Daily Papers

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

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

Exposure to large language model output is rapidly increasing. How will seeing AI-generated ideas affect human ideas? We conducted an experiment (800+ participants, 40+ countries) where participants viewed creative ideas that were from ChatGPT or prior experimental participants and then brainstormed their own idea. We varied the number of AI-generated examples (none, low, or high exposure) and if the examples were labeled as 'AI' (disclosure). Our dynamic experiment design -- ideas from prior participants in an experimental condition are used as stimuli for future participants in the same experimental condition -- mimics the interdependent process of cultural creation: creative ideas are built upon prior ideas. Hence, we capture the compounding effects of having LLMs 'in the culture loop'. We find that high AI exposure (but not low AI exposure) did not affect the creativity of individual ideas but did increase the average amount and rate of change of collective idea diversity. AI made ideas different, not better. There were no main effects of disclosure. We also found that self-reported creative people were less influenced by knowing an idea was from AI, and that participants were more likely to knowingly adopt AI ideas when the task was difficult. Our findings suggest that introducing AI ideas into society may increase collective diversity but not individual creativity.

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

Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. In this paper, we introduce BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function as in Bayesian optimization. Moreover, BioDiscoveryAgent, using Claude 3.5 Sonnet, achieves an average of 21% improvement in predicting relevant genetic perturbations across six datasets, and a 46% improvement in the harder task of non-essential gene perturbation, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb more than twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' efficacy.

It is well-known that inverse dynamics models can improve tracking performance in robot control. These models need to precisely capture the robot dynamics, which consist of well-understood components, e.g., rigid body dynamics, and effects that remain challenging to capture, e.g., stick-slip friction and mechanical flexibilities. Such effects exhibit hysteresis and partial observability, rendering them, particularly challenging to model. Hence, hybrid models, which combine a physical prior with data-driven approaches are especially well-suited in this setting. We present a novel hybrid model formulation that enables us to identify fully physically consistent inertial parameters of a rigid body dynamics model which is paired with a recurrent neural network architecture, allowing us to capture unmodeled partially observable effects using the network memory. We compare our approach against state-of-the-art inverse dynamics models on a 7 degree of freedom manipulator. Using data sets obtained through an optimal experiment design approach, we study the accuracy of offline torque prediction and generalization capabilities of joint learning methods. In control experiments on the real system, we evaluate the model as a feed-forward term for impedance control and show the feedback gains can be drastically reduced to achieve a given tracking accuracy.

Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

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

In reinforcement learning (RL), rewards of states are typically considered additive, and following the Markov assumption, they are independent of states visited previously. In many important applications, such as coverage control, experiment design and informative path planning, rewards naturally have diminishing returns, i.e., their value decreases in light of similar states visited previously. To tackle this, we propose submodular RL (SubRL), a paradigm which seeks to optimize more general, non-additive (and history-dependent) rewards modelled via submodular set functions which capture diminishing returns. Unfortunately, in general, even in tabular settings, we show that the resulting optimization problem is hard to approximate. On the other hand, motivated by the success of greedy algorithms in classical submodular optimization, we propose SubPO, a simple policy gradient-based algorithm for SubRL that handles non-additive rewards by greedily maximizing marginal gains. Indeed, under some assumptions on the underlying Markov Decision Process (MDP), SubPO recovers optimal constant factor approximations of submodular bandits. Moreover, we derive a natural policy gradient approach for locally optimizing SubRL instances even in large state- and action- spaces. We showcase the versatility of our approach by applying SubPO to several applications, such as biodiversity monitoring, Bayesian experiment design, informative path planning, and coverage maximization. Our results demonstrate sample efficiency, as well as scalability to high-dimensional state-action spaces.

Urban causal research is essential for understanding the complex dynamics of cities and informing evidence-based policies. However, it is challenged by the inefficiency and bias of hypothesis generation, barriers to multimodal data complexity, and the methodological fragility of causal experimentation. Recent advances in large language models (LLMs) present an opportunity to rethink how urban causal analysis is conducted. This Perspective examines current urban causal research by analyzing taxonomies that categorize research topics, data sources, and methodological approaches to identify structural gaps. We then introduce an LLM-driven conceptual framework, AutoUrbanCI, composed of four distinct modular agents responsible for hypothesis generation, data engineering, experiment design and execution, and results interpretation with policy recommendations. We propose evaluation criteria for rigor and transparency and reflect on implications for human-AI collaboration, equity, and accountability. We call for a new research agenda that embraces AI-augmented workflows not as replacements for human expertise but as tools to broaden participation, improve reproducibility, and unlock more inclusive forms of urban causal reasoning.

As scientific research becomes increasingly complex, innovative tools are needed to manage vast data, facilitate interdisciplinary collaboration, and accelerate discovery. Large language models (LLMs) are now evolving into LLM-based scientific agents that automate critical tasks, ranging from hypothesis generation and experiment design to data analysis and simulation. Unlike general-purpose LLMs, these specialized agents integrate domain-specific knowledge, advanced tool sets, and robust validation mechanisms, enabling them to handle complex data types, ensure reproducibility, and drive scientific breakthroughs. This survey provides a focused review of the architectures, design, benchmarks, applications, and ethical considerations surrounding LLM-based scientific agents. We highlight why they differ from general agents and the ways in which they advance research across various scientific fields. By examining their development and challenges, this survey offers a comprehensive roadmap for researchers and practitioners to harness these agents for more efficient, reliable, and ethically sound scientific discovery.

Scientific Research, vital for improving human life, is hindered by its inherent complexity, slow pace, and the need for specialized experts. To enhance its productivity, we propose a ResearchAgent, a large language model-powered research idea writing agent, which automatically generates problems, methods, and experiment designs while iteratively refining them based on scientific literature. Specifically, starting with a core paper as the primary focus to generate ideas, our ResearchAgent is augmented not only with relevant publications through connecting information over an academic graph but also entities retrieved from an entity-centric knowledge store based on their underlying concepts, mined and shared across numerous papers. In addition, mirroring the human approach to iteratively improving ideas with peer discussions, we leverage multiple ReviewingAgents that provide reviews and feedback iteratively. Further, they are instantiated with human preference-aligned large language models whose criteria for evaluation are derived from actual human judgments. We experimentally validate our ResearchAgent on scientific publications across multiple disciplines, showcasing its effectiveness in generating novel, clear, and valid research ideas based on human and model-based evaluation results.

Modelling compositional meaning for sentences using empirical distributional methods has been a challenge for computational linguists. We implement the abstract categorical model of Coecke et al. (arXiv:1003.4394v1 [cs.CL]) using data from the BNC and evaluate it. The implementation is based on unsupervised learning of matrices for relational words and applying them to the vectors of their arguments. The evaluation is based on the word disambiguation task developed by Mitchell and Lapata (2008) for intransitive sentences, and on a similar new experiment designed for transitive sentences. Our model matches the results of its competitors in the first experiment, and betters them in the second. The general improvement in results with increase in syntactic complexity showcases the compositional power of our model.

Bayesian Optimization (BO) is a foundational strategy in the field of engineering design optimization for efficiently handling black-box functions with many constraints and expensive evaluations. This paper introduces a fast and accurate BO framework that leverages Pre-trained Transformers for Bayesian Optimization (PFN4sBO) to address constrained optimization problems in engineering. Unlike traditional BO methods that rely heavily on Gaussian Processes (GPs), our approach utilizes Prior-data Fitted Networks (PFNs), a type of pre-trained transformer, to infer constraints and optimal solutions without requiring any iterative retraining. We demonstrate the effectiveness of PFN-based BO through a comprehensive benchmark consisting of fifteen test problems, encompassing synthetic, structural, and engineering design challenges. Our findings reveal that PFN-based BO significantly outperforms Constrained Expected Improvement and Penalty-based GP methods by an order of magnitude in speed while also outperforming them in accuracy in identifying feasible, optimal solutions. This work showcases the potential of integrating machine learning with optimization techniques in solving complex engineering challenges, heralding a significant leap forward for optimization methodologies, opening up the path to using PFN-based BO to solve other challenging problems, such as enabling user-guided interactive BO, adaptive experiment design, or multi-objective design optimization. Additionally, we establish a benchmark for evaluating BO algorithms in engineering design, offering a robust platform for future research and development in the field. This benchmark framework for evaluating new BO algorithms in engineering design will be published at https://github.com/rosenyu304/BOEngineeringBenchmark.

