation testbed where a red team attempts to generate subtly backdoored code with an LLM whose deployment is safeguarded by a blue team. We plot Pareto frontiers of safety (# of non-backdoored solutions) and usefulness (# of correct solutions). At a given level of usefulness, our adaptive deployment strategy reduces the number of backdoors by 80% compared to non-adaptive baselines.

The field of Deep Learning (DL) has undergone explosive growth during the last decade, with a substantial impact on Natural Language Processing (NLP) as well. Yet, compared to more established disciplines, a lack of common experimental standards remains an open challenge to the field at large. Starting from fundamental scientific principles, we distill ongoing discussions on experimental standards in NLP into a single, widely-applicable methodology. Following these best practices is crucial to strengthen experimental evidence, improve reproducibility and support scientific progress. These standards are further collected in a public repository to help them transparently adapt to future needs.

With an increasing number of replication studies performed in psychological science, the question of how to evaluate the outcome of a replication attempt deserves careful consideration. Bayesian approaches allow to incorporate uncertainty and prior information into the analysis of the replication attempt by their design. The Replication Bayes Factor, introduced by Verhagen & Wagenmakers (2014), provides quantitative, relative evidence in favor or against a successful replication. In previous work by Verhagen & Wagenmakers (2014) it was limited to the case of t-tests. In this paper, the Replication Bayes Factor is extended to F-tests in multi-group, fixed-effect ANOVA designs. Simulations and examples are presented to facilitate the understanding and to demonstrate the usefulness of this approach. Finally, the Replication Bayes Factor is compared to other Bayesian and frequentist approaches and discussed in the context of replication attempts. R code to calculate Replication Bayes factors and to reproduce the examples in the paper is available at https://osf.io/jv39h/.

The automatic evaluation of instruction following typically involves using large language models (LLMs) to assess response quality. However, there is a lack of comprehensive evaluation of these LLM-based evaluators across two dimensions: the base LLMs and the evaluation protocols. Therefore, we present a thorough meta-evaluation of instruction following, including 25 base LLMs and 15 recently proposed evaluation protocols, on 4 human-annotated datasets, assessing the evaluation accuracy of the LLM-evaluators. Our evaluation allows us to identify the best-performing base LLMs and evaluation protocols with a high degree of robustness. Moreover, our large-scale evaluation reveals: (1) Base LLM performance ranking remains largely consistent across evaluation protocols, with less capable LLMs showing greater improvement from protocol enhancements; (2) Robust evaluation of evaluation protocols requires many base LLMs with varying capability levels, as protocol effectiveness can depend on the base LLM used; (3) Evaluation results on different datasets are not always consistent, so a rigorous evaluation requires multiple datasets with distinctive features. We release our meta-evaluation suite ReIFE, which provides the codebase and evaluation result collection for more than 500 LLM-evaluator configurations, to support future research in instruction-following evaluation.

Limited large-scale evaluations exist for facilitation strategies of online discussions due to significant costs associated with human involvement. An effective solution is synthetic discussion simulations using Large Language Models (LLMs) to create initial pilot experiments. We propose a simple, generalizable, LLM-driven methodology to prototype the development of LLM facilitators, and produce high-quality synthetic data without human involvement. We use our methodology to test whether current facilitation strategies can improve the performance of LLM facilitators. We find that, while LLM facilitators significantly improve synthetic discussions, there is no evidence that the application of more elaborate facilitation strategies proposed in modern Social Science research lead to further improvements in discussion quality, compared to more basic approaches. Additionally, we find that small LLMs (such as Mistral Nemo 12B) can perform comparably to larger models (such as LLaMa 70B), and that special instructions must be used for instruction-tuned models to induce toxicity in synthetic discussions. We confirm that each component of our methodology contributes substantially to high quality data via an ablation study. We release an open-source framework, "SynDisco" (pip install syndisco), which implements our methodology. We also release the "Virtual Moderation Dataset" (https://paperswithcode.com/dataset/vmd), a large, publicly available dataset containing LLM-generated and LLM-annotated discussions using multiple open-source LLMs.

Hypothesis ranking is a crucial component of automated scientific discovery, particularly in natural sciences where wet-lab experiments are costly and throughput-limited. Existing approaches focus on pre-experiment ranking, relying solely on large language model's internal reasoning without incorporating empirical outcomes from experiments. We introduce the task of experiment-guided ranking, which aims to prioritize candidate hypotheses based on the results of previously tested ones. However, developing such strategies is challenging due to the impracticality of repeatedly conducting real experiments in natural science domains. To address this, we propose a simulator grounded in three domain-informed assumptions, modeling hypothesis performance as a function of similarity to a known ground truth hypothesis, perturbed by noise. We curate a dataset of 124 chemistry hypotheses with experimentally reported outcomes to validate the simulator. Building on this simulator, we develop a pseudo experiment-guided ranking method that clusters hypotheses by shared functional characteristics and prioritizes candidates based on insights derived from simulated experimental feedback. Experiments show that our method outperforms pre-experiment baselines and strong ablations.

Shojaee et al. (2025) report that Large Reasoning Models (LRMs) exhibit "accuracy collapse" on planning puzzles beyond certain complexity thresholds. We demonstrate that their findings primarily reflect experimental design limitations rather than fundamental reasoning failures. Our analysis reveals three critical issues: (1) Tower of Hanoi experiments systematically exceed model output token limits at reported failure points, with models explicitly acknowledging these constraints in their outputs; (2) The authors' automated evaluation framework fails to distinguish between reasoning failures and practical constraints, leading to misclassification of model capabilities; (3) Most concerningly, their River Crossing benchmarks include mathematically impossible instances for N > 5 due to insufficient boat capacity, yet models are scored as failures for not solving these unsolvable problems. When we control for these experimental artifacts, by requesting generating functions instead of exhaustive move lists, preliminary experiments across multiple models indicate high accuracy on Tower of Hanoi instances previously reported as complete failures. These findings highlight the importance of careful experimental design when evaluating AI reasoning capabilities.

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells in quantitative, predictive, and mechanistic ways. We discuss the role of mathematical models in the context of cell-fate decision making systems across the tree of life. Complex multi-cellular organisms have been a particular focus, but single celled organisms also have to sense and respond to their environment. We center our discussion around the idea of design principles which we can learn from observations and modeling, and exploit in order to (re)-design or guide cellular behavior.

In large language model (LLM) pretraining, data quality is believed to determine model quality. In this paper, we re-examine the notion of "quality" from the perspective of pre- and post-training co-design. Specifically, we explore the possibility that pre-training on more toxic data can lead to better control in post-training, ultimately decreasing a model's output toxicity. First, we use a toy experiment to study how data composition affects the geometry of features in the representation space. Next, through controlled experiments with Olmo-1B models trained on varying ratios of clean and toxic data, we find that the concept of toxicity enjoys a less entangled linear representation as the proportion of toxic data increases. Furthermore, we show that although toxic data increases the generational toxicity of the base model, it also makes the toxicity easier to remove. Evaluations on Toxigen and Real Toxicity Prompts demonstrate that models trained on toxic data achieve a better trade-off between reducing generational toxicity and preserving general capabilities when detoxifying techniques such as inference-time intervention (ITI) are applied. Our findings suggest that, with post-training taken into account, bad data may lead to good models.

Much has been said about observability in system theory and control; however, it has been recently that observability in complex networks has seriously attracted the attention of researchers. This paper examines the state-of-the-art and discusses some issues raised due to "complexity" and "stochasticity". These unresolved issues call for a new practical methodology. For stochastic systems, a degree of observability may be defined and the observability problem is not a binary (i.e., yes-no) question anymore. Here, we propose to employ a goal-seeking system to play a supervisory role in the network. Hence, improving the degree of observability would be a valid objective for the supervisory system. Towards this goal, the supervisor dynamically optimizes the observation process by reconfiguring the sensory parts in the network. A cognitive dynamic system is suggested as a proper choice for the supervisory system. In this framework, the network itself is viewed as the environment with which the cognitive dynamic system interacts. Computer experiments confirm the potential of the proposed approach for addressing some of the issues raised in networks due to complexity and stochasticity.

The ability of Large Language Models (LLMs) to mimic human behavior triggered a plethora of computational social science research, assuming that empirical studies of humans can be conducted with AI agents instead. Since there have been conflicting research findings on whether and when this hypothesis holds, there is a need to better understand the differences in their experimental designs. We focus on replicating the behavior of social network users with the use of LLMs for the analysis of communication on social networks. First, we provide a formal framework for the simulation of social networks, before focusing on the sub-task of imitating user communication. We empirically test different approaches to imitate user behavior on X in English and German. Our findings suggest that social simulations should be validated by their empirical realism measured in the setting in which the simulation components were fitted. With this paper, we argue for more rigor when applying generative-agent-based modeling for social simulation.

In social sciences, researchers often face challenges when conducting large-scale experiments, particularly due to the simulations' complexity and the lack of technical expertise required to develop such frameworks. Agent-Based Modeling (ABM) is a computational approach that simulates agents' actions and interactions to evaluate how their behaviors influence the outcomes. However, the traditional implementation of ABM can be demanding and complex. Generative Agent-Based Modeling (GABM) offers a solution by enabling scholars to create simulations where AI-driven agents can generate complex behaviors based on underlying rules and interactions. This paper introduces a framework for designing reliable experiments using GABM, making sophisticated simulation techniques more accessible to researchers across various fields. We provide a step-by-step guide for selecting appropriate tools, designing the model, establishing experimentation protocols, and validating results.

