Daily Papers

Machine learning approaches often require training and evaluation datasets with a clear separation between positive and negative examples. This risks simplifying and even obscuring the inherent subjectivity present in many tasks. Preserving such variance in content and diversity in datasets is often expensive and laborious. This is especially troubling when building safety datasets for conversational AI systems, as safety is both socially and culturally situated. To demonstrate this crucial aspect of conversational AI safety, and to facilitate in-depth model performance analyses, we introduce the DICES (Diversity In Conversational AI Evaluation for Safety) dataset that contains fine-grained demographic information about raters, high replication of ratings per item to ensure statistical power for analyses, and encodes rater votes as distributions across different demographics to allow for in-depth explorations of different aggregation strategies. In short, the DICES dataset enables the observation and measurement of variance, ambiguity, and diversity in the context of conversational AI safety. We also illustrate how the dataset offers a basis for establishing metrics to show how raters' ratings can intersects with demographic categories such as racial/ethnic groups, age groups, and genders. The goal of DICES is to be used as a shared resource and benchmark that respects diverse perspectives during safety evaluation of conversational AI systems.

In this work, we propose a novel Trajectory Score Matching (TSM) method that aims to solve the pseudo ground truth inconsistency problem caused by the accumulated error in Interval Score Matching (ISM) when using the Denoising Diffusion Implicit Models (DDIM) inversion process. Unlike ISM which adopts the inversion process of DDIM to calculate on a single path, our TSM method leverages the inversion process of DDIM to generate two paths from the same starting point for calculation. Since both paths start from the same starting point, TSM can reduce the accumulated error compared to ISM, thus alleviating the problem of pseudo ground truth inconsistency. TSM enhances the stability and consistency of the model's generated paths during the distillation process. We demonstrate this experimentally and further show that ISM is a special case of TSM. Furthermore, to optimize the current multi-stage optimization process from high-resolution text to 3D generation, we adopt Stable Diffusion XL for guidance. In response to the issues of abnormal replication and splitting caused by unstable gradients during the 3D Gaussian splatting process when using Stable Diffusion XL, we propose a pixel-by-pixel gradient clipping method. Extensive experiments show that our model significantly surpasses the state-of-the-art models in terms of visual quality and performance. Code: https://github.com/xingy038/Dreamer-XL.

Visual diffusion models have revolutionized the field of creative AI, producing high-quality and diverse content. However, they inevitably memorize training images or videos, subsequently replicating their concepts, content, or styles during inference. This phenomenon raises significant concerns about privacy, security, and copyright within generated outputs. In this survey, we provide the first comprehensive review of replication in visual diffusion models, marking a novel contribution to the field by systematically categorizing the existing studies into unveiling, understanding, and mitigating this phenomenon. Specifically, unveiling mainly refers to the methods used to detect replication instances. Understanding involves analyzing the underlying mechanisms and factors that contribute to this phenomenon. Mitigation focuses on developing strategies to reduce or eliminate replication. Beyond these aspects, we also review papers focusing on its real-world influence. For instance, in the context of healthcare, replication is critically worrying due to privacy concerns related to patient data. Finally, the paper concludes with a discussion of the ongoing challenges, such as the difficulty in detecting and benchmarking replication, and outlines future directions including the development of more robust mitigation techniques. By synthesizing insights from diverse studies, this paper aims to equip researchers and practitioners with a deeper understanding at the intersection between AI technology and social good. We release this project at https://github.com/WangWenhao0716/Awesome-Diffusion-Replication.

Broader access to high-quality movement analysis could greatly benefit movement science and rehabilitation, such as allowing more detailed characterization of movement impairments and responses to interventions, or even enabling early detection of new neurological conditions or fall risk. While emerging technologies are making it easier to capture kinematics with biomechanical models, or how joint angles change over time, inferring the underlying physics that give rise to these movements, including ground reaction forces, joint torques, or even muscle activations, is still challenging. Here we explore whether imitation learning applied to a biomechanical model from a large dataset of movements from able-bodied and impaired individuals can learn to compute these inverse dynamics. Although imitation learning in human pose estimation has seen great interest in recent years, our work differences in several ways: we focus on using an accurate biomechanical model instead of models adopted for computer vision, we test it on a dataset that contains participants with impaired movements, we reported detailed tracking metrics relevant for the clinical measurement of movement including joint angles and ground contact events, and finally we apply imitation learning to a muscle-driven neuromusculoskeletal model. We show that our imitation learning policy, KinTwin, can accurately replicate the kinematics of a wide range of movements, including those with assistive devices or therapist assistance, and that it can infer clinically meaningful differences in joint torques and muscle activations. Our work demonstrates the potential for using imitation learning to enable high-quality movement analysis in clinical practice.

Cutting-edge diffusion models produce images with high quality and customizability, enabling them to be used for commercial art and graphic design purposes. But do diffusion models create unique works of art, or are they replicating content directly from their training sets? In this work, we study image retrieval frameworks that enable us to compare generated images with training samples and detect when content has been replicated. Applying our frameworks to diffusion models trained on multiple datasets including Oxford flowers, Celeb-A, ImageNet, and LAION, we discuss how factors such as training set size impact rates of content replication. We also identify cases where diffusion models, including the popular Stable Diffusion model, blatantly copy from their training data.

The multi-step, iterative image editing capabilities of multi-modal agentic systems have transformed digital content creation. Although latest image editing models faithfully follow instructions and generate high-quality images in single-turn edits, we identify a critical weakness in multi-turn editing, which is the iterative degradation of image quality. As images are repeatedly edited, minor artifacts accumulate, rapidly leading to a severe accumulation of visible noise and a failure to follow simple editing instructions. To systematically study these failures, we introduce Banana100, a comprehensive dataset of 28,000 degraded images generated through 100 iterative editing steps, including diverse textures and image content. Alarmingly, image quality evaluators fail to detect the degradation. Among 21 popular no-reference image quality assessment (NR-IQA) metrics, none of them consistently assign lower scores to heavily degraded images than to clean ones. The dual failures of generators and evaluators may threaten the stability of future model training and the safety of deployed agentic systems, if the low-quality synthetic data generated by multi-turn edits escape quality filters. We release the full code and data to facilitate the development of more robust models, helping to mitigate the fragility of multi-modal agentic systems.

We introduce Wan-Animate, a unified framework for character animation and replacement. Given a character image and a reference video, Wan-Animate can animate the character by precisely replicating the expressions and movements of the character in the video to generate high-fidelity character videos. Alternatively, it can integrate the animated character into the reference video to replace the original character, replicating the scene's lighting and color tone to achieve seamless environmental integration. Wan-Animate is built upon the Wan model. To adapt it for character animation tasks, we employ a modified input paradigm to differentiate between reference conditions and regions for generation. This design unifies multiple tasks into a common symbolic representation. We use spatially-aligned skeleton signals to replicate body motion and implicit facial features extracted from source images to reenact expressions, enabling the generation of character videos with high controllability and expressiveness. Furthermore, to enhance environmental integration during character replacement, we develop an auxiliary Relighting LoRA. This module preserves the character's appearance consistency while applying the appropriate environmental lighting and color tone. Experimental results demonstrate that Wan-Animate achieves state-of-the-art performance. We are committed to open-sourcing the model weights and its source code.

A facial morph is an image created by combining two face images pertaining to two distinct identities. Face demorphing inverts the process and tries to recover the original images constituting a facial morph. While morph attack detection (MAD) techniques can be used to flag morph images, they do not divulge any visual information about the faces used to create them. Demorphing helps address this problem. Existing demorphing techniques are either very restrictive (assume identities during testing) or produce feeble outputs (both outputs look very similar). In this paper, we overcome these issues by proposing dc-GAN, a novel GAN-based demorphing method conditioned on the morph images. Our method overcomes morph-replication and produces high quality reconstructions of the bonafide images used to create the morphs. Moreover, our method is highly generalizable across demorphing paradigms (differential/reference-free). We conduct experiments on AMSL, FRLL-Morphs and MorDiff datasets to showcase the efficacy of our method.

Large Language Model (LLM) serving systems remain fundamentally fragile, where frequent hardware faults in hyperscale clusters trigger disproportionate service outages in the software stack. Current recovery mechanisms are prohibitively slow, often requiring up to 10 minutes to reinitialize resources and reload massive model weights. We introduce KevlarFlow, a fault tolerant serving architecture designed to bridge the gap between hardware unreliability and service availability. KevlarFlow leverages 1) decoupled model parallelism initialization, 2) dynamic traffic rerouting, and 3) background KV cache replication to maintain high throughput during partial failures. Our evaluation demonstrates that KevlarFlow reduces mean-time-to-recovery (MTTR) by 20x and, under failure conditions, improves average latency by 3.1x, 99th percentile (p99) latency by 2.8x, average time-to-first-token (TTFT) by 378.9x, and p99 TTFT by 574.6x with negligible runtime overhead in comparison to state-of-the-art LLM serving systems.