The integration of artificial intelligence into journalistic practices represents a transformative shift in how news is gathered, analyzed, and disseminated. Large language models (LLMs), particularly those with agentic capabilities, offer unprecedented opportunities for enhancing journalistic workflows while simultaneously presenting complex challenges for newsroom integration. This research explores how agentic LLMs can support journalists' workflows, based on insights from journalist interviews and from the development of an LLM-based automation tool performing information filtering, summarization, and reporting. The paper details automated aggregation and summarization systems for journalists, presents a technical overview and evaluation of a user-centric LLM-driven reporting system (TeleFlash), and discusses both addressed and unmet journalist needs, with an outlook on future directions for AI-driven tools in journalism.

Layout generation is a task to synthesize a harmonious layout with elements characterized by attributes such as category, position, and size. Human designers experiment with the placement and modification of elements to create aesthetic layouts, however, we observed that current discrete diffusion models (DDMs) struggle to correct inharmonious layouts after they have been generated. In this paper, we first provide novel insights into layout sticking phenomenon in DDMs and then propose a simple yet effective layout-assessment module Layout-Corrector, which works in conjunction with existing DDMs to address the layout sticking problem. We present a learning-based module capable of identifying inharmonious elements within layouts, considering overall layout harmony characterized by complex composition. During the generation process, Layout-Corrector evaluates the correctness of each token in the generated layout, reinitializing those with low scores to the ungenerated state. The DDM then uses the high-scored tokens as clues to regenerate the harmonized tokens. Layout-Corrector, tested on common benchmarks, consistently boosts layout-generation performance when in conjunction with various state-of-the-art DDMs. Furthermore, our extensive analysis demonstrates that the Layout-Corrector (1) successfully identifies erroneous tokens, (2) facilitates control over the fidelity-diversity trade-off, and (3) significantly mitigates the performance drop associated with fast sampling.

This study explores the impact of AI-generated digital self-clones on improving online presentation skills. We carried out a mixed-design experiment involving 44 international students, comparing self-recorded videos (control) with self-clone videos (AI group) for English presentation practice. The AI videos utilized voice cloning, face swapping, lip-sync, and body-language simulation to refine participants' original presentations in terms of repetition, filler words, and pronunciation. Machine-rated scores indicated enhancements in speech performance for both groups. Though the groups didn't significantly differ, the AI group exhibited a heightened depth of reflection, self-compassion, and a meaningful transition from a corrective to an enhancive approach to self-critique. Within the AI group, congruence between self-perception and AI self-clones resulted in diminished speech anxiety and increased enjoyment. Our findings recommend the ethical employment of digital self-clones to enhance the emotional and cognitive facets of skill development.

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

As fine-grained visual classification (FGVC) being developed for decades, great works related have exposed a key direction -- finding discriminative local regions and revealing subtle differences. However, unlike identifying visual contents within static images, for recognizing objects in the real physical world, discriminative information is not only present within seen local regions but also hides in other unseen perspectives. In other words, in addition to focusing on the distinguishable part from the whole, for efficient and accurate recognition, it is required to infer the key perspective with a few glances, e.g., people may recognize a "Benz AMG GT" with a glance of its front and then know that taking a look at its exhaust pipe can help to tell which year's model it is. In this paper, back to reality, we put forward the problem of active fine-grained recognition (AFGR) and complete this study in three steps: (i) a hierarchical, multi-view, fine-grained vehicle dataset is collected as the testbed, (ii) a simple experiment is designed to verify that different perspectives contribute differently for FGVC and different categories own different discriminative perspective, (iii) a policy-gradient-based framework is adopted to achieve efficient recognition with active view selection. Comprehensive experiments demonstrate that the proposed method delivers a better performance-efficient trade-off than previous FGVC methods and advanced neural networks.

Rigging and skinning are essential steps to create realistic 3D animations, often requiring significant expertise and manual effort. Traditional attempts at automating these processes rely heavily on geometric heuristics and often struggle with objects of complex geometry. Recent data-driven approaches show potential for better generality, but are often constrained by limited training data. We present the Anymate Dataset, a large-scale dataset of 230K 3D assets paired with expert-crafted rigging and skinning information -- 70 times larger than existing datasets. Using this dataset, we propose a learning-based auto-rigging framework with three sequential modules for joint, connectivity, and skinning weight prediction. We systematically design and experiment with various architectures as baselines for each module and conduct comprehensive evaluations on our dataset to compare their performance. Our models significantly outperform existing methods, providing a foundation for comparing future methods in automated rigging and skinning. Code and dataset can be found at https://anymate3d.github.io/.

Model fingerprinting has emerged as a powerful tool for model owners to identify their shared model given API access. However, to lower false discovery rate, fight fingerprint leakage, and defend against coalitions of model users attempting to bypass detection, we argue that {\em scalability} is critical, i.e., scaling up the number of fingerprints one can embed into a model. Hence, we pose scalability as a crucial requirement for fingerprinting schemes. We experiment with fingerprint design at a scale significantly larger than previously considered, and introduce a new method, dubbed Perinucleus sampling, to generate scalable, persistent, and harmless fingerprints. We demonstrate that this scheme can add 24,576 fingerprints to a Llama-3.1-8B model -- two orders of magnitude more than existing schemes -- without degrading the model's utility. Our inserted fingerprints persist even after supervised fine-tuning on standard post-training data. We further address security risks for fingerprinting, and theoretically and empirically show how a scalable fingerprinting scheme like ours can mitigate these risks.

Dark matter makes up approximately 85% of total matter in our universe, yet it has never been directly observed in any laboratory on Earth. The origin of dark matter is one of the most important questions in contemporary physics, and a convincing detection of dark matter would be a Nobel-Prize-level breakthrough in fundamental science. The ABRACADABRA experiment was specifically designed to search for dark matter. Although it has not yet made a discovery, ABRACADABRA has produced several dark matter search results widely endorsed by the physics community. The experiment generates ultra-long time-series data at a rate of 10 million samples per second, where the dark matter signal would manifest itself as a sinusoidal oscillation mode within the ultra-long time series. In this paper, we present the TIDMAD -- a comprehensive data release from the ABRACADABRA experiment including three key components: an ultra-long time series dataset divided into training, validation, and science subsets; a carefully-designed denoising score for direct model benchmarking; and a complete analysis framework which produces a community-standard dark matter search result suitable for publication as a physics paper. This data release enables core AI algorithms to extract the signal and produce real physics results thereby advancing fundamental science. The data downloading and associated analysis scripts are available at https://github.com/jessicafry/TIDMAD

In this work, we introduce OmniDrones, an efficient and flexible platform tailored for reinforcement learning in drone control, built on Nvidia's Omniverse Isaac Sim. It employs a bottom-up design approach that allows users to easily design and experiment with various application scenarios on top of GPU-parallelized simulations. It also offers a range of benchmark tasks, presenting challenges ranging from single-drone hovering to over-actuated system tracking. In summary, we propose an open-sourced drone simulation platform, equipped with an extensive suite of tools for drone learning. It includes 4 drone models, 5 sensor modalities, 4 control modes, over 10 benchmark tasks, and a selection of widely used RL baselines. To showcase the capabilities of OmniDrones and to support future research, we also provide preliminary results on these benchmark tasks. We hope this platform will encourage further studies on applying RL to practical drone systems.