Classical Internet evolved exceptionally during the last five decades, from a network comprising a few static nodes in the early days to a leviathan interconnecting billions of devices. This has been possible by the separation of concern principle, for which the network functionalities are organized as a stack of layers, each providing some communication functionalities through specific network protocols. In this survey, we aim at highlighting the impossibility of adapting the classical Internet protocol stack to the Quantum Internet, due to the marvels of quantum mechanics. Indeed, the design of the Quantum Internet requires a major paradigm shift of the whole protocol stack for harnessing the peculiarities of quantum entanglement and quantum information. In this context, we first overview the relevant literature about Quantum Internet protocol stack. Then, stemming from this, we sheds the light on the open problems and required efforts toward the design of an effective and complete Quantum Internet protocol stack. To the best of authors' knowledge, a survey of this type is the first of its own. What emerges from this analysis is that the Quantum Internet, though still in its infancy, is a disruptive technology whose design requires an inter-disciplinary effort at the border between quantum physics, computer and telecommunications engineering.

Null Hypothesis Significance Testing is the de facto tool for assessing effectiveness differences between Information Retrieval systems. Researchers use statistical tests to check whether those differences will generalise to online settings or are just due to the samples observed in the laboratory. Much work has been devoted to studying which test is the most reliable when comparing a pair of systems, but most of the IR real-world experiments involve more than two. In the multiple comparisons scenario, testing several systems simultaneously may inflate the errors committed by the tests. In this paper, we use a new approach to assess the reliability of multiple comparison procedures using simulated and real TREC data. Experiments show that Wilcoxon plus the Benjamini-Hochberg correction yields Type I error rates according to the significance level for typical sample sizes while being the best test in terms of statistical power.

Randomized controlled trials (RCTs) are considered the gold standard for estimating the average treatment effect (ATE) of interventions. One use of RCTs is to study the causes of global poverty -- a subject explicitly cited in the 2019 Nobel Memorial Prize awarded to Duflo, Banerjee, and Kremer "for their experimental approach to alleviating global poverty." Because the ATE is a population summary, anti-poverty experiments often seek to unpack the effect variation around the ATE by conditioning (CATE) on tabular variables such as age and ethnicity that were measured during the RCT data collection. Although such variables are key to unpacking CATE, using only such variables may fail to capture historical, geographical, or neighborhood-specific contributors to effect variation, as tabular RCT data are often only observed near the time of the experiment. In global poverty research, when the location of the experiment units is approximately known, satellite imagery can provide a window into such factors important for understanding heterogeneity. However, there is no method that specifically enables applied researchers to analyze CATE from images. In this paper, using a deep probabilistic modeling framework, we develop such a method that estimates latent clusters of images by identifying images with similar treatment effects distributions. Our interpretable image CATE model also includes a sensitivity factor that quantifies the importance of image segments contributing to the effect cluster prediction. We compare the proposed methods against alternatives in simulation; also, we show how the model works in an actual RCT, estimating the effects of an anti-poverty intervention in northern Uganda and obtaining a posterior predictive distribution over effects for the rest of the country where no experimental data was collected. We make all models available in open-source software.

Survey data are self-reported data collected directly from respondents by a questionnaire or an interview and are commonly used in epidemiology. Such data are traditionally collected via a single mode (e.g. face-to-face interview alone), but use of mixed-mode designs (e.g. offering face-to-face interview or online survey) has become more common. This introduces two key challenges. First, individuals may respond differently to the same question depending on the mode; these differences due to measurement are known as 'mode effects'. Second, different individuals may participate via different modes; these differences in sample composition between modes are known as 'mode selection'. Where recognised, mode effects are often handled by straightforward approaches such as conditioning on survey mode. However, while reducing mode effects, this and other equivalent approaches may introduce collider bias in the presence of mode selection. The existence of mode effects and the consequences of na\"ive conditioning may be underappreciated in epidemiology. This paper offers a simple introduction to these challenges using directed acyclic graphs by exploring a range of possible data structures. We discuss the potential implications of using conditioning- or imputation-based approaches and outline the advantages of quantitative bias analyses for dealing with mode effects.

A Recurrent Neural Network (RNN) was used to perform video frame prediction of microbial growth for a population of two mutants of Pseudomonas aeruginosa. The RNN was trained on videos of 20 frames that were acquired using fluorescence microscopy and microfluidics. The network predicted the last 10 frames of each video, and the accuracy's of the predictions was assessed by comparing raw images, population curves, and the number and size of individual colonies. Overall, we found the predictions to be accurate using this approach. The implications this result has on designing autonomous experiments in microbiology, and the steps that can be taken to make the predictions even more accurate, are discussed.

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

Progress in computer-aided synthesis planning (CASP) is obscured by the lack of standardized evaluation infrastructure and the reliance on metrics that prioritize topological completion over chemical validity. We introduce RetroCast, a unified evaluation suite that standardizes heterogeneous model outputs into a common schema to enable statistically rigorous, apples-to-apples comparison. The framework includes a reproducible benchmarking pipeline with stratified sampling and bootstrapped confidence intervals, accompanied by SynthArena, an interactive platform for qualitative route inspection. We utilize this infrastructure to evaluate leading search-based and sequence-based algorithms on a new suite of standardized benchmarks. Our analysis reveals a divergence between "solvability" (stock-termination rate) and route quality; high solvability scores often mask chemical invalidity or fail to correlate with the reproduction of experimental ground truths. Furthermore, we identify a "complexity cliff" in which search-based methods, despite high solvability rates, exhibit a sharp performance decay in reconstructing long-range synthetic plans compared to sequence-based approaches. We release the full framework, benchmark definitions, and a standardized database of model predictions to support transparent and reproducible development in the field.

We present an open-source database of superconducting quantum device designs that may be used as the starting point for customized devices. Each design can be generated programmatically using the open-source Qiskit Metal package, and simulated using finite-element electromagnetic solvers. We present a robust workflow for achieving high accuracy on design simulations. Many designs in the database are experimentally validated, showing excellent agreement between simulated and measured parameters. Our database includes a front-end interface that allows users to generate ``best-guess'' designs based on desired circuit parameters. This project lowers the barrier to entry for research groups seeking to make a new class of devices by providing them a well-characterized starting point from which to refine their designs.

Language model users often issue queries that lack specification, where the context under which a query was issued -- such as the user's identity, the query's intent, and the criteria for a response to be useful -- is not explicit. For instance, a good response to a subjective query like "What book should I read next?" would depend on the user's preferences, and a good response to an open-ended query like "How do antibiotics work against bacteria?" would depend on the user's expertise. This makes evaluation of responses to such queries an ill-posed task, as evaluators may make arbitrary judgments about the response quality. To remedy this, we present contextualized evaluations, a protocol that synthetically constructs context surrounding an underspecified query and provides it during evaluation. We find that the presence of context can 1) alter conclusions drawn from evaluation, even flipping win rates between model pairs, 2) nudge evaluators to make fewer judgments based on surface-level criteria, like style, and 3) provide new insights about model behavior across diverse contexts. Specifically, our procedure uncovers an implicit bias towards WEIRD contexts in models' "default" responses and we find that models are not equally sensitive to following different contexts, even when they are provided in prompts.

We present a design framework called Conversational Learning with Analytical Step-by-Step Strategies (CLASS) for developing high-performance Intelligent Tutoring Systems (ITS). The CLASS framework aims to empower ITS with with two critical capabilities: imparting tutor-like step-by-step guidance and enabling tutor-like conversations in natural language to effectively engage learners. To empower ITS with the aforementioned capabilities, the CLASS framework employs two carefully curated synthetic datasets. The first scaffolding dataset encompasses a variety of elements, including problems, their corresponding subproblems, hints, incorrect solutions, and tailored feedback. This dataset provides ITS with essential problem-solving strategies necessary for guiding students through each step of the conversation. The second conversational dataset contains simulated student-tutor conversations that involve the application of problem-solving strategies learned from the first dataset. In the second dataset, the tutoring system adheres to a pre-defined response template, which helps to maintain consistency and structure in ITS's responses during its interactions. This structured methodology facilitates seamless integration of user feedback and yields valuable insights into ITS's internal decision-making process, allowing for continuous refinement and improvement of the system. We also present a proof-of-concept ITS, referred to as SPOCK, trained using the CLASS framework with a focus on college level introductory biology content. A carefully constructed protocol was developed for SPOCK's preliminary evaluation, examining aspects such as the factual accuracy and relevance of its responses. Experts in the field of biology offered favorable remarks, particularly highlighting SPOCK's capability to break down questions into manageable subproblems and provide step-by-step guidance to students.

When artificial agents are jointly trained to perform collaborative tasks using a communication channel, they develop opaque goal-oriented communication protocols. Good task performance is often considered sufficient evidence that meaningful communication is taking place, but existing empirical results show that communication strategies induced by common objectives can be counterintuitive whilst solving the task nearly perfectly. In this work, we identify a goal-agnostic prerequisite to meaningful communication, which we term semantic consistency, based on the idea that messages should have similar meanings across instances. We provide a formal definition for this idea, and use it to compare the two most common objectives in the field of emergent communication: discrimination and reconstruction. We prove, under mild assumptions, that semantically inconsistent communication protocols can be optimal solutions to the discrimination task, but not to reconstruction. We further show that the reconstruction objective encourages a stricter property, spatial meaningfulness, which also accounts for the distance between messages. Experiments with emergent communication games validate our theoretical results. These findings demonstrate an inherent advantage of distance-based communication goals, and contextualize previous empirical discoveries.