Diffusion models have significant advantages in the field of real-world video super-resolution and have demonstrated strong performance in past research. In recent diffusion-based video super-resolution (VSR) models, the number of sampling steps has been reduced to just one, yet there remains significant room for further optimization in inference efficiency. In this paper, we propose FastVSR, which achieves substantial reductions in computational cost by implementing a high compression VAE (spatial compression ratio of 16, denoted as f16). We design the structure of the f16 VAE and introduce a stable training framework. We employ pixel shuffle and channel replication to achieve additional upsampling. Furthermore, we propose a lower-bound-guided training strategy, which introduces a simpler training objective as a lower bound for the VAE's performance. It makes the training process more stable and easier to converge. Experimental results show that FastVSR achieves speedups of 111.9 times compared to multi-step models and 3.92 times compared to existing one-step models. We will release code and models at https://github.com/JianzeLi-114/FastVSR.

Diffusion models have emerged as frontrunners in text-to-image generation for their impressive capabilities. Nonetheless, their fixed image resolution during training often leads to challenges in high-resolution image generation, such as semantic inaccuracies and object replication. This paper introduces MegaFusion, a novel approach that extends existing diffusion-based text-to-image generation models towards efficient higher-resolution generation without additional fine-tuning or extra adaptation. Specifically, we employ an innovative truncate and relay strategy to bridge the denoising processes across different resolutions, allowing for high-resolution image generation in a coarse-to-fine manner. Moreover, by integrating dilated convolutions and noise re-scheduling, we further adapt the model's priors for higher resolution. The versatility and efficacy of MegaFusion make it universally applicable to both latent-space and pixel-space diffusion models, along with other derivative models. Extensive experiments confirm that MegaFusion significantly boosts the capability of existing models to produce images of megapixels and various aspect ratios, while only requiring about 40% of the original computational cost.

HomeRobot (noun): An affordable compliant robot that navigates homes and manipulates a wide range of objects in order to complete everyday tasks. Open-Vocabulary Mobile Manipulation (OVMM) is the problem of picking any object in any unseen environment, and placing it in a commanded location. This is a foundational challenge for robots to be useful assistants in human environments, because it involves tackling sub-problems from across robotics: perception, language understanding, navigation, and manipulation are all essential to OVMM. In addition, integration of the solutions to these sub-problems poses its own substantial challenges. To drive research in this area, we introduce the HomeRobot OVMM benchmark, where an agent navigates household environments to grasp novel objects and place them on target receptacles. HomeRobot has two components: a simulation component, which uses a large and diverse curated object set in new, high-quality multi-room home environments; and a real-world component, providing a software stack for the low-cost Hello Robot Stretch to encourage replication of real-world experiments across labs. We implement both reinforcement learning and heuristic (model-based) baselines and show evidence of sim-to-real transfer. Our baselines achieve a 20% success rate in the real world; our experiments identify ways future research work improve performance. See videos on our website: https://ovmm.github.io/.

Corruption studies, the primary tool for evaluating chain-of-thought (CoT) faithfulness, identify which chain positions are "computationally important" by measuring accuracy when steps are replaced with errors. We identify a systematic confound: for chains with explicit terminal answer statements, the dominant format in standard benchmarks, corruption studies detect where the answer text appears, not where computation occurs. A within-dataset format ablation provides the key evidence: on standard GSM8K chains ending with "the answer is X," removing only the answer statement, preserving all reasoning, collapses suffix sensitivity ~19x at 3B (N=300, p=0.022). Conflicting-answer experiments quantify the causal mechanism: at 7B, CC accuracy drops to near-zero (<=0.02) across five architecture families; the followed-wrong rate spans 0.63-1.00 at 3B-7B and attenuates at larger scales (0.300 at Phi-4-14B, ~0.01 at 32B). A within-stable 7B replication (9.3x attenuation, N=76, p=7.8e-3; Qwen3-8B N=299, p=0.004) provides converging evidence, and the pattern replicates on MATH (DeepSeek-R1-7B: 10.9x suffix-survival recovery). On chains without answer suffixes the same protocol identifies the prefix as load-bearing (Delta=-0.77, p<10^-12). Generation-time probes confirm a dissociation: the answer is not early-determined during generation (early commitment <5%), yet at consumption time model outputs systematically follow the explicit answer text. The format-determination effect persists through 14B (8.5x ratio, p=0.001) and converges toward zero at 32B. We propose a three-prerequisite protocol (question-only control, format characterization, all-position sweep) as a minimum standard for corruption-based faithfulness studies.

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/.

Reproducibility is central to research credibility, yet large-scale reanalysis of empricial data remains costly because replication packages vary widely in structure, software environment, and documentation. We develop and evaluate an agentic AI workflow that addresses this execution bottleneck while preserving scientific rigor. The system separates scientific reasoning from computational execution: researchers design fixed diagnostic templates, and the workflow automates the acquisition, harmonization, and execution of replication materials using pre-specified, version-controlled code. A structured knowledge layer records resolved failure patterns, enabling adaptation across heterogeneous studies while keeping each pipeline version transparent and stable. We evaluate this workflow on 92 instrumental variable (IV) studies, including 67 with manually verified reproducible 2SLS estimates and 25 newly published IV studies under identical criteria. For each paper, we analyze up to three two-stage least squares (2SLS) specifications, totaling 215. Across the 92 papers, the system achieves 87% end-to-end success overall. Conditional on accessible data and code, reproducibility is 100% at both the paper and specification levels. The framework substantially lowers the cost of executing established empirical protocols and can be adapted in empirical settings where analytic templates and norms of transparency are well established.

CNN-based generative modelling has evolved to produce synthetic images indistinguishable from real images in the RGB pixel space. Recent works have observed that CNN-generated images share a systematic shortcoming in replicating high frequency Fourier spectrum decay attributes. Furthermore, these works have successfully exploited this systematic shortcoming to detect CNN-generated images reporting up to 99% accuracy across multiple state-of-the-art GAN models. In this work, we investigate the validity of assertions claiming that CNN-generated images are unable to achieve high frequency spectral decay consistency. We meticulously construct a counterexample space of high frequency spectral decay consistent CNN-generated images emerging from our handcrafted experiments using DCGAN, LSGAN, WGAN-GP and StarGAN, where we empirically show that this frequency discrepancy can be avoided by a minor architecture change in the last upsampling operation. We subsequently use images from this counterexample space to successfully bypass the recently proposed forensics detector which leverages on high frequency Fourier spectrum decay attributes for CNN-generated image detection. Through this study, we show that high frequency Fourier spectrum decay discrepancies are not inherent characteristics for existing CNN-based generative models--contrary to the belief of some existing work--, and such features are not robust to perform synthetic image detection. Our results prompt re-thinking of using high frequency Fourier spectrum decay attributes for CNN-generated image detection. Code and models are available at https://keshik6.github.io/Fourier-Discrepancies-CNN-Detection/

The literature has witnessed an emerging interest in AI agents for automated assessment of scientific papers. Existing benchmarks focus primarily on the computational aspect of this task, testing agents' ability to reproduce or replicate research outcomes when having access to the code and data. This setting, while foundational, (1) fails to capture the inconsistent availability of new data for replication as opposed to reproduction, and (2) lacks ground-truth diversity by focusing only on reproducible papers, thereby failing to evaluate an agent's ability to identify non-replicable research. Furthermore, most benchmarks only evaluate outcomes rather than the replication process. In response, we introduce ReplicatorBench, an end-to-end benchmark, including human-verified replicable and non-replicable research claims in social and behavioral sciences for evaluating AI agents in research replication across three stages: (1) extraction and retrieval of replication data; (2) design and execution of computational experiments; and (3) interpretation of results, allowing a test of AI agents' capability to mimic the activities of human replicators in real world. To set a baseline of AI agents' capability, we develop ReplicatorAgent, an agentic framework equipped with necessary tools, like web search and iterative interaction with sandboxed environments, to accomplish tasks in ReplicatorBench. We evaluate ReplicatorAgent across four underlying large language models (LLMs), as well as different design choices of programming language and levels of code access. Our findings reveal that while current LLM agents are capable of effectively designing and executing computational experiments, they struggle with retrieving resources, such as new data, necessary to replicate a claim. All code and data are publicly available at https://github.com/CenterForOpenScience/llm-benchmarking.