Deep learning models have a risk of utilizing spurious clues to make predictions, such as recognizing actions based on the background scene. This issue can severely degrade the open-set action recognition performance when the testing samples have different scene distributions from the training samples. To mitigate this problem, we propose a novel method, called Scene-debiasing Open-set Action Recognition (SOAR), which features an adversarial scene reconstruction module and an adaptive adversarial scene classification module. The former prevents the decoder from reconstructing the video background given video features, and thus helps reduce the background information in feature learning. The latter aims to confuse scene type classification given video features, with a specific emphasis on the action foreground, and helps to learn scene-invariant information. In addition, we design an experiment to quantify the scene bias. The results indicate that the current open-set action recognizers are biased toward the scene, and our proposed SOAR method better mitigates such bias. Furthermore, our extensive experiments demonstrate that our method outperforms state-of-the-art methods, and the ablation studies confirm the effectiveness of our proposed modules.

While the capabilities of large language models (LLMs) have progressed significantly, their use in high-stakes applications have been limited due to risks of hallucination. One key approach in reducing hallucination is retrieval-augmented generation (RAG), but even in such setups, LLMs may still hallucinate when presented with questions outside of the knowledge base. Such behavior is unacceptable in high-stake applications where LLMs are expected to abstain from answering queries it does not have sufficient context on. In this work, we present a novel methodology for systematically evaluating out-of-knowledge base (OOKB) robustness of LLMs (whether LLMs know or do not know) in the RAG setting, without the need for manual annotation of gold standard answers. We implement our methodology in knowornot, an open-source library that enables users to develop their own customized evaluation data and pipelines for OOKB robustness. knowornot comprises four main features. Firstly, it provides a unified, high-level API that streamlines the process of setting up and running robustness benchmarks. Secondly, its modular architecture emphasizes extensibility and flexibility, allowing users to easily integrate their own LLM clients and RAG settings. Thirdly, its rigorous data modeling design ensures experiment reproducibility, reliability and traceability. Lastly, it implements a comprehensive suite of tools for users to customize their pipelines. We demonstrate the utility of knowornot by developing a challenging benchmark, PolicyBench, which spans four Question-Answer (QA) chatbots on government policies, and analyze its OOKB robustness. The source code of knowornot is available https://github.com/govtech-responsibleai/KnowOrNot.

Recently, multimodal contrastive learning (MMCL) approaches, such as CLIP, have achieved a remarkable success in learning representations that are robust against distribution shift and generalize to new domains. Despite the empirical success, the mechanism behind learning such generalizable representations is not understood. In this work, we rigorously analyze this problem and uncover two mechanisms behind MMCL's robustness: intra-class contrasting, which allows the model to learn features with a high variance, and inter-class feature sharing, where annotated details in one class help learning other classes better. Both mechanisms prevent spurious features that are over-represented in the training data to overshadow the generalizable core features. This yields superior zero-shot classification accuracy under distribution shift. Furthermore, we theoretically demonstrate the benefits of using rich captions on robustness and explore the effect of annotating different types of details in the captions. We validate our theoretical findings through experiments, including a well-designed synthetic experiment and an experiment involving training CLIP models on MSCOCO/Conceptual Captions and evaluating them on shifted ImageNets.

While the progress of machine translation of written text has come far in the past several years thanks to the increasing availability of parallel corpora and corpora-based training technologies, automatic translation of spoken text and dialogues remains challenging even for modern systems. In this paper, we aim to boost the machine translation quality of conversational texts by introducing a newly constructed Japanese-English business conversation parallel corpus. A detailed analysis of the corpus is provided along with challenging examples for automatic translation. We also experiment with adding the corpus in a machine translation training scenario and show how the resulting system benefits from its use.

Large-Language Models like GPT-3 have the potential to enable HCI designers and researchers to create more human-like and helpful chatbots for specific applications. But evaluating the feasibility of these chatbots and designing prompts that optimize GPT-3 for a specific task is challenging. We present a case study in tackling these questions, applying GPT-3 to a brief 5-minute chatbot that anyone can talk to better manage their mood. We report a randomized factorial experiment with 945 participants on Mechanical Turk that tests three dimensions of prompt design to initialize the chatbot (identity, intent, and behaviour), and present both quantitative and qualitative analyses of conversations and user perceptions of the chatbot. We hope other HCI designers and researchers can build on this case study, for other applications of GPT-3 based chatbots to specific tasks, and build on and extend the methods we use for prompt design, and evaluation of the prompt design.

Attention mechanism in graph neural networks is designed to assign larger weights to important neighbor nodes for better representation. However, what graph attention learns is not understood well, particularly when graphs are noisy. In this paper, we propose a self-supervised graph attention network (SuperGAT), an improved graph attention model for noisy graphs. Specifically, we exploit two attention forms compatible with a self-supervised task to predict edges, whose presence and absence contain the inherent information about the importance of the relationships between nodes. By encoding edges, SuperGAT learns more expressive attention in distinguishing mislinked neighbors. We find two graph characteristics influence the effectiveness of attention forms and self-supervision: homophily and average degree. Thus, our recipe provides guidance on which attention design to use when those two graph characteristics are known. Our experiment on 17 real-world datasets demonstrates that our recipe generalizes across 15 datasets of them, and our models designed by recipe show improved performance over baselines.

A central challenge of the clean energy transition is the development of catalysts for low-emissions technologies. Recent advances in Machine Learning for quantum chemistry drastically accelerate the computation of catalytic activity descriptors such as adsorption energies. Here we introduce AdsorbRL, a Deep Reinforcement Learning agent aiming to identify potential catalysts given a multi-objective binding energy target, trained using offline learning on the Open Catalyst 2020 and Materials Project data sets. We experiment with Deep Q-Network agents to traverse the space of all ~160,000 possible unary, binary and ternary compounds of 55 chemical elements, with very sparse rewards based on adsorption energy known for only between 2,000 and 3,000 catalysts per adsorbate. To constrain the actions space, we introduce Random Edge Traversal and train a single-objective DQN agent on the known states subgraph, which we find strengthens target binding energy by an average of 4.1 eV. We extend this approach to multi-objective, goal-conditioned learning, and train a DQN agent to identify materials with the highest (respectively lowest) adsorption energies for multiple simultaneous target adsorbates. We experiment with Objective Sub-Sampling, a novel training scheme aimed at encouraging exploration in the multi-objective setup, and demonstrate simultaneous adsorption energy improvement across all target adsorbates, by an average of 0.8 eV. Overall, our results suggest strong potential for Deep Reinforcement Learning applied to the inverse catalysts design problem.

We describe the design and performance of the near-infrared (1.51--1.70 micron), fiber-fed, multi-object (300 fibers), high resolution (R = lambda/delta lambda ~ 22,500) spectrograph built for the Apache Point Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ~ 10^5 red giant stars that systematically sampled all Milky Way populations (bulge, disk, and halo) to study the Galaxy's chemical and kinematical history. It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 -- 2014 using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV, as well as a second spectrograph, a close copy of the first, operating at the 2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several fiber-fed, multi-object, high resolution spectrographs have been built for visual wavelength spectroscopy, the APOGEE spectrograph is one of the first such instruments built for observations in the near-infrared. The instrument's successful development was enabled by several key innovations, including a "gang connector" to allow simultaneous connections of 300 fibers; hermetically sealed feedthroughs to allow fibers to pass through the cryostat wall continuously; the first cryogenically deployed mosaic volume phase holographic grating; and a large refractive camera that includes mono-crystalline silicon and fused silica elements with diameters as large as ~ 400 mm. This paper contains a comprehensive description of all aspects of the instrument including the fiber system, optics and opto-mechanics, detector arrays, mechanics and cryogenics, instrument control, calibration system, optical performance and stability, lessons learned, and design changes for the second instrument.

Knowledge distillation (KD) aims to transfer knowledge from a large teacher model to a smaller student model. Previous work applying KD in the field of large language models (LLMs) typically focused on the post-training phase, where the student LLM learns directly from instructions and corresponding responses generated by the teacher model. In this paper, we extend KD to the pre-training phase of LLMs, named pre-training distillation (PD). We first conduct a preliminary experiment using GLM-4-9B as the teacher LLM to distill a 1.9B parameter student LLM, validating the effectiveness of PD. Considering the key impact factors of distillation, we systematically explore the design space of pre-training distillation across four aspects: logits processing, loss selection, scaling law, and offline or online logits. We conduct extensive experiments to explore the design space of pre-training distillation and find better configurations and interesting conclusions, such as larger student LLMs generally benefiting more from pre-training distillation, while a larger teacher LLM does not necessarily guarantee better results. We hope our exploration of the design space will inform future practices in pre-training distillation.