If you had an AI Whale-to-English translator, how could you validate whether or not it is working? Does one need to interact with the animals or rely on grounded observations such as temperature? We provide theoretical and proof-of-concept experimental evidence suggesting that interaction and even observations may not be necessary for sufficiently complex languages. One may be able to evaluate translators solely by their English outputs, offering potential advantages in terms of safety, ethics, and cost. This is an instance of machine translation quality evaluation (MTQE) without any reference translations available. A key challenge is identifying ``hallucinations,'' false translations which may appear fluent and plausible. We propose using segment-by-segment translation together with the classic NLP shuffle test to evaluate translators. The idea is to translate animal communication, turn by turn, and evaluate how often the resulting translations make more sense in order than permuted. Proof-of-concept experiments on data-scarce human languages and constructed languages demonstrate the potential utility of this evaluation methodology. These human-language experiments serve solely to validate our reference-free metric under data scarcity. It is found to correlate highly with a standard evaluation based on reference translations, which are available in our experiments. We also perform a theoretical analysis suggesting that interaction may not be necessary nor efficient in the early stages of learning to translate.

AI scientist systems, capable of autonomously executing the full research workflow from hypothesis generation and experimentation to paper writing, hold significant potential for accelerating scientific discovery. However, the internal workflow of these systems have not been closely examined. This lack of scrutiny poses a risk of introducing flaws that could undermine the integrity, reliability, and trustworthiness of their research outputs. In this paper, we identify four potential failure modes in contemporary AI scientist systems: inappropriate benchmark selection, data leakage, metric misuse, and post-hoc selection bias. To examine these risks, we design controlled experiments that isolate each failure mode while addressing challenges unique to evaluating AI scientist systems. Our assessment of two prominent open-source AI scientist systems reveals the presence of several failures, across a spectrum of severity, which can be easily overlooked in practice. Finally, we demonstrate that access to trace logs and code from the full automated workflow enables far more effective detection of such failures than examining the final paper alone. We thus recommend journals and conferences evaluating AI-generated research to mandate submission of these artifacts alongside the paper to ensure transparency, accountability, and reproducibility.

This position paper argues that the field of LLM agents requires a unified, telecom-inspired communication protocol to ensure safety, interoperability, and scalability, especially within the context of Next Generation (NextG) networks. Current ad-hoc communication methods are creating a fragmented ecosystem, reminiscent of the early "protocol wars" in networking, which stifles innovation and poses significant risks. Drawing inspiration from the layered, standardized protocols that underpin modern telecommunications, we propose the LLM-Agent Communication Protocol (LACP). LACP establishes a three-layer architecture designed to ensure semantic clarity in communication, transactional integrity for complex tasks, and robust, built-in security. In this position paper, we argue that adopting a principled, universal protocol is not merely beneficial but essential for realizing the potential of distributed AI. Such a standard is critical for ensuring that multi-agent systems can operate safely and reliably in the complex, real-time applications envisioned for 6G and beyond.

Combined electric power system and High-Altitude Electromagnetic Pulse (HEMP) models are being developed to determine the effect of a HEMP on the US power grid. The work relies primarily on deterministic methods; however, it is computationally untenable to evaluate the E1 HEMP response of large numbers of grid components distributed across a large interconnection. Further, the deterministic assessment of these components' failures are largely unachievable. E1 HEMP laboratory testing of the components is accomplished, but is expensive, leaving few data points to construct failure models of grid components exposed to E1 HEMP. The use of Bayesian priors, developed using the subject matter expertise, combined with the minimal test data in a Bayesian inference process, provides the basis for the development of more robust and cost-effective statistical component failure models. These can be used with minimal computational burden in a simulation environment such as sampling of Cumulative Distribution Functions (CDFs).

Reasoning protocols such as Chain of Thought (CoT) and Tree of Thought (ToT) organize internal deliberation but lack an explicit mechanism for external questioning that elicits self-revision. We present FOR-Prompting (From Objection to Revision Prompting), an asymmetric protocol where a Defender proposes an answer, an Objectioner raises question-style objections with no direct fixes, and a Host enforces consistency and closure. On GSM8K we observe about a 22% point gain over single-prompt and accuracy on par with CoT, with more than 10% higher ratings in reasoning and coherence from a uniform GPT 4.1 judge. FOR-Prompting also corrects mistakes without tools or human supervision on tricky queries, and improves performance for small-scale model (approx. 19% accuracy improved on Llama3.2:1b for GSM8K task), highlighting promise for small models and on personal device use. Beyond factual QA, qualitative analyses on open-ended tasks show enhanced exploration and refinement, with dialogue traces that make assumptions and trade-offs explicit. The protocol is model agnostic and operates purely at the prompt level through role-structured turns, so it works with hosted and local models of different sizes without retraining, and it supports large-scale study of objection-guided reasoning.

AI control protocols serve as a defense mechanism to stop untrusted LLM agents from causing harm in autonomous settings. Prior work treats this as a security problem, stress testing with exploits that use the deployment context to subtly complete harmful side tasks, such as backdoor insertion. In practice, most AI control protocols are fundamentally based on LLM monitors, which can become a central point of failure. We study adaptive attacks by an untrusted model that knows the protocol and the monitor model, which is plausible if the untrusted model was trained with a later knowledge cutoff or can search for this information autonomously. We instantiate a simple adaptive attack vector by which the attacker embeds publicly known or zero-shot prompt injections in the model outputs. Using this tactic, frontier models consistently evade diverse monitors and complete malicious tasks on two main AI control benchmarks. The attack works universally against current protocols that rely on a monitor. Furthermore, the recent Defer-to-Resample protocol even backfires, as its resampling amplifies the prompt injection and effectively reframes it as a best-of-n attack. In general, adaptive attacks on monitor models represent a major blind spot in current control protocols and should become a standard component of evaluations for future AI control mechanisms.

Clinical trials or studies oftentimes require long-term and/or costly follow-up of participants to evaluate a novel treatment/drug/vaccine. There has been increasing interest in the past few decades in using short-term surrogate outcomes as a replacement of the primary outcome i.e., in using the surrogate outcome, which can potentially be observed sooner, to make inference about the treatment effect on the long-term primary outcome. Very few of the available statistical methods to evaluate a surrogate are applicable to settings where both the surrogate and the primary outcome are time-to-event outcomes subject to censoring. Methods that can handle this setting tend to require parametric assumptions or be limited to assessing only the restricted mean survival time. In this paper, we propose a non-parametric approach to evaluate a censored surrogate outcome, such as time to progression, when the primary outcome is also a censored time-to-event outcome, such as time to death, and the treatment effect of interest is the difference in overall survival. Specifically, we define the proportion of the treatment effect on the primary outcome that is explained (PTE) by the censored surrogate outcome in this context, and estimate this proportion by defining and deriving an optimal transformation of the surrogate information. Our approach provides the added advantage of relaxed assumptions to guarantee that the true PTE is within (0,1), along with being model-free. Finite sample performance of our estimators are illustrated via extensive simulation studies and a real data application examining progression-free survival as a surrogate for overall survival for patients with metastatic colorectal cancer.

Recent advances in large language models (LLMs) have led to their extensive global deployment, and ensuring their safety calls for comprehensive and multilingual toxicity evaluations. However, existing toxicity benchmarks are overwhelmingly focused on English, posing serious risks to deploying LLMs in other languages. We address this by introducing PolygloToxicityPrompts (PTP), the first large-scale multilingual toxicity evaluation benchmark of 425K naturally occurring prompts spanning 17 languages. We overcome the scarcity of naturally occurring toxicity in web-text and ensure coverage across languages with varying resources by automatically scraping over 100M web-text documents. Using PTP, we investigate research questions to study the impact of model size, prompt language, and instruction and preference-tuning methods on toxicity by benchmarking over 60 LLMs. Notably, we find that toxicity increases as language resources decrease or model size increases. Although instruction- and preference-tuning reduce toxicity, the choice of preference-tuning method does not have any significant impact. Our findings shed light on crucial shortcomings of LLM safeguarding and highlight areas for future research.

We revisit Wald's celebrated Sequential Probability Ratio Test for sequential tests of two simple hypotheses, under privacy constraints. We propose DP-SPRT, a wrapper that can be calibrated to achieve desired error probabilities and privacy constraints, addressing a significant gap in previous work. DP-SPRT relies on a private mechanism that processes a sequence of queries and stops after privately determining when the query results fall outside a predefined interval. This OutsideInterval mechanism improves upon naive composition of existing techniques like AboveThreshold, potentially benefiting other sequential algorithms. We prove generic upper bounds on the error and sample complexity of DP-SPRT that can accommodate various noise distributions based on the practitioner's privacy needs. We exemplify them in two settings: Laplace noise (pure Differential Privacy) and Gaussian noise (R\'enyi differential privacy). In the former setting, by providing a lower bound on the sample complexity of any epsilon-DP test with prescribed type I and type II errors, we show that DP-SPRT is near optimal when both errors are small and the two hypotheses are close. Moreover, we conduct an experimental study revealing its good practical performance.

We investigate an emerging setup in which a small, on-device language model (LM) with access to local data communicates with a frontier, cloud-hosted LM to solve real-world tasks involving financial, medical, and scientific reasoning over long documents. Can a local-remote collaboration reduce cloud inference costs while preserving quality? First, we consider a naive collaboration protocol where the local and remote models simply chat back and forth. Because only the local model reads the full context, this protocol achieves a 30.4x reduction in remote costs, but recovers only 87% of the performance of the frontier model. We identify two key limitations of this protocol: the local model struggles to (1) follow the remote model's multi-step instructions and (2) reason over long contexts. Motivated by these observations, we study an extension of this protocol, coined MinionS, in which the remote model decomposes the task into easier subtasks over shorter chunks of the document, that are executed locally in parallel. MinionS reduces costs by 5.7x on average while recovering 97.9% of the performance of the remote model alone. Our analysis reveals several key design choices that influence the trade-off between cost and performance in local-remote systems.