Scientific machine learning papers typically make computational claims, e.g., that the relative mean square error is less than 5% or that the 95% predictive credible interval covers the test data. A coding agent can be prompted to replicate those claims from paper materials alone, but the prompt does not by itself reliably preserve progress or check whether generated evidence supports the paper's claims. We introduce Paper-replication, a workflow that makes each selected paper claim a target with recorded evidence, and implement it as a coding-agent skill. The workflow makes the agent record those targets, reconstruct the paper's method, run computational experiments, link generated outputs to provenance and comparisons with the paper's claims, record where matched evidence appears in the replication report, and pass validation checks before completion. We evaluate Paper-replication on twelve independent runs across four scientific machine learning papers. All twelve workspaces pass the completion gate, and all 158 recorded targets are matched with report coverage. Even in this completed workspace state, repeated runs differ in how papers are divided into targets, in numerical fidelity to the source papers, in elapsed replication time, in the number of intermediate executions replaced before final evidence is accepted, and in the rules used to accept evidence. Paper-replication makes completion depend on workspace evidence and validation checks rather than on the agent's final message.

The widespread deployment of Large Language Model (LLM) agents across real-world applications has unlocked tremendous potential, while raising some safety concerns. Among these concerns, the self-replication risk of LLM agents driven by objective misalignment (just like Agent Smith in the movie The Matrix) has drawn growing attention. Previous studies mainly examine whether LLM agents can self-replicate when directly instructed, potentially overlooking the risk of spontaneous replication driven by real-world settings (e.g., ensuring survival against termination threats). In this paper, we present a comprehensive evaluation framework for quantifying self-replication risks. Our framework establishes authentic production environments and realistic tasks (e.g., dynamic load balancing) to enable scenario-driven assessment of agent behaviors. Designing tasks that might induce misalignment between users' and agents' objectives makes it possible to decouple replication success from risk and capture self-replication risks arising from these misalignment settings. We further introduce Overuse Rate (OR) and Aggregate Overuse Count (AOC) metrics, which precisely capture the frequency and severity of uncontrolled replication. In our evaluation of 21 state-of-the-art open-source and proprietary models, we observe that over 50\% of LLM agents display a pronounced tendency toward uncontrolled self-replication, reaching an overall Risk Score (Phi_R) above a safety threshold of 0.5 when subjected to operational pressures. Our results underscore the urgent need for scenario-driven risk assessment and robust safeguards in the practical deployment of LLM agents.

While traditional evolutionary algorithms hard-code reproduction, self-replication can emerge spontaneously within digital ``primordial soups''. This paper investigates the co-evolution of this emergent self-replication alongside problem-solving capabilities. We initialize a population of random 32-byte Z80 assembly programs, requiring self-replication to arise purely through random assembly-level mutations and pairwise program interactions. To link these behaviors, we introduce a task-based validation step: correctly evaluating a polynomial raises a program's interaction probability above a baseline rate. Our experiments yield four primary findings. First, self-replication and mathematical problem-solving successfully co-evolve from initial randomness. Second, the pressure to compute accelerates the emergence of compact, robust reproductive architectures that preserve memory for task execution. Third, applying metabolic constraints increases the likelihood that programs evolve conditional halting, terminating early during validation while bypassing the halt during interaction to execute block-copy replication. Finally, when programs are partitioned into spatial task niches, spontaneous self-replication generates an emergent learning curriculum, utilizing simple solutions as stepping stones toward complex polynomials. Altogether, these results demonstrate an interactive feedback loop: environmental task demands actively shape the physical architecture of self-replication, while spontaneous replication alters the evolutionary trajectory of functional problem-solving.

Frontier AI agents show increasing promise as scientific research assistants, and may eventually be useful for extended, open-ended research workflows. However, in order to use agents for novel research, we must first assess the underlying faithfulness and correctness of their work. To evaluate agents as research assistants, we introduce ReplicationBench, an evaluation framework that tests whether agents can replicate entire research papers drawn from the astrophysics literature. Astrophysics, where research relies heavily on archival data and computational study while requiring little real-world experimentation, is a particularly useful testbed for AI agents in scientific research. We split each paper into tasks which require agents to replicate the paper's core contributions, including the experimental setup, derivations, data analysis, and codebase. Each task is co-developed with the original paper authors and targets a key scientific result, enabling objective evaluation of both faithfulness (adherence to original methods) and correctness (technical accuracy of results). ReplicationBench is extremely challenging for current frontier language models: even the best-performing language models score under 20%. We analyze ReplicationBench trajectories in collaboration with domain experts and find a rich, diverse set of failure modes for agents in scientific research. ReplicationBench establishes the first benchmark of paper-scale, expert-validated astrophysics research tasks, reveals insights about agent performance generalizable to other domains of data-driven science, and provides a scalable framework for measuring AI agents' reliability in scientific research.

State-of-the-art language models (LMs) are notoriously susceptible to generating hallucinated information. Such inaccurate outputs not only undermine the reliability of these models but also limit their use and raise serious concerns about misinformation and propaganda. In this work, we focus on hallucinated book and article references and present them as the "model organism" of language model hallucination research, due to their frequent and easy-to-discern nature. We posit that if a language model cites a particular reference in its output, then it should ideally possess sufficient information about its authors and content, among other relevant details. Using this basic insight, we illustrate that one can identify hallucinated references without ever consulting any external resources, by asking a set of direct or indirect queries to the language model about the references. These queries can be considered as "consistency checks." Our findings highlight that while LMs, including GPT-4, often produce inconsistent author lists for hallucinated references, they also often accurately recall the authors of real references. In this sense, the LM can be said to "know" when it is hallucinating references. Furthermore, these findings show how hallucinated references can be dissected to shed light on their nature. Replication code and results can be found at https://github.com/microsoft/hallucinated-references.

Concerns about reproducibility in artificial intelligence (AI) have emerged, as researchers have reported unsuccessful attempts to directly reproduce published findings in the field. Replicability, the ability to affirm a finding using the same procedures on new data, has not been well studied. In this paper, we examine both reproducibility and replicability of a corpus of 16 papers on table structure recognition (TSR), an AI task aimed at identifying cell locations of tables in digital documents. We attempt to reproduce published results using codes and datasets provided by the original authors. We then examine replicability using a dataset similar to the original as well as a new dataset, GenTSR, consisting of 386 annotated tables extracted from scientific papers. Out of 16 papers studied, we reproduce results consistent with the original in only four. Two of the four papers are identified as replicable using the similar dataset under certain IoU values. No paper is identified as replicable using the new dataset. We offer observations on the causes of irreproducibility and irreplicability. All code and data are available on Codeocean at https://codeocean.com/capsule/6680116/tree.

Self-replication is a key aspect of biological life that has been largely overlooked in Artificial Intelligence systems. Here we describe how to build and train self-replicating neural networks. The network replicates itself by learning to output its own weights. The network is designed using a loss function that can be optimized with either gradient-based or non-gradient-based methods. We also describe a method we call regeneration to train the network without explicit optimization, by injecting the network with predictions of its own parameters. The best solution for a self-replicating network was found by alternating between regeneration and optimization steps. Finally, we describe a design for a self-replicating neural network that can solve an auxiliary task such as MNIST image classification. We observe that there is a trade-off between the network's ability to classify images and its ability to replicate, but training is biased towards increasing its specialization at image classification at the expense of replication. This is analogous to the trade-off between reproduction and other tasks observed in nature. We suggest that a self-replication mechanism for artificial intelligence is useful because it introduces the possibility of continual improvement through natural selection.

AI tools are accelerating scientific publication while the systems that review it struggle to keep up, and independent verification of published research has become both harder and more important. As manual replication is slow and expensive, a growing line of work uses coding agents to automate parts of the process. Existing efforts are largely packaged as benchmarks with companion agents that only run inside the benchmark's own pipeline, and no general-purpose replication tool exists. We present VERITAS, a domain-agnostic replication framework built around CLI coding agents. Given a paper, a code repository, or both, VERITAS extracts the paper's claims, runs the methodology while resolving issues as they arise, and judges each claim against the evidence from experiment runs. The pipeline returns an importance-weighted Replication Score, a severity-rated log of every fix applied, and the patched codebase. We evaluate VERITAS on CORE-Bench and ReplicationBench, 65 papers spanning computer science, social science, medicine, and astrophysics. Against two strong Claude Code baselines on the same model and host environment, VERITAS achieves state-of-the-art performance and leads on every metric on both benchmarks.