Visual Language Models (VLMs) demonstrate impressive capabilities in processing multimodal inputs, yet applications such as visual agents, which require handling multiple images and high-resolution videos, demand enhanced long-range modeling. Moreover, existing open-source VLMs lack systematic exploration into extending their context length, and commercial models often provide limited details. To tackle this, we aim to establish an effective solution that enhances long context performance of VLMs while preserving their capacities in short context scenarios. Towards this goal, we make the best design choice through extensive experiment settings from data curation to context window extending and utilizing: (1) we analyze data sources and length distributions to construct ETVLM - a data recipe to balance the performance across scenarios; (2) we examine existing position extending methods, identify their limitations and propose M-RoPE++ as an enhanced approach; we also choose to solely instruction-tune the backbone with mixed-source data; (3) we discuss how to better utilize extended context windows and propose hybrid-resolution training. Built on the Qwen-VL series model, we propose Giraffe, which is effectively extended to 128K lengths. Evaluated on extensive long context VLM benchmarks such as VideoMME and Viusal Haystacks, our Giraffe achieves state-of-the-art performance among similarly sized open-source long VLMs and is competitive with commercial model GPT-4V. We will open-source the code, data, and models.

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

The Apache Point Observatory Galactic Evolution Experiment (APOGEE), one of the programs in the Sloan Digital Sky Survey III (SDSS-III), has now completed its systematic, homogeneous spectroscopic survey sampling all major populations of the Milky Way. After a three year observing campaign on the Sloan 2.5-m Telescope, APOGEE has collected a half million high resolution (R~22,500), high S/N (>100), infrared (1.51-1.70 microns) spectra for 146,000 stars, with time series information via repeat visits to most of these stars. This paper describes the motivations for the survey and its overall design---hardware, field placement, target selection, operations---and gives an overview of these aspects as well as the data reduction, analysis and products. An index is also given to the complement of technical papers that describe various critical survey components in detail. Finally, we discuss the achieved survey performance and illustrate the variety of potential uses of the data products by way of a number of science demonstrations, which span from time series analysis of stellar spectral variations and radial velocity variations from stellar companions, to spatial maps of kinematics, metallicity and abundance patterns across the Galaxy and as a function of age, to new views of the interstellar medium, the chemistry of star clusters, and the discovery of rare stellar species. As part of SDSS-III Data Release 12, all of the APOGEE data products are now publicly available.

Neutron tagging in Gadolinium-doped water may play a significant role in reducing backgrounds from atmospheric neutrinos in next generation proton-decay searches using megaton-scale Water Cherenkov detectors. Similar techniques might also be useful in the detection of supernova neutrinos. Accurate determination of neutron tagging efficiencies will require a detailed understanding of the number of neutrons produced by neutrino interactions in water as a function of momentum transferred. We propose the Atmospheric Neutrino Neutron Interaction Experiment (ANNIE), designed to measure the neutron yield of atmospheric neutrino interactions in gadolinium-doped water. An innovative aspect of the ANNIE design is the use of precision timing to localize interaction vertices in the small fiducial volume of the detector. We propose to achieve this by using early production of LAPPDs (Large Area Picosecond Photodetectors). This experiment will be a first application of these devices demonstrating their feasibility for Water Cherenkov neutrino detectors.

Neutron tagging in Gadolinium-doped water may play a significant role in reducing backgrounds from atmospheric neutrinos in next generation proton-decay searches using megaton-scale Water Cherenkov detectors. Similar techniques might also be useful in the detection of supernova neutrinos. Accurate determination of neutron tagging efficiencies will require a detailed understanding of the number of neutrons produced by neutrino interactions in water as a function of momentum transferred. We propose the Atmospheric Neutrino Neutron Interaction Experiment (ANNIE), designed to measure the neutron yield of atmospheric neutrino interactions in gadolinium-doped water. An innovative aspect of the ANNIE design is the use of precision timing to localize interaction vertices in the small fiducial volume of the detector. We propose to achieve this by using early production of LAPPDs (Large Area Picosecond Photodetectors). This experiment will be a first application of these devices demonstrating their feasibility for Water Cherenkov neutrino detectors.

A Sense/Compute/Control (SCC) application is one that interacts with the physical environment. Such applications are pervasive in domains such as building automation, assisted living, and autonomic computing. Developing an SCC application is complex because: (1) the implementation must address both the interaction with the environment and the application logic; (2) any evolution in the environment must be reflected in the implementation of the application; (3) correctness is essential, as effects on the physical environment can have irreversible consequences. The SCC architectural pattern and the DiaSpec domain-specific design language propose a framework to guide the design of such applications. From a design description in DiaSpec, the DiaSpec compiler is capable of generating a programming framework that guides the developer in implementing the design and that provides runtime support. In this paper, we report on an experiment using DiaSpec (both the design language and compiler) to develop a standard robotics application. We discuss the benefits and problems of using DiaSpec in a robotics setting and present some changes that would make DiaSpec a better framework in this setting.

Large language models (LLMs) achieve remarkable fluency across linguistic and reasoning tasks but remain systematically prone to hallucination. Prevailing accounts attribute hallucinations to data gaps, limited context, or optimization errors. We argue instead that hallucination is a structural outcome of the transformer architecture. As coherence engines, transformers are compelled to produce fluent continuations, with self-attention simulating the relational structure of meaning but lacking the existential grounding of temporality, mood, and care that stabilizes human understanding. On this basis, we distinguish ontological hallucination, arising when continuations require disclosure of beings in world, and residual reasoning hallucination, where models mimic inference by recycling traces of human reasoning in text. We illustrate these patterns through case studies aligned with Heideggerian categories and an experiment across twelve LLMs showing how simulated "self-preservation" emerges under extended prompts. Our contribution is threefold: (1) a comparative account showing why existing explanations are insufficient; (2) a predictive taxonomy of hallucination linked to existential structures with proposed benchmarks; and (3) design directions toward "truth-constrained" architectures capable of withholding or deferring when disclosure is absent. We conclude that hallucination is not an incidental defect but a defining limit of transformer-based models, an outcome scaffolding can mask but never resolve.

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

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

The significant advancements of Large Language Models (LLMs) in generative tasks have led to a growing body of work exploring LLM-based embedding models. While these models, employing different pooling and attention strategies, have achieved state-of-the-art performance on public embedding benchmarks, questions still arise about what constitutes an effective design for LLM-based embedding models. However, these models are often trained on different datasets, using different LLM base models or training settings. Moreover, evaluations on public embedding benchmarks often fail to report statistical significance, making it difficult to determine which designs truly contribute to final performance. This complicates the process for practitioners seeking optimal training recipes for LLM-based embedding models. In this study, we conduct a large-scale experiment by training a series of LLM-based embedding models using the same training data and base model but differing in their pooling and attention strategies. The results show that there is no one-size-fits-all solution: while bidirectional attention and an additional trainable pooling layer outperform in text similarity and information retrieval tasks, they do not significantly surpass simpler designs like EOS-last token pooling and default causal attention in clustering and classification tasks. Furthermore, we propose a new pooling strategy, Multi-Layers Trainable Pooling, which transforms the outputs of all hidden layers, rather than just the last layer, using a cross-attention network. This method proves to be statistically superior in text similarity and retrieval tasks compared to existing pooling methods. Overall, this paper sheds light on effective training strategies for LLM-based embedding models.