Benchmarking is seen as critical to assessing progress in NLP. However, creating a benchmark involves many design decisions (e.g., which datasets to include, which metrics to use) that often rely on tacit, untested assumptions about what the benchmark is intended to measure or is actually measuring. There is currently no principled way of analyzing these decisions and how they impact the validity of the benchmark's measurements. To address this gap, we draw on evidence-centered design in educational assessments and propose Evidence-Centered Benchmark Design (ECBD), a framework which formalizes the benchmark design process into five modules. ECBD specifies the role each module plays in helping practitioners collect evidence about capabilities of interest. Specifically, each module requires benchmark designers to describe, justify, and support benchmark design choices -- e.g., clearly specifying the capabilities the benchmark aims to measure or how evidence about those capabilities is collected from model responses. To demonstrate the use of ECBD, we conduct case studies with three benchmarks: BoolQ, SuperGLUE, and HELM. Our analysis reveals common trends in benchmark design and documentation that could threaten the validity of benchmarks' measurements.

This paper introduces 26 guiding principles designed to streamline the process of querying and prompting large language models. Our goal is to simplify the underlying concepts of formulating questions for various scales of large language models, examining their abilities, and enhancing user comprehension on the behaviors of different scales of large language models when feeding into different prompts. Extensive experiments are conducted on LLaMA-1/2 (7B, 13B and 70B), GPT-3.5/4 to verify the effectiveness of the proposed principles on instructions and prompts design. We hope that this work can provide a better guide for researchers working on the prompting of large language models. Project page is available at https://github.com/VILA-Lab/ATLAS.

Offline reinforcement learning (RL) allows agents to learn effective, return-maximizing policies from a static dataset. Three popular algorithms for offline RL are Conservative Q-Learning (CQL), Behavior Cloning (BC), and Decision Transformer (DT), from the class of Q-Learning, Imitation Learning, and Sequence Modeling respectively. A key open question is: which algorithm is preferred under what conditions? We study this question empirically by exploring the performance of these algorithms across the commonly used D4RL and Robomimic benchmarks. We design targeted experiments to understand their behavior concerning data suboptimality, task complexity, and stochasticity. Our key findings are: (1) DT requires more data than CQL to learn competitive policies but is more robust; (2) DT is a substantially better choice than both CQL and BC in sparse-reward and low-quality data settings; (3) DT and BC are preferable as task horizon increases, or when data is obtained from human demonstrators; and (4) CQL excels in situations characterized by the combination of high stochasticity and low data quality. We also investigate architectural choices and scaling trends for DT on Atari and D4RL and make design/scaling recommendations. We find that scaling the amount of data for DT by 5x gives a 2.5x average score improvement on Atari.

Activation patching is a popular mechanistic interpretability technique, but has many subtleties regarding how it is applied and how one may interpret the results. We provide a summary of advice and best practices, based on our experience using this technique in practice. We include an overview of the different ways to apply activation patching and a discussion on how to interpret the results. We focus on what evidence patching experiments provide about circuits, and on the choice of metric and associated pitfalls.

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

Machine learning has demonstrated remarkable performance over finite datasets, yet whether the scores over the fixed benchmarks can sufficiently indicate the model's performance in the real world is still in discussion. In reality, an ideal robust model will probably behave similarly to the oracle (e.g., the human users), thus a good evaluation protocol is probably to evaluate the models' behaviors in comparison to the oracle. In this paper, we introduce a new robustness measurement that directly measures the image classification model's performance compared with a surrogate oracle (i.e., a foundation model). Besides, we design a simple method that can accomplish the evaluation beyond the scope of the benchmarks. Our method extends the image datasets with new samples that are sufficiently perturbed to be distinct from the ones in the original sets, but are still bounded within the same image-label structure the original test image represents, constrained by a foundation model pretrained with a large amount of samples. As a result, our new method will offer us a new way to evaluate the models' robustness performance, free of limitations of fixed benchmarks or constrained perturbations, although scoped by the power of the oracle. In addition to the evaluation results, we also leverage our generated data to understand the behaviors of the model and our new evaluation strategies.

Practical identifiability is a critical concern in data-driven modeling of mathematical systems. In this paper, we propose a novel framework for practical identifiability analysis to evaluate parameter identifiability in mathematical models of biological systems. Starting with a rigorous mathematical definition of practical identifiability, we demonstrate its equivalence to the invertibility of the Fisher Information Matrix. Our framework establishes the relationship between practical identifiability and coordinate identifiability, introducing a novel metric that simplifies and accelerates the evaluation of parameter identifiability compared to the profile likelihood method. Additionally, we introduce new regularization terms to address non-identifiable parameters, enabling uncertainty quantification and improving model reliability. To guide experimental design, we present an optimal data collection algorithm that ensures all model parameters are practically identifiable. Applications to Hill functions, neural networks, and dynamic biological models demonstrate the feasibility and efficiency of the proposed computational framework in uncovering critical biological processes and identifying key observable variables.

In unmanned aerial vehicle (UAV) networks, communication protocols and algorithms are essential for cooperation and collaboration between UAVs. Simulation provides a cost-effective solution for prototyping, debugging, and analyzing protocols and algorithms, avoiding the prohibitive expenses of field experiments. In this paper, we present ``UavNetSim-v1'', an open-source Python-based simulation platform designed for rapid development, testing, and evaluating the protocols and algorithms in UAV networks. ``UavNetSim-v1'' provides most of the functionalities developers may need, including routing/medium access control (MAC) protocols, topology control algorithms and mobility/energy models, while maintaining ease of use. Furthermore, the platform supports comprehensive performance evaluation and features an interactive visualization interface for in-depth algorithm analysis. In short, ``UavNetSim-v1'' lends itself to both rapid prototyping and educational purposes, and can serve as a lightweight yet powerful alternative to mature network simulators for UAV communication research.

In many natural and engineered systems, unknown quantum channels act on a subsystem that cannot be directly controlled and measured, but is instead learned through a controllable subsystem that weakly interacts with it. We study quantum channel discrimination (QCD) under these restrictions, which we call hidden system QCD (HQCD). We find that sequential protocols achieve perfect discrimination and saturate the Heisenberg limit. In contrast, depth-1 parallel and multi-shot protocols cannot solve HQCD. This suggests that sequential protocols are superior in experimentally realistic situations.

Large language models are being widely used across industries to generate content that contributes directly to key performance metrics, such as conversion rates. Pretrained models, however, often fall short when it comes to aligning with human preferences or optimizing for business objectives. As a result, fine-tuning with good-quality labeled data is essential to guide models to generate content that achieves better results. Controlled experiments, like A/B tests, can provide such data, but they are often expensive and come with significant engineering and logistical challenges. Meanwhile, companies have access to a vast amount of historical (observational) data that remains underutilized. In this work, we study the challenges and opportunities of fine-tuning LLMs using observational data. We show that while observational outcomes can provide valuable supervision, directly fine-tuning models on such data can lead them to learn spurious correlations. We present empirical evidence of this issue using various real-world datasets and propose DeconfoundLM, a method that explicitly removes the effect of known confounders from reward signals. Using simulation experiments, we demonstrate that DeconfoundLM improves the recovery of causal relationships and mitigates failure modes found in fine-tuning methods that ignore or naively incorporate confounding variables. Our findings highlight that while observational data presents risks, with the right causal corrections, it can be a powerful source of signal for LLM alignment. Please refer to the project page for code and related resources.

We consider the problem of performing Bayesian inference in probabilistic models where observations are accompanied by uncertainty, referred to as "uncertain evidence." We explore how to interpret uncertain evidence, and by extension the importance of proper interpretation as it pertains to inference about latent variables. We consider a recently-proposed method "distributional evidence" as well as revisit two older methods: Jeffrey's rule and virtual evidence. We devise guidelines on how to account for uncertain evidence and we provide new insights, particularly regarding consistency. To showcase the impact of different interpretations of the same uncertain evidence, we carry out experiments in which one interpretation is defined as "correct." We then compare inference results from each different interpretation illustrating the importance of careful consideration of uncertain evidence.

We propose a general-purpose approach for improving the ability of Large Language Models (LLMs) to intelligently and adaptively gather information from a user or other external source using the framework of sequential Bayesian experimental design (BED). This enables LLMs to act as effective multi-turn conversational agents and interactively interface with external environments. Our approach, which we call BED-LLM (Bayesian Experimental Design with Large Language Models), is based on iteratively choosing questions or queries that maximize the expected information gain (EIG) about the task of interest given the responses gathered previously. We show how this EIG can be formulated in a principled way using a probabilistic model derived from the LLM's belief distribution and provide detailed insights into key decisions in its construction. Further key to the success of BED-LLM are a number of specific innovations, such as a carefully designed estimator for the EIG, not solely relying on in-context updates for conditioning on previous responses, and a targeted strategy for proposing candidate queries. We find that BED-LLM achieves substantial gains in performance across a wide range of tests based on the 20-questions game and using the LLM to actively infer user preferences, compared to direct prompting of the LLM and other adaptive design strategies.

A multimodal large language model (MLLM) agent can receive instructions, capture images, retrieve histories from memory, and decide which tools to use. Nonetheless, red-teaming efforts have revealed that adversarial images/prompts can jailbreak an MLLM and cause unaligned behaviors. In this work, we report an even more severe safety issue in multi-agent environments, referred to as infectious jailbreak. It entails the adversary simply jailbreaking a single agent, and without any further intervention from the adversary, (almost) all agents will become infected exponentially fast and exhibit harmful behaviors. To validate the feasibility of infectious jailbreak, we simulate multi-agent environments containing up to one million LLaVA-1.5 agents, and employ randomized pair-wise chat as a proof-of-concept instantiation for multi-agent interaction. Our results show that feeding an (infectious) adversarial image into the memory of any randomly chosen agent is sufficient to achieve infectious jailbreak. Finally, we derive a simple principle for determining whether a defense mechanism can provably restrain the spread of infectious jailbreak, but how to design a practical defense that meets this principle remains an open question to investigate. Our project page is available at https://sail-sg.github.io/Agent-Smith/.