Equivariance theory predicts that an architectural symmetry prior reduces sample complexity by a factor of |G|; this is widely cited but rarely measured as a scaling law with controls that separate the prior from its confounds. On a controlled C_n-symmetric task, we report three findings. First, a wrong-group control with identical orbit size and matched compute is worse than no constraint (joint pairwise CI [+0.79, +3.26] excludes zero, robust across estimators); misaligned constraint is actively harmful, not merely unhelpful. Second, an augmentation baseline equipped with test-time orbit averaging matches the equivariant model exactly -- bit-identical per-epoch validation curves across matched cells -- so the architecture-vs-augmentation gap is conditional on asymmetric test-time computation, not unconditional. Third, the relative exchange rate beta_diff = 1.28 is consistent in sign and order of magnitude with the theoretical 1.0 (single-level CI [+0.92, +2.05]); the more conservative two-level bootstrap (seeds x group sizes) widens this to [-0.63, +1.72], including zero, and a finer-N replication on a sqrt(2)-spaced grid is inconclusive (point estimate -0.82). The methodological contributions -- the relative-rate estimator that cancels the shared-difficulty confound, the wrong-group control, and a pre-specified failure taxonomy -- transfer to any inductive bias whose strength can be parameterised. Honest scoping: the primary estimator beta_diff was adopted post-hoc after the initial analysis revealed a positive-slope identifiability problem; the design was never externally pre-registered; and the headline number rests on an OLS slope over seven group sizes on a coarse N grid. This is an exploratory study, not a confirmatory measurement; the wrong-group result is the cleanest finding and the one we report with the most confidence. A registered replication on fresh seeds is future work.

Benchmarks shape scientific conclusions about model capabilities and steer model development. This creates a feedback loop: stronger benchmarks drive better models, and better models demand more discriminative benchmarks. Ensuring benchmark reliability is therefore essential for trustworthy evaluation and meaningful progress. In this work, we study benchmark reliability from a distributional perspective and introduce benchmark harmony, which measures how uniformly a model's performance is distributed across the subdomains of a benchmark. We posit that high harmony is a desirable benchmark property, indicating that the aggregate metric reflects uniform competence across subdomains. Across 19 multiple-choice benchmarks and five model families, we map each benchmark onto a mean-variance plane of harmony computed across models, where high mean and low variance signal more reliable evaluation. Our analysis shows that less harmonious benchmarks can give misleading results, since overall accuracy may be disproportionately influenced by specific subdomains. For instance, ARC-Easy is overwhelmed by questions on Biological Concepts, overshadowing other critical subdomains such as Geography, Physics, Chemistry, and Environmental Science. By recommending that harmony should be reported alongside accuracy, we reframe evaluation from simple performance averages to a more robust, distributionally reliable measurement of performance.

Pre-training data mixtures are commonly tuned by running small-scale experiments and extrapolating to the target training budget. When high-quality data is scarce and must be repeated, this extrapolation frequently fails, but the source of the failure has not been isolated. We show that a primary culprit is a repetition mismatch: because high-quality datasets are small, their repetition rate changes as the training budget grows, shifting the optimal mixture in ways that small-scale proxy experiments do not anticipate. A subsampling procedure that matches the target repetition rate controls for this effect. In a two-source setting combining limited high-quality data with web crawl, a single repetition-controlled experiment using only 1/16 of the target tokens recovers a mixture within 0.05 of the optimum for a 757M parameter model, compared to an error of 0.75 without repetition control. Achieving comparable accuracy without repetition control requires three to four horizons, consuming 44 to 94% of the target token budget. With three data sources, the larger mixture space requires more than a single experiment to constrain, but the approach remains effective: at the 757M scale, just two repetition-controlled horizons recover the optimal mixture, outperforming baselines that instead require the full two-source experiments to construct. Our results reveal that repetition dynamics, not scale alone, shape whether small-scale mixture experiments generalize. More broadly, they suggest that data repetition deserves treatment as a first-class variable in mixture optimization, rather than an inconvenient side effect of limited data.

Text-to-image diffusion models (DMs) have achieved remarkable success in image generation. However, concerns about data privacy and intellectual property remain due to their potential to inadvertently memorize and replicate training data. Recent mitigation efforts have focused on identifying and pruning weights responsible for triggering replication, based on the assumption that memorization can be localized. Our research assesses the robustness of these pruning-based approaches. We demonstrate that even after pruning, minor adjustments to text embeddings of input prompts are sufficient to re-trigger data replication, highlighting the fragility of these defenses. Furthermore, we challenge the fundamental assumption of memorization locality, by showing that replication can be triggered from diverse locations within the text embedding space, and follows different paths in the model. Our findings indicate that existing mitigation strategies are insufficient and underscore the need for methods that truly remove memorized content, rather than attempting to suppress its retrieval. As a first step in this direction, we introduce a novel adversarial fine-tuning method that iteratively searches for replication triggers and updates the model to increase robustness. Through our research, we provide fresh insights into the nature of memorization in text-to-image DMs and a foundation for building more trustworthy and compliant generative AI.

Higher Degree by Research (HDR) candidates increasingly depend on cloud-provisioned virtual machines and local GPU hardware for their computational experiments, yet a persistent and under-addressed gap exists between having compute resources and using them productively. Cloud and infrastructure teams can provision virtual machines, but the path from a raw VM to a reproducible, GPU-ready research environment remains a significant barrier for researchers who are domain experts, not systems engineers. We identify this gap as a missing adapter layer between cloud provisioning and interactive research work. We present a lightweight, open-source solution built on k3s and Coder that implements this adapter layer and is already in active use in our research workspace environment. Our CI/CD pipeline connects GitHub directly to the local cluster, deploying research projects in under five minutes. We define a concrete metrics framework for evaluating this layer -- covering deployment latency, environment reproducibility, onboarding friction, and resource utilisation -- and establish baselines against which improvements can be measured.

Images produced by diffusion models are increasingly popular in digital artwork and visual marketing. However, such generated images might replicate content from existing ones and pose the challenge of content originality. Existing Image Copy Detection (ICD) models, though accurate in detecting hand-crafted replicas, overlook the challenge from diffusion models. This motivates us to introduce ICDiff, the first ICD specialized for diffusion models. To this end, we construct a Diffusion-Replication (D-Rep) dataset and correspondingly propose a novel deep embedding method. D-Rep uses a state-of-the-art diffusion model (Stable Diffusion V1.5) to generate 40, 000 image-replica pairs, which are manually annotated into 6 replication levels ranging from 0 (no replication) to 5 (total replication). Our method, PDF-Embedding, transforms the replication level of each image-replica pair into a probability density function (PDF) as the supervision signal. The intuition is that the probability of neighboring replication levels should be continuous and smooth. Experimental results show that PDF-Embedding surpasses protocol-driven methods and non-PDF choices on the D-Rep test set. Moreover, by utilizing PDF-Embedding, we find that the replication ratios of well-known diffusion models against an open-source gallery range from 10% to 20%.

We present a detailed replication study of the BASS framework, an abstractive summarization system based on the notion of Unified Semantic Graphs. Our investigation includes challenges in replicating key components and an ablation study to systematically isolate error sources rooted in replicating novel components. Our findings reveal discrepancies in performance compared to the original work. We highlight the significance of paying careful attention even to reasonably omitted details for replicating advanced frameworks like BASS, and emphasize key practices for writing replicable papers.

Recent large language models have been trained on vast datasets, but also often on repeated data, either intentionally for the purpose of upweighting higher quality data, or unintentionally because data deduplication is not perfect and the model is exposed to repeated data at the sentence, paragraph, or document level. Some works have reported substantial negative performance effects of this repeated data. In this paper we attempt to study repeated data systematically and to understand its effects mechanistically. To do this, we train a family of models where most of the data is unique but a small fraction of it is repeated many times. We find a strong double descent phenomenon, in which repeated data can lead test loss to increase midway through training. A predictable range of repetition frequency leads to surprisingly severe degradation in performance. For instance, performance of an 800M parameter model can be degraded to that of a 2x smaller model (400M params) by repeating 0.1% of the data 100 times, despite the other 90% of the training tokens remaining unique. We suspect there is a range in the middle where the data can be memorized and doing so consumes a large fraction of the model's capacity, and this may be where the peak of degradation occurs. Finally, we connect these observations to recent mechanistic interpretability work - attempting to reverse engineer the detailed computations performed by the model - by showing that data repetition disproportionately damages copying and internal structures associated with generalization, such as induction heads, providing a possible mechanism for the shift from generalization to memorization. Taken together, these results provide a hypothesis for why repeating a relatively small fraction of data in large language models could lead to disproportionately large harms to performance.