Mu3e is an experiment currently under construction at the Paul Scherrer Institute in Switzerland, designed to search for the Lepton Flavor Violating (LFV) decay mu^+ rightarrow e^+e^-e^+. In extensions of the Standard Model (SM) that account for neutrino masses, this decay is theoretically allowed but occurs only through extremely rare loop processes, with a predicted branching ratio of approximately O(10^{-54}). Such a small probability implies that any observation of this decay would provide clear evidence for physics beyond the SM. The Mu3e experiment aims to probe the mu^+ rightarrow e^+e^-e^+ decay with a sensitivity of approximately O(10^{-15}) in its Phase-1 and plans to achieve a sensitivity of O(10^{-16}) after future upgrades. To reach its Phase-1 ambitious goals, Mu3e is going to use the most intense continuous muon beam in the world, generating 10^{8} muon stops per second in the target placed at the center of the Mu3e. Mu3e will use three main technologies for particle detection. The tracking will done through ultra-thin (50 - 70 mu m) pixel detectors based on MuPix11 sensors. These are high-voltage monolithic active pixel sensors (HV-MAPS) with a sim 23~mum spatial resolution. The timing will be done through scintillating fibres (sim 250 ps) and tiles (sim 40 ps), coupled to silicon photomultipliers and read out by MuTRiG3 ASICs. A triggerless DAQ system based on FPGAs will collect data from the detectors, which will then undergo reconstruction in a GPU filter farm. The assembly of the detectors has started, with a detector commissioning beam time planned for 2025. This document reports on the status of the construction, installation, and data-taking plans for the near future.

Multimodal Large Language Models (MLLMs) hold promise for accelerating scientific discovery by interpreting complex experimental procedures. However, their true capabilities are poorly understood, as existing benchmarks neglect the fine-grained and long-horizon nature of authentic laboratory work, especially in wet-lab settings. To bridge this gap, we introduce ExpVid, the first benchmark designed to systematically evaluate MLLMs on scientific experiment videos. Curated from peer-reviewed video publications, ExpVid features a new three-level task hierarchy that mirrors the scientific process: (1) Fine-grained Perception of tools, materials, and actions; (2) Procedural Understanding of step order and completeness; and (3) Scientific Reasoning that connects the full experiment to its published conclusions. Our vision-centric annotation pipeline, combining automated generation with multi-disciplinary expert validation, ensures that tasks require visual grounding. We evaluate 19 leading MLLMs on ExpVid and find that while they excel at coarse-grained recognition, they struggle with disambiguating fine details, tracking state changes over time, and linking experimental procedures to scientific outcomes. Our results reveal a notable performance gap between proprietary and open-source models, particularly in high-order reasoning. ExpVid not only provides a diagnostic tool but also charts a roadmap for developing MLLMs capable of becoming trustworthy partners in scientific experimentation.

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

Engineering design optimization seeks to automatically determine the shapes, topologies, or parameters of components that maximize performance under given conditions. This process often depends on physics-based simulations, which are difficult to install, computationally expensive, and require domain-specific expertise. To mitigate these challenges, we introduce EngiBench, the first open-source library and datasets spanning diverse domains for data-driven engineering design. EngiBench provides a unified API and a curated set of benchmarks -- covering aeronautics, heat conduction, photonics, and more -- that enable fair, reproducible comparisons of optimization and machine learning algorithms, such as generative or surrogate models. We also release EngiOpt, a companion library offering a collection of such algorithms compatible with the EngiBench interface. Both libraries are modular, letting users plug in novel algorithms or problems, automate end-to-end experiment workflows, and leverage built-in utilities for visualization, dataset generation, feasibility checks, and performance analysis. We demonstrate their versatility through experiments comparing state-of-the-art techniques across multiple engineering design problems, an undertaking that was previously prohibitively time-consuming to perform. Finally, we show that these problems pose significant challenges for standard machine learning methods due to highly sensitive and constrained design manifolds.

AI and reinforcement learning (RL) have improved many areas, but are not yet widely adopted in economic policy design, mechanism design, or economics at large. At the same time, current economic methodology is limited by a lack of counterfactual data, simplistic behavioral models, and limited opportunities to experiment with policies and evaluate behavioral responses. Here we show that machine-learning-based economic simulation is a powerful policy and mechanism design framework to overcome these limitations. The AI Economist is a two-level, deep RL framework that trains both agents and a social planner who co-adapt, providing a tractable solution to the highly unstable and novel two-level RL challenge. From a simple specification of an economy, we learn rational agent behaviors that adapt to learned planner policies and vice versa. We demonstrate the efficacy of the AI Economist on the problem of optimal taxation. In simple one-step economies, the AI Economist recovers the optimal tax policy of economic theory. In complex, dynamic economies, the AI Economist substantially improves both utilitarian social welfare and the trade-off between equality and productivity over baselines. It does so despite emergent tax-gaming strategies, while accounting for agent interactions and behavioral change more accurately than economic theory. These results demonstrate for the first time that two-level, deep RL can be used for understanding and as a complement to theory for economic design, unlocking a new computational learning-based approach to understanding economic policy.

The Chinese Spelling Correction (CSC) task focuses on detecting and correcting spelling errors in sentences. Current research primarily explores two approaches: traditional multimodal pre-trained models and large language models (LLMs). However, LLMs face limitations in CSC, particularly over-correction, making them suboptimal for this task. While existing studies have investigated the use of phonetic and graphemic information in multimodal CSC models, effectively leveraging these features to enhance correction performance remains a challenge. To address this, we propose the Multimodal Analysis for Character Usage (MACU) experiment, identifying potential improvements for multimodal correctison. Based on empirical findings, we introduce NamBert, a novel multimodal model for Chinese spelling correction. Experiments on benchmark datasets demonstrate NamBert's superiority over SOTA methods. We also conduct a comprehensive comparison between NamBert and LLMs, systematically evaluating their strengths and limitations in CSC. Our code and model are available at https://github.com/iioSnail/NamBert.

Detailed detector simulation is the major consumer of CPU resources at LHCb, having used more than 90% of the total computing budget during Run 2 of the Large Hadron Collider at CERN. As data is collected by the upgraded LHCb detector during Run 3 of the LHC, larger requests for simulated data samples are necessary, and will far exceed the pledged resources of the experiment, even with existing fast simulation options. An evolution of technologies and techniques to produce simulated samples is mandatory to meet the upcoming needs of analysis to interpret signal versus background and measure efficiencies. In this context, we propose Lamarr, a Gaudi-based framework designed to offer the fastest solution for the simulation of the LHCb detector. Lamarr consists of a pipeline of modules parameterizing both the detector response and the reconstruction algorithms of the LHCb experiment. Most of the parameterizations are made of Deep Generative Models and Gradient Boosted Decision Trees trained on simulated samples or alternatively, where possible, on real data. Embedding Lamarr in the general LHCb Gauss Simulation framework allows combining its execution with any of the available generators in a seamless way. Lamarr has been validated by comparing key reconstructed quantities with Detailed Simulation. Good agreement of the simulated distributions is obtained with two-order-of-magnitude speed-up of the simulation phase.

Remote photoplethysmography (rPPG) is a non-contact technique for measuring human physiological signals. Due to its convenience and non-invasiveness, it has demonstrated broad application potential in areas such as health monitoring and emotion recognition. In recent years, the release of numerous public datasets has significantly advanced the performance of rPPG algorithms under ideal lighting conditions. However, the effectiveness of current rPPG methods in realistic nighttime scenarios with dynamic lighting variations remains largely unknown. Moreover, there is a severe lack of datasets specifically designed for such challenging environments, which has substantially hindered progress in this area of research. To address this gap, we present and release a large-scale rPPG dataset collected under dynamic lighting conditions at night, named DLCN. The dataset comprises approximately 13 hours of video data and corresponding synchronized physiological signals from 98 participants, covering four representative nighttime lighting scenarios. DLCN offers high diversity and realism, making it a valuable resource for evaluating algorithm robustness in complex conditions. Built upon the proposed Happy-rPPG Toolkit, we conduct extensive experiments and provide a comprehensive analysis of the challenges faced by state-of-the-art rPPG methods when applied to DLCN. The dataset and code are publicly available at https://github.com/dalaoplan/Happp-rPPG-Toolkit.