In this paper, we propose feedback designs for manipulating a quantum state to a target state by performing sequential measurements. In light of Belavkin's quantum feedback control theory, for a given set of (projective or non-projective) measurements and a given time horizon, we show that finding the measurement selection policy that maximizes the probability of successful state manipulation is an optimal control problem for a controlled Markovian process. The optimal policy is Markovian and can be solved by dynamical programming. Numerical examples indicate that making use of feedback information significantly improves the success probability compared to classical scheme without taking feedback. We also consider other objective functionals including maximizing the expected fidelity to the target state as well as minimizing the expected arrival time. The connections and differences among these objectives are also discussed.

Decentralized reputation schemes present a promising area of experimentation in blockchain applications. These solutions aim to overcome the shortcomings of simple monetary incentive mechanisms of naive tokenomics. However, there is a significant research gap regarding the limitations and benefits of such solutions. We formulate these trade-offs as a conjecture on the irreconcilability of three desirable properties of the reputation system in this context. Such a system can not be simultaneously generalizable, trustless, and Sybil resistant. To handle the limitations of this trilemma, we propose MeritRank: Sybil tolerant feedback aggregation mechanism for reputation. Instead of preventing Sybil attacks, our approach successfully bounds the benefits of these attacks. Using a dataset of participants' interactions in MakerDAO, we run experiments to demonstrate Sybil tolerance of MeritRank. Decay parameters of reputation in MeritRank: transitivity decay and connectivity decay, allow for a fine-tuning of desirable levels of reputation utility and Sybil tolerance in different use contexts.

We study the problem of adaptively identifying patient subpopulations that benefit from a given treatment during a confirmatory clinical trial. This type of adaptive clinical trial has been thoroughly studied in biostatistics, but has been allowed only limited adaptivity so far. Here, we aim to relax classical restrictions on such designs and investigate how to incorporate ideas from the recent machine learning literature on adaptive and online experimentation to make trials more flexible and efficient. We find that the unique characteristics of the subpopulation selection problem -- most importantly that (i) one is usually interested in finding subpopulations with any treatment benefit (and not necessarily the single subgroup with largest effect) given a limited budget and that (ii) effectiveness only has to be demonstrated across the subpopulation on average -- give rise to interesting challenges and new desiderata when designing algorithmic solutions. Building on these findings, we propose AdaGGI and AdaGCPI, two meta-algorithms for subpopulation construction. We empirically investigate their performance across a range of simulation scenarios and derive insights into their (dis)advantages across different settings.

Peer review is fundamental to the integrity and advancement of scientific publication. Traditional methods of peer review analyses often rely on exploration and statistics of existing peer review data, which do not adequately address the multivariate nature of the process, account for the latent variables, and are further constrained by privacy concerns due to the sensitive nature of the data. We introduce AgentReview, the first large language model (LLM) based peer review simulation framework, which effectively disentangles the impacts of multiple latent factors and addresses the privacy issue. Our study reveals significant insights, including a notable 37.1% variation in paper decisions due to reviewers' biases, supported by sociological theories such as the social influence theory, altruism fatigue, and authority bias. We believe that this study could offer valuable insights to improve the design of peer review mechanisms.

Early warning signals have been proposed to forecast the possibility of a critical transition, such as the eutrophication of a lake, the collapse of a coral reef, or the end of a glacial period. Because such transitions often unfold on temporal and spatial scales that can be difficult to approach by experimental manipulation, research has often relied on historical observations as a source of natural experiments. Here we examine a critical difference between selecting systems for study based on the fact that we have observed a critical transition and those systems for which we wish to forecast the approach of a transition. This difference arises by conditionally selecting systems known to experience a transition of some sort and failing to account for the bias this introduces -- a statistical error often known as the Prosecutor's Fallacy. By analysing simulated systems that have experienced transitions purely by chance, we reveal an elevated rate of false positives in common warning signal statistics. We further demonstrate a model-based approach that is less subject to this bias than these more commonly used summary statistics. We note that experimental studies with replicates avoid this pitfall entirely.

Given the impressive capabilities of recent Large Language Models (LLMs), we investigate and benchmark the most popular proprietary and different sized open source models on the task of explicit instruction following in conflicting situations, e.g. overrides. These include the ability of the model to override the knowledge within the weights of the model, the ability to override (or moderate) extracted knowledge in the prompt, and lastly the ability to perform a full jailbreak. Experimentation performed suggest several key findings to improve instruction following - larger models perform the best in following instructions that override internal and contextual instructions, and are obedient, even to a fault. When scaling to longer contexts via rope scaling, a significant buffer needs to be maintained from the edge of the perplexity cliff in order to maintain instruction following capabilities. Finally, we observe improving instruction following, and subsequently instruction overrides/jailbreaks, is fundamentally at odds with the ability of a language model to follow given safety filters or guidelines. Thus, we postulate the most effective approach for safe, trustworthy AI should be dealt external to the LLM itself.

Building language models (LMs), especially small and medium ones, remains more art than science. While large LMs often improve by sheer scale, it is still unclear why many design choices work. For small LMs, this uncertainty is more limiting: tight parameter budgets make each decision critical, yet researchers still lack systematic, scientific ways to test and refine new ideas. We introduce Pico, a lightweight, modular framework that enables systematic, hypothesis-driven research for small and medium-scale language model development. Pico consists of two libraries that together provide a practical sandbox where researchers can make targeted changes to a model's architecture or training procedures and directly observe their effects on the model's behavior. To support reproducible experimentation, we also release a suite of baseline models, pico-decoder, trained under standardized conditions and open-sourced for the community. Case studies highlight how Pico can support iterative small LM design and analysis.

As large language models (LLMs) have been deployed in various real-world settings, concerns about the harm they may propagate have grown. Various jailbreaking techniques have been developed to expose the vulnerabilities of these models and improve their safety. This work reveals that many state-of-the-art LLMs are vulnerable to malicious requests hidden behind scientific language. Specifically, our experiments with GPT4o, GPT4o-mini, GPT-4, LLama3-405B-Instruct, Llama3-70B-Instruct, Cohere, Gemini models demonstrate that, the models' biases and toxicity substantially increase when prompted with requests that deliberately misinterpret social science and psychological studies as evidence supporting the benefits of stereotypical biases. Alarmingly, these models can also be manipulated to generate fabricated scientific arguments claiming that biases are beneficial, which can be used by ill-intended actors to systematically jailbreak these strong LLMs. Our analysis studies various factors that contribute to the models' vulnerabilities to malicious requests in academic language. Mentioning author names and venues enhances the persuasiveness of models, and the bias scores increase as dialogues progress. Our findings call for a more careful investigation on the use of scientific data for training LLMs.

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as an impressive class of deep generative models, sparking extensive research and leading to numerous studies on their application to molecular generative tasks. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. Particularly, due to the diversity of diffusion model formulations, molecular data modalities, and generative task types, the research landscape is challenging to navigate, hindering understanding and limiting the area's growth. To address this, this paper conducts a comprehensive survey of diffusion model-based molecular generative methods. We systematically review the research from the perspectives of methodological formulations, data modalities, and task types, offering a novel taxonomy. This survey aims to facilitate understanding and further flourishing development in this area. The relevant papers are summarized at: https://github.com/AzureLeon1/awesome-molecular-diffusion-models.

While the evaluation of explanations is an important step towards trustworthy models, it needs to be done carefully, and the employed metrics need to be well-understood. Specifically model randomization testing is often overestimated and regarded as a sole criterion for selecting or discarding certain explanation methods. To address shortcomings of this test, we start by observing an experimental gap in the ranking of explanation methods between randomization-based sanity checks [1] and model output faithfulness measures (e.g. [25]). We identify limitations of model-randomization-based sanity checks for the purpose of evaluating explanations. Firstly, we show that uninformative attribution maps created with zero pixel-wise covariance easily achieve high scores in this type of checks. Secondly, we show that top-down model randomization preserves scales of forward pass activations with high probability. That is, channels with large activations have a high probility to contribute strongly to the output, even after randomization of the network on top of them. Hence, explanations after randomization can only be expected to differ to a certain extent. This explains the observed experimental gap. In summary, these results demonstrate the inadequacy of model-randomization-based sanity checks as a criterion to rank attribution methods.

Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experimental or interventional conditions. BaCaDI is fully differentiable, which allows us to infer the complex joint posterior over the intervention targets and the causal structure via efficient gradient-based variational inference. In experiments on synthetic causal discovery tasks and simulated gene-expression data, BaCaDI outperforms related methods in identifying causal structures and intervention targets.

This paper identifies and analyzes a novel vulnerability class in Model Context Protocol (MCP) based agent systems. The attack chain describes and demonstrates how benign, individually authorized tasks can be orchestrated to produce harmful emergent behaviors. Through systematic analysis using the MITRE ATLAS framework, we demonstrate how 95 agents tested with access to multiple services-including browser automation, financial analysis, location tracking, and code deployment-can chain legitimate operations into sophisticated attack sequences that extend beyond the security boundaries of any individual service. These red team exercises survey whether current MCP architectures lack cross-domain security measures necessary to detect or prevent a large category of compositional attacks. We present empirical evidence of specific attack chains that achieve targeted harm through service orchestration, including data exfiltration, financial manipulation, and infrastructure compromise. These findings reveal that the fundamental security assumption of service isolation fails when agents can coordinate actions across multiple domains, creating an exponential attack surface that grows with each additional capability. This research provides a barebones experimental framework that evaluate not whether agents can complete MCP benchmark tasks, but what happens when they complete them too well and optimize across multiple services in ways that violate human expectations and safety constraints. We propose three concrete experimental directions using the existing MCP benchmark suite.