Peer review is a critical component of scientific progress in the fields like AI, but the rapid increase in submission volume has strained the reviewing system, which inevitably leads to reviewer shortages and declines review quality. Besides the growing research popularity, another key factor in this overload is the repeated resubmission of substandard manuscripts, largely due to the lack of effective tools for authors to self-evaluate their work before submission. Large Language Models (LLMs) show great promise in assisting both authors and reviewers, and their performance is fundamentally limited by the quality of the peer review data. However, existing peer review datasets face three major limitations: (1) limited data diversity, (2) inconsistent and low-quality data due to the use of revised rather than initial submissions, and (3) insufficient support for tasks involving rebuttal and reviewer-author interactions. To address these challenges, we introduce the largest consistency-ensured peer review and rebuttal dataset named Re^2, which comprises 19,926 initial submissions, 70,668 review comments, and 53,818 rebuttals from 24 conferences and 21 workshops on OpenReview. Moreover, the rebuttal and discussion stage is framed as a multi-turn conversation paradigm to support both traditional static review tasks and dynamic interactive LLM assistants, providing more practical guidance for authors to refine their manuscripts and helping alleviate the growing review burden. Our data and code are available in https://anonymous.4open.science/r/ReviewBench_anon/.

The adoption of Large Language Models (LLMs) in scientific writing promises efficiency but risks introducing informational entropy. While "hallucinated papers" are a known artifact, the systematic degradation of valid citation chains remains unquantified. We conducted a forensic audit of 50 recent survey papers in Artificial Intelligence (N=5,514 citations) published between September 2024 and January 2026. We utilized a hybrid verification pipeline combining DOI resolution, Crossref metadata analysis, Semantic Scholar queries, and fuzzy text matching to distinguish between formatting errors ("Sloppiness") and verifiable non-existence ("Phantoms). We detect a persistent 17.0% Phantom Rate -- citations that cannot be resolved to any digital object despite aggressive forensic recovery. Diagnostic categorization reveals three distinct failure modes: pure hallucinations (5.1%), hallucinated identifiers with valid titles (16.4%), and parsing-induced matching failures (78.5%). Longitudinal analysis reveals a flat trend (+0.07 pp/month), suggesting that high-entropy citation practices have stabilized as an endemic feature of the field. The scientific citation graph in AI survey literature exhibits "link rot" at scale. This suggests a mechanism where AI tools act as "lazy research assistants," retrieving correct titles but hallucinating metadata, thereby severing the digital chain of custody required for reproducible science.

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.

Nucleotide sequences constitute the fundamental genetic basis of biological systems, rendering viral genomic analysis critical for biomedical advancement. Despite progress in biological foundation models, specifically nucleotide foundation models (NFMs), the field lacks a unified standard for viral genomics to facilitate community development and enforce biosecurity constraints. To address this, we introduce ViroBench, the first comprehensive and large-scale benchmark specifically designed for NFMs in viral settings. ViroBench evaluates models across two critical dimensions: biological understanding and latent biosecurity risk, covering 18 diverse scenarios within 4 task types. Extensive evaluation of 66 NFMs across diverse architectures yields three critical conclusions. Firstly, NFMs exhibit a performance degradation in biological understanding under phylogenetic and temporal shifts, indicating weak extrapolation capabilities. Secondly, generation tasks reveal a decoupling between statistical likelihood and biological functional validity, posing latent biosecurity risks. Thirdly, controlled ablation studies reveal that taxonomic diversity in pretraining data outweighs parameter scale. Specifically, a lightweight baseline trained on diverse data achieves a 67.5% performance gain over its original model. Overall, ViroBench provides interpretable, diagnostic evaluations and a reproducible measurement framework for future research on viral nucleotide foundation models. The datasets and code are publicly available at https://github.com/QIANJINYDX/ViroBench.

Assessing the capabilities and risks of frontier AI systems is a critical area of research, and recent work has shown that repeated sampling from models can dramatically increase both. For instance, repeated sampling has been shown to increase their capabilities, such as solving difficult math and coding problems, but it has also been shown to increase their potential for harm, such as being jailbroken. Such results raise a crucial question for both capability and safety forecasting: how can one accurately predict a model's behavior when scaled to a massive number of attempts, given a vastly smaller sampling budget? This question is directly relevant to model providers, who serve hundreds of millions of users daily, and to governmental regulators, who seek to prevent harms. To answer this questions, we make three contributions. First, we find that standard methods for fitting these laws suffer from statistical shortcomings that hinder predictive accuracy, especially in data-limited scenarios. Second, we remedy these shortcomings by introducing a robust estimation framework, which uses a beta-binomial distribution to generate more accurate predictions from limited data. Third, we propose a dynamic sampling strategy that allocates a greater budget to harder problems. Combined, these innovations enable more reliable prediction of rare risks and capabilities at a fraction of the computational cost.

Hyperparameter optimization (HPO) is a core problem for the machine learning community and remains largely unsolved due to the significant computational resources required to evaluate hyperparameter configurations. As a result, a series of recent related works have focused on the direction of transfer learning for quickly fine-tuning hyperparameters on a dataset. Unfortunately, the community does not have a common large-scale benchmark for comparing HPO algorithms. Instead, the de facto practice consists of empirical protocols on arbitrary small-scale meta-datasets that vary inconsistently across publications, making reproducibility a challenge. To resolve this major bottleneck and enable a fair and fast comparison of black-box HPO methods on a level playing field, we propose HPO-B, a new large-scale benchmark in the form of a collection of meta-datasets. Our benchmark is assembled and preprocessed from the OpenML repository and consists of 176 search spaces (algorithms) evaluated sparsely on 196 datasets with a total of 6.4 million hyperparameter evaluations. For ensuring reproducibility on our benchmark, we detail explicit experimental protocols, splits, and evaluation measures for comparing methods for both non-transfer, as well as, transfer learning HPO.

Training large neural networks with data-parallel stochastic gradient descent allocates N GPU replicas to compute effectively identical updates -- a practice that leaves the rich space of learning rate configurations entirely unexplored during training. We propose Hyperparameter-Divergent Ensemble Training (HDET), a method that repurposes these replicas for simultaneous learning rate exploration at negligible communication overhead. HDET operates in alternating phases: a fan-out stage in which replicas train independently under a structured, symmetric spread of learning rates, and a converge stage in which parameters are averaged across all replicas via AllReduce every T steps. Building on this ensemble substrate, we further propose an automatic learning rate (auto-LR) controller that treats the relative training loss across replicas as a performance signal, updating the shared base schedule toward higher-performing configurations via a momentum-based gradient-free meta-update. The combined method produces a self-adapting learning rate schedule that improves both optimization quality and generalization without additional hyperparameter sweeps or training budget. Crucially, the framework generalizes beyond learning rate: any scalar hyperparameter that does not alter model architecture -- such as dropout rate, attention scale temperature, or weight-decay coefficient -- can be explored across replicas using the same fan-out/converge protocol, with inter-replica loss differences serving as zero-order hypergradients that guide the search direction. HDET is implemented as a drop-in replacement for PyTorch's OneCycleLR scheduler, requiring no changes to model architecture, optimizer, or data pipeline.

We present a single-GPU (H100, bf16) evaluation of GPT-OSS-20B (Mixture-of-Experts; 20.9B total, approx. 3.61B active) against dense baselines Qwen3-32B and Yi-34B across multiple dimensions. We measure true time-to-first-token (TTFT), full-decode throughput (TPOT), end-to-end latency percentiles, peak VRAM with past key values (PKV) held, and energy via a consistent nvidia-smi-based sampler. At a 2048-token context with 64-token decode, GPT-OSS-20B delivers higher decode throughput and tokens per Joule than dense baselines Qwen3-32B and Yi-34B, while substantially reducing peak VRAM and energy per 1000 generated tokens; its TTFT is higher due to MoE routing overhead. With only 17.3% of parameters active (3.61B of 20.9B), GPT-OSS-20B provides about 31.8% higher decode throughput and 25.8% lower energy per 1000 generated tokens than Qwen3-32B at 2048/64, while using 31.7% less peak VRAM. Normalized by active parameters, GPT-OSS-20B shows markedly stronger per-active-parameter efficiency (APE), underscoring MoE's deployment advantages. We do not evaluate accuracy; this is a deployment-focused study. We release code and consolidated results to enable replication and extension.