Understanding visually-rich business documents to extract structured data and automate business workflows has been receiving attention both in academia and industry. Although recent multi-modal language models have achieved impressive results, we find that existing benchmarks do not reflect the complexity of real documents seen in industry. In this work, we identify the desiderata for a more comprehensive benchmark and propose one we call Visually Rich Document Understanding (VRDU). VRDU contains two datasets that represent several challenges: rich schema including diverse data types as well as hierarchical entities, complex templates including tables and multi-column layouts, and diversity of different layouts (templates) within a single document type. We design few-shot and conventional experiment settings along with a carefully designed matching algorithm to evaluate extraction results. We report the performance of strong baselines and offer three observations: (1) generalizing to new document templates is still very challenging, (2) few-shot performance has a lot of headroom, and (3) models struggle with hierarchical fields such as line-items in an invoice. We plan to open source the benchmark and the evaluation toolkit. We hope this helps the community make progress on these challenging tasks in extracting structured data from visually rich documents.

We show that domain-general automatic evaluators can significantly improve the performance of agents for web navigation and device control. We experiment with multiple evaluation models that trade off between inference cost, modularity of design, and accuracy. We validate the performance of these models in several popular benchmarks for digital agents, finding between 74.4 and 92.9% agreement with oracle evaluation metrics. Finally, we use these evaluators to improve the performance of existing agents via fine-tuning and inference-time guidance. Without any additional supervision, we improve state-of-the-art performance by 29% on the popular benchmark WebArena, and achieve a 75% relative improvement in a challenging domain transfer scenario.

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

Large language models (LLMs) pre-trained on massive corpora have demonstrated impressive few-shot learning ability on many NLP tasks. A common practice is to recast the task into a text-to-text format such that generative LLMs of natural language (NL-LLMs) like GPT-3 can be prompted to solve it. However, it is nontrivial to perform information extraction (IE) tasks with NL-LLMs since the output of the IE task is usually structured and therefore is hard to be converted into plain text. In this paper, we propose to recast the structured output in the form of code instead of natural language and utilize generative LLMs of code (Code-LLMs) such as Codex to perform IE tasks, in particular, named entity recognition and relation extraction. In contrast to NL-LLMs, we show that Code-LLMs can be well-aligned with these IE tasks by designing code-style prompts and formulating these IE tasks as code generation tasks. Experiment results on seven benchmarks show that our method consistently outperforms fine-tuning moderate-size pre-trained models specially designed for IE tasks (e.g., UIE) and prompting NL-LLMs under few-shot settings. We further conduct a series of in-depth analyses to demonstrate the merits of leveraging Code-LLMs for IE tasks.

Recent advancements in Gaussian-based human body reconstruction have achieved notable success in creating animatable avatars. However, there are ongoing challenges to fully exploit the SMPL model's prior knowledge and enhance the visual fidelity of these models to achieve more refined avatar reconstructions. In this paper, we introduce AniGaussian which addresses the above issues with two insights. First, we propose an innovative pose guided deformation strategy that effectively constrains the dynamic Gaussian avatar with SMPL pose guidance, ensuring that the reconstructed model not only captures the detailed surface nuances but also maintains anatomical correctness across a wide range of motions. Second, we tackle the expressiveness limitations of Gaussian models in representing dynamic human bodies. We incorporate rigid-based priors from previous works to enhance the dynamic transform capabilities of the Gaussian model. Furthermore, we introduce a split-with-scale strategy that significantly improves geometry quality. The ablative study experiment demonstrates the effectiveness of our innovative model design. Through extensive comparisons with existing methods, AniGaussian demonstrates superior performance in both qualitative result and quantitative metrics.

The shift towards electrification and autonomous driving in the automotive industry results in more and more automotive wire harnesses being installed in modern automobiles, which stresses the great significance of guaranteeing the quality of automotive wire harness assembly. The mating of connectors is essential in the final assembly of automotive wire harnesses due to the importance of connectors on wire harness connection and signal transmission. However, the current manual operation of mating connectors leads to severe problems regarding assembly quality and ergonomics, where the robotized assembly has been considered, and different vision-based solutions have been proposed to facilitate a better perception of the robot control system on connectors. Nonetheless, there has been a lack of deep learning-based solutions for detecting automotive wire harness connectors in previous literature. This paper presents a deep learning-based connector detection for robotized automotive wire harness assembly. A dataset of twenty automotive wire harness connectors was created to train and evaluate a two-stage and a one-stage object detection model, respectively. The experiment results indicate the effectiveness of deep learning-based connector detection for automotive wire harness assembly but are limited by the design of the exteriors of connectors.

Polymeric nano- and micro-scale particles have critical roles in tackling critical healthcare and energy challenges with their miniature characteristics. However, tailoring their synthesis process to meet specific design targets has traditionally depended on domain expertise and costly trial-and-errors. Recently, modeling strategies, particularly Bayesian optimization (BO), have been proposed to aid materials discovery for maximized/minimized properties. Coming from practical demands, this study for the first time integrates constrained and composite Bayesian optimization (CCBO) to perform efficient target value optimization under black-box feasibility constraints and limited data for laboratory experimentation. Using a synthetic problem that simulates electrospraying, a model nanomanufacturing process, CCBO strategically avoided infeasible conditions and efficiently optimized particle production towards predefined size targets, surpassing standard BO pipelines and providing decisions comparable to human experts. Further laboratory experiments validated CCBO capability to guide the rational synthesis of poly(lactic-co-glycolic acid) (PLGA) particles with diameters of 300 nm and 3.0 mum via electrospraying. With minimal initial data and unknown experiment constraints, CCBO reached the design targets within 4 iterations. Overall, the CCBO approach presents a versatile and holistic optimization paradigm for next-generation target-driven particle synthesis empowered by artificial intelligence (AI).

We introduce a new type of test, called a Turing Experiment (TE), for evaluating how well a language model, such as GPT-3, can simulate different aspects of human behavior. Unlike the Turing Test, which involves simulating a single arbitrary individual, a TE requires simulating a representative sample of participants in human subject research. We give TEs that attempt to replicate well-established findings in prior studies. We design a methodology for simulating TEs and illustrate its use to compare how well different language models are able to reproduce classic economic, psycholinguistic, and social psychology experiments: Ultimatum Game, Garden Path Sentences, Milgram Shock Experiment, and Wisdom of Crowds. In the first three TEs, the existing findings were replicated using recent models, while the last TE reveals a "hyper-accuracy distortion" present in some language models.

Column type annotation is the task of annotating the columns of a relational table with the semantic type of the values contained in each column. Column type annotation is an important pre-processing step for data search and data integration in the context of data lakes. State-of-the-art column type annotation methods either rely on matching table columns to properties of a knowledge graph or fine-tune pre-trained language models such as BERT for column type annotation. In this work, we take a different approach and explore using ChatGPT for column type annotation. We evaluate different prompt designs in zero- and few-shot settings and experiment with providing task definitions and detailed instructions to the model. We further implement a two-step table annotation pipeline which first determines the class of the entities described in the table and depending on this class asks ChatGPT to annotate columns using only the relevant subset of the overall vocabulary. Using instructions as well as the two-step pipeline, ChatGPT reaches F1 scores of over 85% in zero- and one-shot setups. To reach a similar F1 score a RoBERTa model needs to be fine-tuned with 356 examples. This comparison shows that ChatGPT is able deliver competitive results for the column type annotation task given no or only a minimal amount of task-specific demonstrations.

Efficient image tokenization with high compression ratios remains a critical challenge for training generative models. We present SoftVQ-VAE, a continuous image tokenizer that leverages soft categorical posteriors to aggregate multiple codewords into each latent token, substantially increasing the representation capacity of the latent space. When applied to Transformer-based architectures, our approach compresses 256x256 and 512x512 images using as few as 32 or 64 1-dimensional tokens. Not only does SoftVQ-VAE show consistent and high-quality reconstruction, more importantly, it also achieves state-of-the-art and significantly faster image generation results across different denoising-based generative models. Remarkably, SoftVQ-VAE improves inference throughput by up to 18x for generating 256x256 images and 55x for 512x512 images while achieving competitive FID scores of 1.78 and 2.21 for SiT-XL. It also improves the training efficiency of the generative models by reducing the number of training iterations by 2.3x while maintaining comparable performance. With its fully-differentiable design and semantic-rich latent space, our experiment demonstrates that SoftVQ-VAE achieves efficient tokenization without compromising generation quality, paving the way for more efficient generative models. Code and model are released.