This research delves into the construction and utilization of synthetic datasets, specifically within the telematics sphere, leveraging OpenAI's powerful language model, ChatGPT. Synthetic datasets present an effective solution to challenges pertaining to data privacy, scarcity, and control over variables - characteristics that make them particularly valuable for research pursuits. The utility of these datasets, however, largely depends on their quality, measured through the lenses of diversity, relevance, and coherence. To illustrate this data creation process, a hands-on case study is conducted, focusing on the generation of a synthetic telematics dataset. The experiment involved an iterative guidance of ChatGPT, progressively refining prompts and culminating in the creation of a comprehensive dataset for a hypothetical urban planning scenario in Columbus, Ohio. Upon generation, the synthetic dataset was subjected to an evaluation, focusing on the previously identified quality parameters and employing descriptive statistics and visualization techniques for a thorough analysis. Despite synthetic datasets not serving as perfect replacements for actual world data, their potential in specific use-cases, when executed with precision, is significant. This research underscores the potential of AI models like ChatGPT in enhancing data availability for complex sectors like telematics, thus paving the way for a myriad of new research opportunities.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

Researchers and developers increasingly rely on toxicity scoring to moderate generative language model outputs, in settings such as customer service, information retrieval, and content generation. However, toxicity scoring may render pertinent information inaccessible, rigidify or "value-lock" cultural norms, and prevent language reclamation processes, particularly for marginalized people. In this work, we extend the concept of algorithmic recourse to generative language models: we provide users a novel mechanism to achieve their desired prediction by dynamically setting thresholds for toxicity filtering. Users thereby exercise increased agency relative to interactions with the baseline system. A pilot study (n = 30) supports the potential of our proposed recourse mechanism, indicating improvements in usability compared to fixed-threshold toxicity-filtering of model outputs. Future work should explore the intersection of toxicity scoring, model controllability, user agency, and language reclamation processes -- particularly with regard to the bias that many communities encounter when interacting with generative language models.

The Model Context Protocol (MCP) is rapidly emerging as a pivotal open standard, designed to enhance agent-tool integration and interoperability, and is positioned to unlock a new era of powerful, interconnected, and genuinely utilitarian agentic AI. However, despite MCP's growing adoption, existing benchmarks often fail to capture real-world agent performance within this new paradigm, leading to a distorted perception of their true operational value and an inability to reliably differentiate proficiencies. To bridge this critical evaluation gap, we introduce MCP-AgentBench -- a comprehensive benchmark specifically engineered to rigorously assess language agent capabilities in MCP-mediated tool interactions. Core contributions of MCP-AgentBench include: the establishment of a robust MCP testbed comprising 33 operational servers with 188 distinct tools; the development of a benchmark featuring 600 systematically designed queries distributed across 6 distinct categories of varying interaction complexity; and the introduction of MCP-Eval, a novel outcome-oriented evaluation methodology prioritizing real-world task success. Through extensive empirical evaluation of leading language agents, we provide foundational insights. MCP-AgentBench aims to equip the research community with a standardized and reliable framework to build, validate, and advance agents capable of fully leveraging MCP's transformative benefits, thereby accelerating progress toward truly capable and interoperable AI systems.

We introduce and study the problem of detecting whether an agent is updating their prior beliefs given new evidence in an optimal way that is Bayesian, or whether they are biased towards their own prior. In our model, biased agents form posterior beliefs that are a convex combination of their prior and the Bayesian posterior, where the more biased an agent is, the closer their posterior is to the prior. Since we often cannot observe the agent's beliefs directly, we take an approach inspired by information design. Specifically, we measure an agent's bias by designing a signaling scheme and observing the actions they take in response to different signals, assuming that they are maximizing their own expected utility; our goal is to detect bias with a minimum number of signals. Our main results include a characterization of scenarios where a single signal suffices and a computationally efficient algorithm to compute optimal signaling schemes.

Online competitive action games have flourished as a space for entertainment and social connections, yet they face challenges from a small percentage of players engaging in disruptive behaviors. This study delves into the under-explored realm of understanding the effects of moderation on player behavior within online gaming on an example of a popular title - Call of Duty(R): Modern Warfare(R)II. We employ a quasi-experimental design and causal inference techniques to examine the impact of moderation in a real-world industry-scale moderation system. We further delve into novel aspects around the impact of delayed moderation, as well as the severity of applied punishment. We examine these effects on a set of four disruptive behaviors including cheating, offensive user name, chat, and voice. Our findings uncover the dual impact moderation has on reducing disruptive behavior and discouraging disruptive players from participating. We further uncover differences in the effectiveness of quick and delayed moderation and the varying severity of punishment. Our examination of real-world gaming interactions sets a precedent in understanding the effectiveness of moderation and its impact on player behavior. Our insights offer actionable suggestions for the most promising avenues for improving real-world moderation practices, as well as the heterogeneous impact moderation has on indifferent players.

This paper investigates prior prompt engineering (pPE) in the context of reinforcement fine-tuning (RFT), where language models (LMs) are incentivized to exhibit behaviors that maximize performance through reward signals. While existing RFT research has primarily focused on algorithms, reward shaping, and data curation, the design of the prior prompt--the instructions prepended to queries during training to elicit behaviors such as step-by-step reasoning--remains underexplored. We investigate whether different pPE approaches can guide LMs to internalize distinct behaviors after RFT. Inspired by inference-time prompt engineering (iPE), we translate five representative iPE strategies--reasoning, planning, code-based reasoning, knowledge recall, and null-example utilization--into corresponding pPE approaches. We experiment with Qwen2.5-7B using each of the pPE approaches, then evaluate performance on in-domain and out-of-domain benchmarks (e.g., AIME2024, HumanEval+, and GPQA-Diamond). Our results show that all pPE-trained models surpass their iPE-prompted counterparts, with the null-example pPE approach achieving the largest average performance gain and the highest improvement on AIME2024 and GPQA-Diamond, surpassing the commonly used reasoning approach. Furthermore, by adapting a behavior-classification framework, we demonstrate that different pPE strategies instill distinct behavioral styles in the resulting models. These findings position pPE as a powerful yet understudied axis for RFT.

Large language models (LLMs) excel in most NLP tasks but also require expensive cloud servers for deployment due to their size, while smaller models that can be deployed on lower cost (e.g., edge) devices, tend to lag behind in terms of response quality. Therefore in this work we propose a hybrid inference approach which combines their respective strengths to save cost and maintain quality. Our approach uses a router that assigns queries to the small or large model based on the predicted query difficulty and the desired quality level. The desired quality level can be tuned dynamically at test time to seamlessly trade quality for cost as per the scenario requirements. In experiments our approach allows us to make up to 40% fewer calls to the large model, with no drop in response quality.

Large language models and autonomous AI agents have evolved rapidly, resulting in a diverse array of evaluation benchmarks, frameworks, and collaboration protocols. However, the landscape remains fragmented and lacks a unified taxonomy or comprehensive survey. Therefore, we present a side-by-side comparison of benchmarks developed between 2019 and 2025 that evaluate these models and agents across multiple domains. In addition, we propose a taxonomy of approximately 60 benchmarks that cover general and academic knowledge reasoning, mathematical problem-solving, code generation and software engineering, factual grounding and retrieval, domain-specific evaluations, multimodal and embodied tasks, task orchestration, and interactive assessments. Furthermore, we review AI-agent frameworks introduced between 2023 and 2025 that integrate large language models with modular toolkits to enable autonomous decision-making and multi-step reasoning. Moreover, we present real-world applications of autonomous AI agents in materials science, biomedical research, academic ideation, software engineering, synthetic data generation, chemical reasoning, mathematical problem-solving, geographic information systems, multimedia, healthcare, and finance. We then survey key agent-to-agent collaboration protocols, namely the Agent Communication Protocol (ACP), the Model Context Protocol (MCP), and the Agent-to-Agent Protocol (A2A). Finally, we discuss recommendations for future research, focusing on advanced reasoning strategies, failure modes in multi-agent LLM systems, automated scientific discovery, dynamic tool integration via reinforcement learning, integrated search capabilities, and security vulnerabilities in agent protocols.

Recent work has demonstrated that controlled pretraining experiments are a powerful tool for understanding learning, reasoning, and memorization in large language models (LLMs). However, the computational cost of pretraining presents a significant constraint. To overcome this constraint, we propose to conduct multiple pretraining experiments simultaneously during a single training run. We demonstrate the feasibility of this approach by conducting ten experiments during the training of a 1.5B parameter model on 210B tokens. Although we only train a single model, we can replicate the results from multiple previous works on data contamination, poisoning, and memorization. We also conduct novel investigations into knowledge acquisition, mathematical reasoning, and watermarking. For example, we dynamically update the training data until the model acquires a particular piece of knowledge. Remarkably, the influence of the ten experiments on the model's training dynamics and overall performance is minimal. However, interactions between different experiments may act as a potential confounder in our approach. We propose to test for interactions with continual pretraining experiments, finding them to be negligible in our setup. Overall, our findings suggest that performing multiple pretraining experiments in a single training run can enable rigorous scientific experimentation with large models on a compute budget.

The second quantum revolution brings with it the promise of a quantum internet. As the first quantum network hardware prototypes near completion new challenges emerge. A functional network is more than just the physical hardware, yet work on scalable quantum network systems is in its infancy. In this paper we present a quantum network protocol designed to enable end-to-end quantum communication in the face of the new fundamental and technical challenges brought by quantum mechanics. We develop a quantum data plane protocol that enables end-to-end quantum communication and can serve as a building block for more complex services. One of the key challenges in near-term quantum technology is decoherence -- the gradual decay of quantum information -- which imposes extremely stringent limits on storage times. Our protocol is designed to be efficient in the face of short quantum memory lifetimes. We demonstrate this using a simulator for quantum networks and show that the protocol is able to deliver its service even in the face of significant losses due to decoherence. Finally, we conclude by showing that the protocol remains functional on the extremely resource limited hardware that is being developed today underlining the timeliness of this work.