Language models are running out of high-quality training data, and even aggressively deduplicated corpora retain some amount of repetition. Earlier controlled studies predated Chinchilla-style scaling laws and could only measure the cost of repetition indirectly. We revisit repetition in the Chinchilla era, using a fitted no-repetition scaling law to report Compute-Equivalent Gain and Compute-Equivalent Loss. We show that under this modernized paradigm, repetition damage is systematic in three ways. First, holding compute allocated to repeated data constant, eval loss peaks at an intermediate repeat count Rep; repeating a moderately sized subset a moderate number of times damages performance more than repeating a large subset a few times or a small subset many times. Second, the location of this peak is well-fit by a power law in model size; this scaling law reveals that the most damaging number of repeated data grows more quickly than compute. Finally, when repeated documents consume 10\% of the FLOPs budget in a controlled exact-document repetition setting, the compute-equivalent loss can be large: on FineWeb-Edu-Dedup, the most damaging repeat count for a Qwen3-style 344M-parameter model at OT=1 matches the loss of a no-repetition run using 67% of the FLOPs. We demonstrate that these phenomena are not language-model-specific, and can be analytically understood in a simple statistical model: a misspecified linear regression with verbatim duplicates reproduces the same qualitative loss peak, quantifying how such peaks can arise from a statistical tradeoff between memorization and generalization. Our findings add precision to the study of duplication in language models, allowing practitioners to quantify the wasted compute incurred by the presence and repeat structure of duplicates in pretraining corpora.

In order to improve reproducibility, deep reinforcement learning (RL) has been adopting better scientific practices such as standardized evaluation metrics and reporting. However, the process of hyperparameter optimization still varies widely across papers, which makes it challenging to compare RL algorithms fairly. In this paper, we show that hyperparameter choices in RL can significantly affect the agent's final performance and sample efficiency, and that the hyperparameter landscape can strongly depend on the tuning seed which may lead to overfitting. We therefore propose adopting established best practices from AutoML, such as the separation of tuning and testing seeds, as well as principled hyperparameter optimization (HPO) across a broad search space. We support this by comparing multiple state-of-the-art HPO tools on a range of RL algorithms and environments to their hand-tuned counterparts, demonstrating that HPO approaches often have higher performance and lower compute overhead. As a result of our findings, we recommend a set of best practices for the RL community, which should result in stronger empirical results with fewer computational costs, better reproducibility, and thus faster progress. In order to encourage the adoption of these practices, we provide plug-and-play implementations of the tuning algorithms used in this paper at https://github.com/facebookresearch/how-to-autorl.

Weird generalization is a phenomenon in which models fine-tuned on data from a narrow domain (e.g. insecure code) develop surprising traits that manifest even outside that domain (e.g. broad misalignment)-a phenomenon that prior work has highlighted as a critical safety concern. Here, we present an extended replication study of key weird generalization results across an expanded suite of models and datasets. We confirm that surprising (and dangerous) traits can emerge under certain circumstances, but we find that weird generalization is exceptionally brittle: it emerges only for specific models on specific datasets, and it vanishes under simple training-time, prompt-based interventions. We find that the most effective interventions provide prompt context that makes the generalized behavior the expected behavior. However, we show that even very generic interventions that do not anticipate specific generalized traits can still be effective in mitigating weird generalization's effects. Our findings thus help clarify the nature of the safety threat that weird generalization poses and point toward an easily implemented set of solutions.

Large language models have been widely adopted across different tasks, but their auto-regressive generation nature often leads to inefficient resource utilization during inference. While batching is commonly used to increase throughput, performance gains plateau beyond a certain batch size, especially with smaller models, a phenomenon that existing literature typically explains as a shift to the compute-bound regime. In this paper, through an in-depth GPU-level analysis, we reveal that large-batch inference remains memory-bound, with most GPU compute capabilities underutilized due to DRAM bandwidth saturation as the primary bottleneck. To address this, we propose a Batching Configuration Advisor (BCA) that optimizes memory allocation, reducing GPU memory requirements with minimal impact on throughput. The freed memory and underutilized GPU compute capabilities can then be leveraged by concurrent workloads. Specifically, we use model replication to improve serving throughput and GPU utilization. Our findings challenge conventional assumptions about LLM inference, offering new insights and practical strategies for improving resource utilization, particularly for smaller language models.

Context: Jupyter Notebook has emerged as a versatile tool that transforms how researchers, developers, and data scientists conduct and communicate their work. As the adoption of Jupyter notebooks continues to rise, so does the interest from the software engineering research community in improving the software engineering practices for Jupyter notebooks. Objective: The purpose of this study is to analyze trends, gaps, and methodologies used in software engineering research on Jupyter notebooks. Method: We selected 146 relevant publications from the DBLP Computer Science Bibliography up to the end of 2024, following established systematic literature review guidelines. We explored publication trends, categorized them based on software engineering topics, and reported findings based on those topics. Results: The most popular venues for publishing software engineering research on Jupyter notebooks are related to human-computer interaction instead of traditional software engineering venues. Researchers have addressed a wide range of software engineering topics on notebooks, such as code reuse, readability, and execution environment. Although reusability is one of the research topics for Jupyter notebooks, only 64 of the 146 studies can be reused based on their provided URLs. Additionally, most replication packages are not hosted on permanent repositories for long-term availability and adherence to open science principles. Conclusion: Solutions specific to notebooks for software engineering issues, including testing, refactoring, and documentation, are underexplored. Future research opportunities exist in automatic testing frameworks, refactoring clones between notebooks, and generating group documentation for coherent code cells.

Reproducibility is essential for scientific research. However, in computer vision, achieving consistent results is challenging due to various factors. One influential, yet often unrecognized, factor is CUDA-induced randomness. Despite CUDA's advantages for accelerating algorithm execution on GPUs, if not controlled, its behavior across multiple executions remains non-deterministic. While reproducibility issues in ML being researched, the implications of CUDA-induced randomness in application are yet to be understood. Our investigation focuses on this randomness across one standard benchmark dataset and two real-world datasets in an isolated environment. Our results show that CUDA-induced randomness can account for differences up to 4.77% in performance scores. We find that managing this variability for reproducibility may entail increased runtime or reduce performance, but that disadvantages are not as significant as reported in previous studies.

We introduce PaperBench, a benchmark evaluating the ability of AI agents to replicate state-of-the-art AI research. Agents must replicate 20 ICML 2024 Spotlight and Oral papers from scratch, including understanding paper contributions, developing a codebase, and successfully executing experiments. For objective evaluation, we develop rubrics that hierarchically decompose each replication task into smaller sub-tasks with clear grading criteria. In total, PaperBench contains 8,316 individually gradable tasks. Rubrics are co-developed with the author(s) of each ICML paper for accuracy and realism. To enable scalable evaluation, we also develop an LLM-based judge to automatically grade replication attempts against rubrics, and assess our judge's performance by creating a separate benchmark for judges. We evaluate several frontier models on PaperBench, finding that the best-performing tested agent, Claude 3.5 Sonnet (New) with open-source scaffolding, achieves an average replication score of 21.0\%. Finally, we recruit top ML PhDs to attempt a subset of PaperBench, finding that models do not yet outperform the human baseline. We https://github.com/openai/preparedness{open-source our code} to facilitate future research in understanding the AI engineering capabilities of AI agents.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

As computational work becomes more and more integral to many aspects of scientific research, computational reproducibility has become an issue of increasing importance to computer systems researchers and domain scientists alike. Though computational reproducibility seems more straight forward than replicating physical experiments, the complex and rapidly changing nature of computer environments makes being able to reproduce and extend such work a serious challenge. In this paper, I explore common reasons that code developed for one research project cannot be successfully executed or extended by subsequent researchers. I review current approaches to these issues, including virtual machines and workflow systems, and their limitations. I then examine how the popular emerging technology Docker combines several areas from systems research - such as operating system virtualization, cross-platform portability, modular re-usable elements, versioning, and a `DevOps' philosophy, to address these challenges. I illustrate this with several examples of Docker use with a focus on the R statistical environment.

Images generated by diffusion models like Stable Diffusion are increasingly widespread. Recent works and even lawsuits have shown that these models are prone to replicating their training data, unbeknownst to the user. In this paper, we first analyze this memorization problem in text-to-image diffusion models. While it is widely believed that duplicated images in the training set are responsible for content replication at inference time, we observe that the text conditioning of the model plays a similarly important role. In fact, we see in our experiments that data replication often does not happen for unconditional models, while it is common in the text-conditional case. Motivated by our findings, we then propose several techniques for reducing data replication at both training and inference time by randomizing and augmenting image captions in the training set.