We investigate the extent to which contemporary Large Language Models (LLMs) can engage in exploration, a core capability in reinforcement learning and decision making. We focus on native performance of existing LLMs, without training interventions. We deploy LLMs as agents in simple multi-armed bandit environments, specifying the environment description and interaction history entirely in-context, i.e., within the LLM prompt. We experiment with GPT-3.5, GPT-4, and Llama2, using a variety of prompt designs, and find that the models do not robustly engage in exploration without substantial interventions: i) Across all of our experiments, only one configuration resulted in satisfactory exploratory behavior: GPT-4 with chain-of-thought reasoning and an externally summarized interaction history, presented as sufficient statistics; ii) All other configurations did not result in robust exploratory behavior, including those with chain-of-thought reasoning but unsummarized history. Although these findings can be interpreted positively, they suggest that external summarization -- which may not be possible in more complex settings -- is important for obtaining desirable behavior from LLM agents. We conclude that non-trivial algorithmic interventions, such as fine-tuning or dataset curation, may be required to empower LLM-based decision making agents in complex settings.

This article explores deep learning models for the automatic identification of registers - text varieties such as news reports and discussion forums - in web-based datasets across 16 languages. Identifying web registers, or genres, is crucial for understanding the content of web-scale datasets, which have become essential in corpus and computational linguistics. Despite recent advances, the full potential of register classifiers in the noisy, unrestricted web remains largely unexplored, particularly in multilingual settings. We experiment with various deep learning models using the Multilingual CORE corpora, newly introduced in this article, which includes 16 languages annotated with a detailed, hierarchical taxonomy of 25 registers designed to cover the entire web. Our classifiers achieve state-of-the-art results using a multi-label approach, demonstrating that competitive performance is possible using a relatively complex register taxonomy. However, all models hit a performance ceiling at approximately 80% F1 score, which we attribute to the non-discrete nature of web registers and the inherent uncertainty in labeling some documents. By pruning ambiguous examples, we enhance model performance to over 90%. Additionally, multilingual models consistently outperform monolingual ones, especially benefiting languages with fewer training examples and smaller registers. Although a zero-shot setting reduces performance by an average of 7%, these drops are not correlated with specific registers or languages. Instead, we find that registers are surprisingly similar across languages.

Embedding-based methods for reasoning in knowledge hypergraphs learn a representation for each entity and relation. Current methods do not capture the procedural rules underlying the relations in the graph. We propose a simple embedding-based model called ReAlE that performs link prediction in knowledge hypergraphs (generalized knowledge graphs) and can represent high-level abstractions in terms of relational algebra operations. We show theoretically that ReAlE is fully expressive and provide proofs and empirical evidence that it can represent a large subset of the primitive relational algebra operations, namely renaming, projection, set union, selection, and set difference. We also verify experimentally that ReAlE outperforms state-of-the-art models in knowledge hypergraph completion, and in representing each of these primitive relational algebra operations. For the latter experiment, we generate a synthetic knowledge hypergraph, for which we design an algorithm based on the Erdos-R'enyi model for generating random graphs.

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

Large Language Models (LLMs) solely trained on next-token prediction learn to solve a wide range of problems involving mathematical reasoning. But how does this ability evolve during training? We show the first analysis of how mathematical reasoning abilities of several open-weight LLMs develop during pre-training and post-training. To this end, we construct MathCAMPS, a synthetic dataset of novel mathematical reasoning problems grounded in 44 fine-grained skills taken from the Common Core curriculum from K to 8th grades. In one experiment, we show that mathematical skills are learned during pre-training in an order that measurably correlates with the human-designed curriculum, even though training data are randomly ordered. We also show a detailed analysis of which mathematical abilities benefit from instruction tuning, a widely used post-training method and, in contrast, which skills suffer. Our work paves the way for an empirical understanding of LLM training dynamics in relation to reasoning.

We propose a novel framework to study asynchronous federated learning optimization with delays in gradient updates. Our theoretical framework extends the standard FedAvg aggregation scheme by introducing stochastic aggregation weights to represent the variability of the clients update time, due for example to heterogeneous hardware capabilities. Our formalism applies to the general federated setting where clients have heterogeneous datasets and perform at least one step of stochastic gradient descent (SGD). We demonstrate convergence for such a scheme and provide sufficient conditions for the related minimum to be the optimum of the federated problem. We show that our general framework applies to existing optimization schemes including centralized learning, FedAvg, asynchronous FedAvg, and FedBuff. The theory here provided allows drawing meaningful guidelines for designing a federated learning experiment in heterogeneous conditions. In particular, we develop in this work FedFix, a novel extension of FedAvg enabling efficient asynchronous federated training while preserving the convergence stability of synchronous aggregation. We empirically demonstrate our theory on a series of experiments showing that asynchronous FedAvg leads to fast convergence at the expense of stability, and we finally demonstrate the improvements of FedFix over synchronous and asynchronous FedAvg.

The Transatomic Power (TAP) reactor has an unusual design for a molten salt reactor technology, building upon the foundation laid by the Molten Salt Reactor Experiment (MSRE). This design introduces three key modifications to enhance efficiency and compactness: a revised fuel salt composition, an alternative moderator material, and moderator pins surrounded by the molten salt fuel. Unlike traditional solid-fueled reactors that rely on excess positive reactivity at the beginning of life, the TAP concept employs a dynamic approach. The core's design, featuring a cylindrical geometry with square assemblies of moderator rods surrounded by flowing fuel salt, provides flexibility in adjusting the moderator-to-fuel ratio during operation - using movable moderator rods - further adding criticality control capability in addition to the control rods system. Shape optimization of the core can play a crucial role in enhancing performance and efficiency. By applying multiphysics continuous shape optimization techniques to key components, such as the unit cells of the TAP reactor or its moderator assemblies, we can fine-tune the reactor's geometry to achieve optimal performance in key physics like neutronics and thermal hydraulics. We explore this aspect using the optimization module in the Multiphysics Object Oriented Simulation Environment (MOOSE) framework which allows for multiphysics continuous shape optimization. The results reported here illustrate the benefits of applying continuous shape optimization in the design of nuclear reactor components and can help in extending the TAP reactor's performance.

Radio Frequency Reinforcement Learning (RFRL) is anticipated to be a widely applicable technology in the next generation of wireless communication systems, particularly 6G and next-gen military communications. Given this, our research is focused on developing a tool to promote the development of RFRL techniques that leverage spectrum sensing. In particular, the tool was designed to address two cognitive radio applications, specifically dynamic spectrum access and jamming. In order to train and test reinforcement learning (RL) algorithms for these applications, a simulation environment is necessary to simulate the conditions that an agent will encounter within the Radio Frequency (RF) spectrum. In this paper, such an environment has been developed, herein referred to as the RFRL Gym. Through the RFRL Gym, users can design their own scenarios to model what an RL agent may encounter within the RF spectrum as well as experiment with different spectrum sensing techniques. Additionally, the RFRL Gym is a subclass of OpenAI gym, enabling the use of third-party ML/RL Libraries. We plan to open-source this codebase to enable other researchers to utilize the RFRL Gym to test their own scenarios and RL algorithms, ultimately leading to the advancement of RL research in the wireless communications domain. This paper describes in further detail the components of the Gym, results from example scenarios, and plans for future additions. Index Terms-machine learning, reinforcement learning, wireless communications, dynamic spectrum access, OpenAI gym

TensorFlow is a machine learning system that operates at large scale and in heterogeneous environments. TensorFlow uses dataflow graphs to represent computation, shared state, and the operations that mutate that state. It maps the nodes of a dataflow graph across many machines in a cluster, and within a machine across multiple computational devices, including multicore CPUs, general-purpose GPUs, and custom designed ASICs known as Tensor Processing Units (TPUs). This architecture gives flexibility to the application developer: whereas in previous "parameter server" designs the management of shared state is built into the system, TensorFlow enables developers to experiment with novel optimizations and training algorithms. TensorFlow supports a variety of applications, with particularly strong support for training and inference on deep neural networks. Several Google services use TensorFlow in production, we have released it as an open-source project, and it has become widely used for machine learning research. In this paper, we describe the TensorFlow dataflow model in contrast to existing systems, and demonstrate the compelling performance that TensorFlow achieves for several real-world applications.