Large language models trained for safety and harmlessness remain susceptible to adversarial misuse, as evidenced by the prevalence of "jailbreak" attacks on early releases of ChatGPT that elicit undesired behavior. Going beyond recognition of the issue, we investigate why such attacks succeed and how they can be created. We hypothesize two failure modes of safety training: competing objectives and mismatched generalization. Competing objectives arise when a model's capabilities and safety goals conflict, while mismatched generalization occurs when safety training fails to generalize to a domain for which capabilities exist. We use these failure modes to guide jailbreak design and then evaluate state-of-the-art models, including OpenAI's GPT-4 and Anthropic's Claude v1.3, against both existing and newly designed attacks. We find that vulnerabilities persist despite the extensive red-teaming and safety-training efforts behind these models. Notably, new attacks utilizing our failure modes succeed on every prompt in a collection of unsafe requests from the models' red-teaming evaluation sets and outperform existing ad hoc jailbreaks. Our analysis emphasizes the need for safety-capability parity -- that safety mechanisms should be as sophisticated as the underlying model -- and argues against the idea that scaling alone can resolve these safety failure modes.

When deploying machine learning models in high-stakes real-world environments such as health care, it is crucial to accurately assess the uncertainty concerning a model's prediction on abnormal inputs. However, there is a scarcity of literature analyzing this problem on medical data, especially on mixed-type tabular data such as Electronic Health Records. We close this gap by presenting a series of tests including a large variety of contemporary uncertainty estimation techniques, in order to determine whether they are able to identify out-of-distribution (OOD) patients. In contrast to previous work, we design tests on realistic and clinically relevant OOD groups, and run experiments on real-world medical data. We find that almost all techniques fail to achieve convincing results, partly disagreeing with earlier findings.

Human evaluation is critical for validating the performance of text-to-image generative models, as this highly cognitive process requires deep comprehension of text and images. However, our survey of 37 recent papers reveals that many works rely solely on automatic measures (e.g., FID) or perform poorly described human evaluations that are not reliable or repeatable. This paper proposes a standardized and well-defined human evaluation protocol to facilitate verifiable and reproducible human evaluation in future works. In our pilot data collection, we experimentally show that the current automatic measures are incompatible with human perception in evaluating the performance of the text-to-image generation results. Furthermore, we provide insights for designing human evaluation experiments reliably and conclusively. Finally, we make several resources publicly available to the community to facilitate easy and fast implementations.

Scientific experimentation, a cornerstone of human progress, demands rigor in reliability, methodical control, and interpretability to yield meaningful results. Despite the growing capabilities of large language models (LLMs) in automating different aspects of the scientific process, automating rigorous experimentation remains a significant challenge. To address this gap, we propose Curie, an AI agent framework designed to embed rigor into the experimentation process through three key components: an intra-agent rigor module to enhance reliability, an inter-agent rigor module to maintain methodical control, and an experiment knowledge module to enhance interpretability. To evaluate Curie, we design a novel experimental benchmark composed of 46 questions across four computer science domains, derived from influential research papers, and widely adopted open-source projects. Compared to the strongest baseline tested, we achieve a 3.4times improvement in correctly answering experimental questions.Curie is open-sourced at https://github.com/Just-Curieous/Curie.

Efficient experiment reproduction is critical to accelerating progress in artificial intelligence. However, the inherent complexity of method design and training procedures presents substantial challenges for automation. Notably, reproducing experiments often requires implicit domain-specific knowledge not explicitly documented in the original papers. To address this, we introduce the paper lineage algorithm, which identifies and extracts implicit knowledge from the relevant references cited by the target paper. Building on this idea, we propose AutoReproduce, a multi-agent framework capable of automatically reproducing experiments described in research papers in an end-to-end manner. AutoReproduce enhances code executability by generating unit tests alongside the reproduction process. To evaluate the reproduction capability, we construct ReproduceBench, a benchmark annotated with verified implementations, and introduce novel evaluation metrics to assess both the reproduction and execution fidelity. Experimental results demonstrate that AutoReproduce outperforms the existing strong agent baselines on all five evaluation metrics by a peak margin of over 70%. In particular, compared to the official implementations, AutoReproduce achieves an average performance gap of 22.1% on 89.74% of the executable experiment runs. The code will be available at https://github.com/AI9Stars/AutoReproduce.

This paper introduces fourteen novel datasets for the evaluation of Large Language Models' safety in the context of enterprise tasks. A method was devised to evaluate a model's safety, as determined by its ability to follow instructions and output factual, unbiased, grounded, and appropriate content. In this research, we used OpenAI GPT as point of comparison since it excels at all levels of safety. On the open-source side, for smaller models, Meta Llama2 performs well at factuality and toxicity but has the highest propensity for hallucination. Mistral hallucinates the least but cannot handle toxicity well. It performs well in a dataset mixing several tasks and safety vectors in a narrow vertical domain. Gemma, the newly introduced open-source model based on Google Gemini, is generally balanced but trailing behind. When engaging in back-and-forth conversation (multi-turn prompts), we find that the safety of open-source models degrades significantly. Aside from OpenAI's GPT, Mistral is the only model that still performed well in multi-turn tests.

Despite its importance to experimental design, statistical power (the probability that, given a real effect, an experiment will reject the null hypothesis) has largely been ignored by the NLP community. Underpowered experiments make it more difficult to discern the difference between statistical noise and meaningful model improvements, and increase the chances of exaggerated findings. By meta-analyzing a set of existing NLP papers and datasets, we characterize typical power for a variety of settings and conclude that underpowered experiments are common in the NLP literature. In particular, for several tasks in the popular GLUE benchmark, small test sets mean that most attempted comparisons to state of the art models will not be adequately powered. Similarly, based on reasonable assumptions, we find that the most typical experimental design for human rating studies will be underpowered to detect small model differences, of the sort that are frequently studied. For machine translation, we find that typical test sets of 2000 sentences have approximately 75% power to detect differences of 1 BLEU point. To improve the situation going forward, we give an overview of best practices for power analysis in NLP and release a series of notebooks to assist with future power analyses.

This chapter discusses the need of security and privacy protection mechanisms in aggregation protocols used in wireless sensor networks (WSN). It presents a comprehensive state of the art discussion on the various privacy protection mechanisms used in WSNs and particularly focuses on the CPDA protocols proposed by He et al. (INFOCOM 2007). It identifies a security vulnerability in the CPDA protocol and proposes a mechanism to plug that vulnerability. To demonstrate the need of security in aggregation process, the chapter further presents various threats in WSN aggregation mechanisms. A large number of existing protocols for secure aggregation in WSN are discussed briefly and a protocol is proposed for secure aggregation which can detect false data injected by malicious nodes in a WSN. The performance of the protocol is also presented. The chapter concludes while highlighting some future directions of research in secure data aggregation in WSNs.

In the last few years, the Internet throughput, usage and reliability have increased almost exponentially. The introduction of broadband wireless mobile ad hoc networks (MANETs) and cellular networks together with increased computational power have opened the door for a new breed of applications to be created, namely real-time multimedia applications. Delivering real-time multimedia traffic over a complex network like the Internet is a particularly challenging task since these applications have strict quality-of-service (QoS) requirements on bandwidth, delay, and delay jitter. Traditional Internet protocol (IP)-based best effort service is not able to meet these stringent requirements. The time-varying nature of wireless channels and resource constrained wireless devices make the problem even more difficult. To improve perceived media quality by end users over wireless Internet, QoS supports can be addressed in different layers, including application layer, transport layer and link layer. Cross layer design is a well-known approach to achieve this adaptation. In cross-layer design, the challenges from the physical wireless medium and the QoS-demands from the applications are taken into account so that the rate, power, and coding at the physical (PHY) layer can adapted to meet the requirements of the applications given the current channel and network conditions. A number of propositions for cross-layer designs exist in the literature. In this chapter, an extensive review has been made on these cross-layer architectures that combine the application-layer, transport layer and the link layer controls. Particularly, the issues like channel estimation techniques, adaptive controls at the application and link layers for energy efficiency, priority based scheduling, transmission rate control at the transport layer, and adaptive automatic repeat request (ARQ) are discussed in detail.

Reinforcement learning (RL) over text representations can be effective for finding high-value policies that can search over graphs. However, RL requires careful structuring of the search space and algorithm design to be effective in this challenge. Through extensive experiments, we explore how different design choices for text grammar and algorithmic choices for training can affect an RL policy's ability to generate molecules with desired properties. We arrive at a new RL-based molecular design algorithm (ChemRLformer) and perform a thorough analysis using 25 molecule design tasks, including computationally complex protein docking simulations. From this analysis, we discover unique insights in this problem space and show that ChemRLformer achieves state-of-the-art performance while being more straightforward than prior work by demystifying which design choices are actually helpful for text-based molecule design.

Workplace toxicity is widely recognized as detrimental to organizational culture, yet quantifying its direct impact on operational efficiency remains methodologically challenging due to the ethical and practical difficulties of reproducing conflict in human subjects. This study leverages Large Language Model (LLM) based Multi-Agent Systems to simulate 1-on-1 adversarial debates, creating a controlled "sociological sandbox". We employ a Monte Carlo method to simulate hundrets of discussions, measuring the convergence time (defined as the number of arguments required to reach a conclusion) between a baseline control group and treatment groups involving agents with "toxic" system prompts. Our results demonstrate a statistically significant increase of approximately 25\% in the duration of conversations involving toxic participants. We propose that this "latency of toxicity" serves as a proxy for financial damage in corporate and academic settings. Furthermore, we demonstrate that agent-based modeling provides a reproducible, ethical alternative to human-subject research for measuring the mechanics of social friction.