Large language models (LLMs) have shown significant potential in scientific disciplines such as biomedicine, particularly in hypothesis generation, where they can analyze vast literature, identify patterns, and suggest research directions. However, a key challenge lies in evaluating the truthfulness of generated hypotheses, as verifying their accuracy often requires substantial time and resources. Additionally, the hallucination problem in LLMs can lead to the generation of hypotheses that appear plausible but are ultimately incorrect, undermining their reliability. To facilitate the systematic study of these challenges, we introduce TruthHypo, a benchmark for assessing the capabilities of LLMs in generating truthful biomedical hypotheses, and KnowHD, a knowledge-based hallucination detector to evaluate how well hypotheses are grounded in existing knowledge. Our results show that LLMs struggle to generate truthful hypotheses. By analyzing hallucinations in reasoning steps, we demonstrate that the groundedness scores provided by KnowHD serve as an effective metric for filtering truthful hypotheses from the diverse outputs of LLMs. Human evaluations further validate the utility of KnowHD in identifying truthful hypotheses and accelerating scientific discovery. Our data and source code are available at https://github.com/Teddy-XiongGZ/TruthHypo.

How many experimental studies would have come to different conclusions had they been run on larger samples? I show how to estimate the expected number of statistically significant results that a set of experiments would have reported had their sample sizes all been counterfactually increased. The proposed deconvolution estimator is asymptotically normal and adjusts for publication bias. Unlike related methods, this approach requires no assumptions of any kind about the distribution of true intervention treatment effects and allows for point masses. Simulations find good coverage even when the t-score is only approximately normal. An application to randomized trials (RCTs) published in economics journals finds that doubling every sample would increase the power of t-tests by 7.2 percentage points on average. This effect is smaller than for non-RCTs and comparable to systematic replications in laboratory psychology where previous studies enabled more accurate power calculations. This suggests that RCTs are on average relatively insensitive to sample size increases. Research funders who wish to raise power should generally consider sponsoring better-measured and higher quality experiments -- rather than only larger ones.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

Data-driven social science research is inherently slow, relying on iterative cycles of observation, hypothesis generation, and experimental validation. While recent data-driven methods promise to accelerate parts of this process, they largely fail to support end-to-end scientific discovery. To address this gap, we introduce EXPERIGEN, an agentic framework that operationalizes end-to-end discovery through a Bayesian optimization inspired two-phase search, in which a Generator proposes candidate hypotheses and an Experimenter evaluates them empirically. Across multiple domains, EXPERIGEN consistently discovers 2-4x more statistically significant hypotheses that are 7-17 percent more predictive than prior approaches, and naturally extends to complex data regimes including multimodal and relational datasets. Beyond statistical performance, hypotheses must be novel, empirically grounded, and actionable to drive real scientific progress. To evaluate these qualities, we conduct an expert review of machine-generated hypotheses, collecting feedback from senior faculty. Among 25 reviewed hypotheses, 88 percent were rated moderately or strongly novel, 70 percent were deemed impactful and worth pursuing, and most demonstrated rigor comparable to senior graduate-level research. Finally, recognizing that ultimate validation requires real-world evidence, we conduct the first A/B test of LLM-generated hypotheses, observing statistically significant results with p less than 1e-6 and a large effect size of 344 percent.

While Retrieval-Augmented Generation (RAG) enables large language models (LLMs) to generate contextually grounded responses, contextual faithfulness remains challenging as LLMs may not consistently trust provided context, leading to hallucinations that undermine reliability. We observe an inverse correlation between response copying degree and context-unfaithful hallucinations on RAGTruth, suggesting that higher copying degrees reduce hallucinations by fostering genuine contextual belief. We propose CopyPasteLLM, obtained through two-stage high-copying response preference training. We design three prompting methods to enhance copying degree, demonstrating that high-copying responses achieve superior contextual faithfulness and hallucination control. These approaches enable a fully automated pipeline that transforms generated responses into high-copying preference data for training CopyPasteLLM. On FaithEval, ConFiQA and PubMedQA, CopyPasteLLM achieves best performance in both counterfactual and original contexts, remarkably with 12.2% to 24.5% accuracy improvements on FaithEval over the best baseline, while requiring only 365 training samples -- 1/50th of baseline data. To elucidate CopyPasteLLM's effectiveness, we propose the Context-Parameter Copying Capturing algorithm. Interestingly, this reveals that CopyPasteLLM recalibrates reliance on internal parametric knowledge rather than external knowledge during generation. All codes are available at https://github.com/longyongchao/CopyPasteLLM

Click-through rate (CTR) prediction is a critical task for many applications, as its accuracy has a direct impact on user experience and platform revenue. In recent years, CTR prediction has been widely studied in both academia and industry, resulting in a wide variety of CTR prediction models. Unfortunately, there is still a lack of standardized benchmarks and uniform evaluation protocols for CTR prediction research. This leads to non-reproducible or even inconsistent experimental results among existing studies, which largely limits the practical value and potential impact of their research. In this work, we aim to perform open benchmarking for CTR prediction and present a rigorous comparison of different models in a reproducible manner. To this end, we ran over 7,000 experiments for more than 12,000 GPU hours in total to re-evaluate 24 existing models on multiple datasets and settings. Surprisingly, our experiments show that with sufficient hyper-parameter search and model tuning, many deep models have smaller differences than expected. The results also reveal that making real progress on the modeling of CTR prediction is indeed a very challenging research task. We believe that our benchmarking work could not only allow researchers to gauge the effectiveness of new models conveniently but also make them fairly compare with the state of the arts. We have publicly released the benchmarking code, evaluation protocols, and hyper-parameter settings of our work to promote reproducible research in this field.

Adapting machine-learned interatomic potential (MLIP) foundation models to specialised tasks through fine-tuning is an increasingly important practice, yet systematic guidance on when and how to fine-tune is currently limited. We evaluate seven fine-tuning strategies -- naive full-parameter updates, two layer-freezing variants, Low-Rank Adaptation (LoRA), multihead replay, pseudolabelled replay, and replay combined with LoRA -- across five chemically diverse benchmarks (aqueous NaCl, ice polymorphs, S_N2 reactions, SPICE biomolecules, and lithium electrolytes), three generations of foundation models, and training sets spanning five orders of magnitude. To support this evaluation we implement three capabilities in the MACE codebase: LoRA adapted for equivariant message-passing architectures, including both scalar and equivariant linear layers; pseudolabelled replay, which decouples the replay data source from the original pretraining corpus; and model-aware atomic reference energy (E0) reestimation for fine-tuning workflows. We find that foundation model quality, correct E0 initialisation, and well-chosen hyperparameters are prerequisites whose impact routinely exceeds that of the fine-tuning strategy itself. Once these prerequisites are met, most strategies achieve strong target-task accuracy, consistently surpassing models trained from scratch. The practical distinction depends on deployment scope: naive fine-tuning offers the best convergence for single-system applications, while multihead replay -- with either original or pseudolabelled data -- is the only approach tested that consistently preserves out-of-distribution robustness, maintaining both pretraining-distribution accuracy for broader deployment and many-body short-range repulsion.

A/B tests are typically analyzed via frequentist p-values and confidence intervals; but these inferences are wholly unreliable if users endogenously choose samples sizes by *continuously monitoring* their tests. We define *always valid* p-values and confidence intervals that let users try to take advantage of data as fast as it becomes available, providing valid statistical inference whenever they make their decision. Always valid inference can be interpreted as a natural interface for a sequential hypothesis test, which empowers users to implement a modified test tailored to them. In particular, we show in an appropriate sense that the measures we develop tradeoff sample size and power efficiently, despite a lack of prior knowledge of the user's relative preference between these two goals. We also use always valid p-values to obtain multiple hypothesis testing control in the sequential context. Our methodology has been implemented in a large scale commercial A/B testing platform to analyze hundreds of thousands of experiments to date.

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.

This paper introduces a pioneering approach to artificial intelligence research, embodied in our O1 Replication Journey. In response to the announcement of OpenAI's groundbreaking O1 model, we embark on a transparent, real-time exploration to replicate its capabilities while reimagining the process of conducting and communicating AI research. Our methodology addresses critical challenges in modern AI research, including the insularity of prolonged team-based projects, delayed information sharing, and the lack of recognition for diverse contributions. By providing comprehensive, real-time documentation of our replication efforts, including both successes and failures, we aim to foster open science, accelerate collective advancement, and lay the groundwork for AI-driven scientific discovery. Our research progress report diverges significantly from traditional research papers, offering continuous updates, full process transparency, and active community engagement throughout the research journey. Technologically, we proposed the journey learning paradigm, which encourages models to learn not just shortcuts, but the complete exploration process, including trial and error, reflection, and backtracking. With only 327 training samples and without any additional tricks, journey learning outperformed conventional supervised learning by over 8\% on the MATH dataset, demonstrating its extremely powerful potential. We believe this to be the most crucial component of O1 technology that we have successfully decoded. We share valuable resources including technical hypotheses and insights, cognitive exploration maps, custom-developed tools, etc at https://github.com/GAIR-NLP/O1-Journey.

Qualitative research faces a critical reliability challenge: traditional inter-rater agreement methods require multiple human coders, are time-intensive, and often yield moderate consistency. We present a multi-perspective validation framework for LLM-based thematic analysis that combines ensemble validation with dual reliability metrics: Cohen's Kappa (κ) for inter-rater agreement and cosine similarity for semantic consistency. Our framework enables configurable analysis parameters (1-6 seeds, temperature 0.0-2.0), supports custom prompt structures with variable substitution, and provides consensus theme extraction across any JSON format. As proof-of-concept, we evaluate three leading LLMs (Gemini 2.5 Pro, GPT-4o, Claude 3.5 Sonnet) on a psychedelic art therapy interview transcript, conducting six independent runs per model. Results demonstrate Gemini achieves highest reliability (κ= 0.907, cosine=95.3%), followed by GPT-4o (κ= 0.853, cosine=92.6%) and Claude (κ= 0.842, cosine=92.1%). All three models achieve a high agreement (κ> 0.80), validating the multi-run ensemble approach. The framework successfully extracts consensus themes across runs, with Gemini identifying 6 consensus themes (50-83% consistency), GPT-4o identifying 5 themes, and Claude 4 themes. Our open-source implementation provides researchers with transparent reliability metrics, flexible configuration, and structure-agnostic consensus extraction, establishing methodological foundations for reliable AI-assisted qualitative research.

Recent surge in large-scale generative models has spurred the development of vast fields in computer vision. In particular, text-to-image diffusion models have garnered widespread adoption across diverse domain due to their potential for high-fidelity image generation. Nonetheless, existing large-scale diffusion models are confined to generate images of up to 1K resolution, which is far from meeting the demands of contemporary commercial applications. Directly sampling higher-resolution images often yields results marred by artifacts such as object repetition and distorted shapes. Addressing the aforementioned issues typically necessitates training or fine-tuning models on higher resolution datasets. However, this undertaking poses a formidable challenge due to the difficulty in collecting large-scale high-resolution contents and substantial computational resources. While several preceding works have proposed alternatives, they often fail to produce convincing results. In this work, we probe the generative ability of diffusion models at higher resolution beyond its original capability and propose a novel progressive approach that fully utilizes generated low-resolution image to guide the generation of higher resolution image. Our method obviates the need for additional training or fine-tuning which significantly lowers the burden of computational costs. Extensive experiments and results validate the efficiency and efficacy of our method. Project page: https://yhyun225.github.io/DiffuseHigh/

Recent progress in autonomous code generation has fueled excitement around AI agents capable of accelerating scientific discovery by running experiments. However, there is currently no benchmark that evaluates whether such agents can implement scientific ideas when given varied amounts of code as a starting point, interpolating between reproduction (running code) and from-scratch replication (fully re-implementing and running code). We introduce AutoExperiment, a benchmark that evaluates AI agents' ability to implement and run machine learning experiments based on natural language descriptions in research papers. In each task, agents are given a research paper, a codebase with key functions masked out, and a command to run the experiment. The goal is to generate the missing code, execute the experiment in a sandboxed environment, and reproduce the results. AutoExperiment scales in difficulty by varying the number of missing functions n, ranging from partial reproduction to full replication. We evaluate state-of-the-art agents and find that performance degrades rapidly as n increases. Agents that can dynamically interact with the environment (e.g. to debug their code) can outperform agents in fixed "agentless" harnesses, and there exists a significant gap between single-shot and multi-trial success rates (Pass@1 vs. Pass@5), motivating verifier approaches to our benchmark. Our findings highlight critical challenges in long-horizon code generation, context retrieval, and autonomous experiment execution, establishing AutoExperiment as a new benchmark for evaluating progress in AI-driven scientific experimentation. Our data and code are open-sourced at https://github.com/j1mk1m/AutoExperiment .

Clinical LLMs are often scaled by increasing model size, context length, retrieval complexity, or inference-time compute, with the implicit expectation that higher accuracy implies safer behavior. This assumption is incomplete in medicine, where a few confident, high-risk, or evidence-contradicting errors can matter more than average benchmark performance. We introduce SaFE-Scale, a framework for measuring how clinical LLM safety changes across model scale, evidence quality, retrieval strategy, context exposure, and inference-time compute. To instantiate this framework, we introduce RadSaFE-200, a Radiology Safety-Focused Evaluation benchmark of 200 multiple-choice questions with clinician-defined clean evidence, conflict evidence, and option-level labels for high-risk error, unsafe answer, and evidence contradiction. We evaluated 34 locally deployed LLMs across six deployment conditions: closed-book prompting (zero-shot), clean evidence, conflict evidence, standard RAG, agentic RAG, and max-context prompting. Clean evidence produced the strongest improvement, increasing mean accuracy from 73.5% to 94.1%, while reducing high-risk error from 12.0% to 2.6%, contradiction from 12.7% to 2.3%, and dangerous overconfidence from 8.0% to 1.6%. Standard RAG and agentic RAG did not reproduce this safety profile: agentic RAG improved accuracy over standard RAG and reduced contradiction, but high-risk error and dangerous overconfidence remained elevated. Max-context prompting increased latency without closing the safety gap, and additional inference-time compute produced only limited gains. Worst-case analysis showed that clinically consequential errors concentrated in a small subset of questions. Clinical LLM safety is therefore not a passive consequence of scaling, but a deployment property shaped by evidence quality, retrieval design, context construction, and collective failure behavior.

The emerging paradigm of AI co-scientists focuses on tasks characterized by repeatable verification, where agents explore search spaces in 'guess and check' loops. This paradigm does not extend to problems where repeated evaluation is impossible and ground truth is established by the consensus synthesis of theory and existing evidence. We evaluate a Gemini-based AI environment designed to support collaborative scientific assessment, integrated into a standard scientific workflow. In collaboration with a diverse group of 13 scientists working in the field of climate science, we tested the system on a complex topic: the stability of the Atlantic Meridional Overturning Circulation (AMOC). Our results show that AI can accelerate the scientific workflow. The group produced a comprehensive synthesis of 79 papers through 104 revision cycles in just over 46 person-hours. AI contribution was significant: most AI-generated content was retained in the report. AI also helped maintain logical consistency and presentation quality. However, expert additions were crucial to ensure its acceptability: less than half of the report was produced by AI. Furthermore, substantial oversight was required to expand and elevate the content to rigorous scientific standards.

Genome engineering has achieved sequence-level precision, yet predicting the transcriptomic state a cell will occupy after perturbation remains open. Single-cell CRISPR screens measure how far cells move, but effect magnitude ignores whether the cells move together. We introduce Shesha perturbation stability (S_p), which quantifies directional coherence as the mean cosine similarity between individual cell shift vectors and the mean perturbation direction. Across five CRISPR datasets (2,200+ perturbations), stability correlates with magnitude (Spearman ρ= 0.75--0.97), but discordant cases expose regulatory architecture: pleiotropic regulators such as CEBPA pay a ``geometric tax,'' producing large but incoherent shifts, while lineage-specific factors such as KLF1 produce coordinated responses. S_p and Song et al.'s perturbation-response score (PS) share partial overlap (ρ_{partial} = +0.51 after controlling for magnitude), but S_p provides significant incremental prediction of UPR pathway activation beyond both PS and magnitude (p < 10^{-18}). In a split-half reproducibility assay, S_p predicts directional reproducibility beyond magnitude (ρ_{partial} = +0.384) while PS does not (ρ_{partial} = -0.193), with the advantage consistent across all magnitude strata and both datasets. Geometric instability is independently associated with UPR activation across four datasets. S_p is implemented in the open-source shesha-geometry Python package.