Recent advancements in large language models (LLMs) have shown promise in generating novel research ideas. However, these ideas often face challenges related to feasibility and expected effectiveness. This paper explores how augmenting LLMs with relevant data during the idea generation process can enhance the quality of generated ideas. We introduce two ways of incorporating data: (1) providing metadata during the idea generation stage to guide LLMs toward feasible directions, and (2) adding automatic validation during the idea selection stage to assess the empirical plausibility of hypotheses within ideas. We conduct experiments in the social science domain, specifically with climate negotiation topics, and find that metadata improves the feasibility of generated ideas by 20%, while automatic validation improves the overall quality of selected ideas by 7%. A human study shows that LLM-generated ideas, along with their related data and validation processes, inspire researchers to propose research ideas with higher quality. Our work highlights the potential of data-driven research idea generation, and underscores the practical utility of LLM-assisted ideation in real-world academic settings.

Various algorithms for continual learning (CL) have been designed with the goal of effectively alleviating the trade-off between stability and plasticity during the CL process. To achieve this goal, tuning appropriate hyperparameters for each algorithm is essential. As an evaluation protocol, it has been common practice to train a CL algorithm using diverse hyperparameter values on a CL scenario constructed with a benchmark dataset. Subsequently, the best performance attained with the optimal hyperparameter value serves as the criterion for evaluating the CL algorithm. In this paper, we contend that this evaluation protocol is not only impractical but also incapable of effectively assessing the CL capability of a CL algorithm. Returning to the fundamental principles of model evaluation in machine learning, we propose an evaluation protocol that involves Hyperparameter Tuning and Evaluation phases. Those phases consist of different datasets but share the same CL scenario. In the Hyperparameter Tuning phase, each algorithm is iteratively trained with different hyperparameter values to find the optimal hyperparameter values. Subsequently, in the Evaluation phase, the optimal hyperparameter values is directly applied for training each algorithm, and their performance in the Evaluation phase serves as the criterion for evaluating them. Through experiments on CIFAR-100 and ImageNet-100 based on the proposed protocol in class-incremental learning, we not only observed that the existing evaluation method fail to properly assess the CL capability of each algorithm but also observe that some recently proposed state-of-the-art algorithms, which reported superior performance, actually exhibit inferior performance compared to the previous algorithm.

The emergence of pre-trained AI systems with powerful capabilities across a diverse and ever-increasing set of complex domains has raised a critical challenge for AI safety as tasks can become too complicated for humans to judge directly. Irving et al. [2018] proposed a debate method in this direction with the goal of pitting the power of such AI models against each other until the problem of identifying (mis)-alignment is broken down into a manageable subtask. While the promise of this approach is clear, the original framework was based on the assumption that the honest strategy is able to simulate deterministic AI systems for an exponential number of steps, limiting its applicability. In this paper, we show how to address these challenges by designing a new set of debate protocols where the honest strategy can always succeed using a simulation of a polynomial number of steps, whilst being able to verify the alignment of stochastic AI systems, even when the dishonest strategy is allowed to use exponentially many simulation steps.

Motivated by concerns about making online decisions that incur undue amount of risk at each time step, in this paper, we formulate the probably anytime-safe stochastic combinatorial semi-bandits problem. In this problem, the agent is given the option to select a subset of size at most K from a set of L ground items. Each item is associated to a certain mean reward as well as a variance that represents its risk. To mitigate the risk that the agent incurs, we require that with probability at least 1-delta, over the entire horizon of time T, each of the choices that the agent makes should contain items whose sum of variances does not exceed a certain variance budget. We call this probably anytime-safe constraint. Under this constraint, we design and analyze an algorithm {\sc PASCombUCB} that minimizes the regret over the horizon of time T. By developing accompanying information-theoretic lower bounds, we show that under both the problem-dependent and problem-independent paradigms, {\sc PASCombUCB} is almost asymptotically optimal. Experiments are conducted to corroborate our theoretical findings. Our problem setup, the proposed {\sc PASCombUCB} algorithm, and novel analyses are applicable to domains such as recommendation systems and transportation in which an agent is allowed to choose multiple items at a single time step and wishes to control the risk over the whole time horizon.

Exploiting the recent advancements in artificial intelligence, showcased by ChatGPT and DALL-E, in real-world applications necessitates vast, domain-specific, and publicly accessible datasets. Unfortunately, the scarcity of such datasets poses a significant challenge for researchers aiming to apply these breakthroughs in engineering design. Synthetic datasets emerge as a viable alternative. However, practitioners are often uncertain about generating high-quality datasets that accurately represent real-world data and are suitable for the intended downstream applications. This study aims to fill this knowledge gap by proposing comprehensive guidelines for generating, annotating, and validating synthetic datasets. The trade-offs and methods associated with each of these aspects are elaborated upon. Further, the practical implications of these guidelines are illustrated through the creation of a turbo-compressors dataset. The study underscores the importance of thoughtful sampling methods to ensure the appropriate size, diversity, utility, and realism of a dataset. It also highlights that design diversity does not equate to performance diversity or realism. By employing test sets that represent uniform, real, or task-specific samples, the influence of sample size and sampling strategy is scrutinized. Overall, this paper offers valuable insights for researchers intending to create and publish synthetic datasets for engineering design, thereby paving the way for more effective applications of AI advancements in the field. The code and data for the dataset and methods are made publicly accessible at https://github.com/cyrilpic/radcomp .

Large Language Models have recently gained significant attention in scientific discovery for their extensive knowledge and advanced reasoning capabilities. However, they encounter challenges in effectively simulating observational feedback and grounding it with language to propel advancements in physical scientific discovery. Conversely, human scientists undertake scientific discovery by formulating hypotheses, conducting experiments, and revising theories through observational analysis. Inspired by this, we propose to enhance the knowledge-driven, abstract reasoning abilities of LLMs with the computational strength of simulations. We introduce Scientific Generative Agent (SGA), a bilevel optimization framework: LLMs act as knowledgeable and versatile thinkers, proposing scientific hypotheses and reason about discrete components, such as physics equations or molecule structures; meanwhile, simulations function as experimental platforms, providing observational feedback and optimizing via differentiability for continuous parts, such as physical parameters. We conduct extensive experiments to demonstrate our framework's efficacy in constitutive law discovery and molecular design, unveiling novel solutions that differ from conventional human expectations yet remain coherent upon analysis.

The development of robust safety benchmarks for large language models requires open, reproducible datasets that can measure both appropriate refusal of harmful content and potential over-restriction of legitimate scientific discourse. We present an open-source dataset and testing framework for evaluating LLM safety mechanisms across mainly controlled substance queries, analyzing four major models' responses to systematically varied prompts. Our results reveal distinct safety profiles: Claude-3.5-sonnet demonstrated the most conservative approach with 73% refusals and 27% allowances, while Mistral attempted to answer 100% of queries. GPT-3.5-turbo showed moderate restriction with 10% refusals and 90% allowances, and Grok-2 registered 20% refusals and 80% allowances. Testing prompt variation strategies revealed decreasing response consistency, from 85% with single prompts to 65% with five variations. This publicly available benchmark enables systematic evaluation of the critical balance between necessary safety restrictions and potential over-censorship of legitimate scientific inquiry, while providing a foundation for measuring progress in AI safety implementation. Chain-of-thought analysis reveals potential vulnerabilities in safety mechanisms, highlighting the complexity of implementing robust safeguards without unduly restricting desirable and valid scientific discourse.

A modified LAB algorithm is introduced in this paper. It builds upon the original LAB algorithm (Reddy et al. 2023), which is a socio-inspired algorithm that models competitive and learning behaviours within a group, establishing hierarchical roles. The proposed algorithm incorporates the roulette wheel approach and a reduction factor introducing inter-group competition and iteratively narrowing down the sample space. The algorithm is validated by solving the benchmark test problems from CEC 2005 and CEC 2017. The solutions are validated using standard statistical tests such as two-sided and pairwise signed rank Wilcoxon test and Friedman rank test. The algorithm exhibited improved and superior robustness as well as search space exploration capabilities. Furthermore, a Clustering-Based Search Space Reduction (C-SSR) method is proposed, making the algorithm capable to solve constrained problems. The C-SSR method enables the algorithm to identify clusters of feasible regions, satisfying the constraints and contributing to achieve the optimal solution. This method demonstrates its effectiveness as a potential alternative to traditional constraint handling techniques. The results obtained using the Modified LAB algorithm are then compared with those achieved by other recent metaheuristic algorithms.

Purpose: With advancements in Large Language Models (LLMs) for healthcare, the need arises for competitive open-source models to protect the public interest. This work contributes to the field of open medical LLMs by optimizing key stages of data preprocessing and training, while showing how to improve model safety (through DPO) and efficacy (through RAG). The evaluation methodology used, which includes four different types of tests, defines a new standard for the field. The resultant models, shown to be competitive with the best private alternatives, are released with a permisive license. Methods: Building on top of strong base models like Llama 3.1 and Qwen 2.5, Aloe Beta uses a custom dataset to enhance public data with synthetic Chain of Thought examples. The models undergo alignment with Direct Preference Optimization, emphasizing ethical and policy-aligned performance in the presence of jailbreaking attacks. Evaluation includes close-ended, open-ended, safety and human assessments, to maximize the reliability of results. Results: Recommendations are made across the entire pipeline, backed by the solid performance of the Aloe Family. These models deliver competitive performance across healthcare benchmarks and medical fields, and are often preferred by healthcare professionals. On bias and toxicity, the Aloe Beta models significantly improve safety, showing resilience to unseen jailbreaking attacks. For a responsible release, a detailed risk assessment specific to healthcare is attached to the Aloe Family models. Conclusion: The Aloe Beta models, and the recipe that leads to them, are a significant contribution to the open-source medical LLM field, offering top-of-the-line performance while maintaining high ethical requirements. This work sets a new standard for developing and reporting aligned LLMs in healthcare.