Multimodal Large Language Models have demonstrated impressive capabilities across tasks, yet they often exhibit difficulty in distinguishing task-relevant from irrelevant signals -- particularly in tasks like Visual Question Answering -- which can lead to susceptibility to misleading or spurious inputs. We refer to this broader limitation as the Cross-Modality Competency Problem -- the model's inability to fairly evaluate all modalities. This vulnerability becomes more evident in modality-specific tasks -- such as image classification or pure text question answering -- where models are expected to rely solely on one modality. In such tasks, spurious information from irrelevant modalities often leads to significant performance degradation. We refer to this failure as Modality Interference, which serves as a concrete and measurable instance of the cross-modality competency problem, and we further design a perturbation-based causal diagnostic experiment to verify and quantify this problem. To mitigate modality interference, we propose a novel framework to finetune MLLMs, including perturbation-based data augmentations with both heuristic perturbations and adversarial perturbations, and a consistency regularization strategy applying on model outputs with original and perturbed inputs. Experiments on multiple benchmark datasets (image-heavy, text-heavy and multimodal tasks) and multiple model families with different scales demonstrate significant improvements in robustness and cross-modality competency, indicating our method's effectiveness in boosting unimodal reasoning ability while enhancing performance on multimodal tasks.

Scientific research demands sophisticated reasoning over multimodal data, a challenge especially prevalent in biology. Despite recent advances in multimodal large language models (MLLMs) for AI-assisted research, existing multimodal reasoning benchmarks only target up to college-level difficulty, while research-level benchmarks emphasize lower-level perception, falling short of the complex multimodal reasoning needed for scientific discovery. To bridge this gap, we introduce MicroVQA, a visual-question answering (VQA) benchmark designed to assess three reasoning capabilities vital in research workflows: expert image understanding, hypothesis generation, and experiment proposal. MicroVQA consists of 1,042 multiple-choice questions (MCQs) curated by biology experts across diverse microscopy modalities, ensuring VQA samples represent real scientific practice. In constructing the benchmark, we find that standard MCQ generation methods induce language shortcuts, motivating a new two-stage pipeline: an optimized LLM prompt structures question-answer pairs into MCQs; then, an agent-based `RefineBot' updates them to remove shortcuts. Benchmarking on state-of-the-art MLLMs reveal a peak performance of 53\%; models with smaller LLMs only slightly underperform top models, suggesting that language-based reasoning is less challenging than multimodal reasoning; and tuning with scientific articles enhances performance. Expert analysis of chain-of-thought responses shows that perception errors are the most frequent, followed by knowledge errors and then overgeneralization errors. These insights highlight the challenges in multimodal scientific reasoning, showing MicroVQA is a valuable resource advancing AI-driven biomedical research. MicroVQA is available at https://huggingface.co/datasets/jmhb/microvqa, and project page at https://jmhb0.github.io/microvqa.

Robot models, particularly those trained with large amounts of data, have recently shown a plethora of real-world manipulation and navigation capabilities. Several independent efforts have shown that given sufficient training data in an environment, robot policies can generalize to demonstrated variations in that environment. However, needing to finetune robot models to every new environment stands in stark contrast to models in language or vision that can be deployed zero-shot for open-world problems. In this work, we present Robot Utility Models (RUMs), a framework for training and deploying zero-shot robot policies that can directly generalize to new environments without any finetuning. To create RUMs efficiently, we develop new tools to quickly collect data for mobile manipulation tasks, integrate such data into a policy with multi-modal imitation learning, and deploy policies on-device on Hello Robot Stretch, a cheap commodity robot, with an external mLLM verifier for retrying. We train five such utility models for opening cabinet doors, opening drawers, picking up napkins, picking up paper bags, and reorienting fallen objects. Our system, on average, achieves 90% success rate in unseen, novel environments interacting with unseen objects. Moreover, the utility models can also succeed in different robot and camera set-ups with no further data, training, or fine-tuning. Primary among our lessons are the importance of training data over training algorithm and policy class, guidance about data scaling, necessity for diverse yet high-quality demonstrations, and a recipe for robot introspection and retrying to improve performance on individual environments. Our code, data, models, hardware designs, as well as our experiment and deployment videos are open sourced and can be found on our project website: https://robotutilitymodels.com

Recent success in deep learning has generated immense interest among practitioners and students, inspiring many to learn about this new technology. While visual and interactive approaches have been successfully developed to help people more easily learn deep learning, most existing tools focus on simpler models. In this work, we present GAN Lab, the first interactive visualization tool designed for non-experts to learn and experiment with Generative Adversarial Networks (GANs), a popular class of complex deep learning models. With GAN Lab, users can interactively train generative models and visualize the dynamic training process's intermediate results. GAN Lab tightly integrates an model overview graph that summarizes GAN's structure, and a layered distributions view that helps users interpret the interplay between submodels. GAN Lab introduces new interactive experimentation features for learning complex deep learning models, such as step-by-step training at multiple levels of abstraction for understanding intricate training dynamics. Implemented using TensorFlow.js, GAN Lab is accessible to anyone via modern web browsers, without the need for installation or specialized hardware, overcoming a major practical challenge in deploying interactive tools for deep learning.

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

We present a new kind of question answering dataset, OpenBookQA, modeled after open book exams for assessing human understanding of a subject. The open book that comes with our questions is a set of 1329 elementary level science facts. Roughly 6000 questions probe an understanding of these facts and their application to novel situations. This requires combining an open book fact (e.g., metals conduct electricity) with broad common knowledge (e.g., a suit of armor is made of metal) obtained from other sources. While existing QA datasets over documents or knowledge bases, being generally self-contained, focus on linguistic understanding, OpenBookQA probes a deeper understanding of both the topic---in the context of common knowledge---and the language it is expressed in. Human performance on OpenBookQA is close to 92%, but many state-of-the-art pre-trained QA methods perform surprisingly poorly, worse than several simple neural baselines we develop. Our oracle experiments designed to circumvent the knowledge retrieval bottleneck demonstrate the value of both the open book and additional facts. We leave it as a challenge to solve the retrieval problem in this multi-hop setting and to close the large gap to human performance.

This paper evaluates whether large language models (LLMs) exhibit cognitive fan effects, similar to those discovered by Anderson in humans, after being pre-trained on human textual data. We conduct two sets of in-context recall experiments designed to elicit fan effects. Consistent with human results, we find that LLM recall uncertainty, measured via token probability, is influenced by the fan effect. Our results show that removing uncertainty disrupts the observed effect. The experiments suggest the fan effect is consistent whether the fan value is induced in-context or in the pre-training data. Finally, these findings provide in-silico evidence that fan effects and typicality are expressions of the same phenomena.

As the context limits of Large Language Models (LLMs) increase, the range of possible applications and downstream functions broadens. In many real-world tasks, decisions depend on details scattered across collections of often disparate documents containing mostly irrelevant information. Long-context LLMs appear well-suited to this form of complex information retrieval and reasoning, which has traditionally proven costly and time-consuming. However, although the development of longer context models has seen rapid gains in recent years, our understanding of how effectively LLMs use their context has not kept pace. To address this, we conduct a set of retrieval experiments designed to evaluate the capabilities of 17 leading LLMs, such as their ability to follow threads of information through the context window. Strikingly, we find that many models are remarkably threadsafe: capable of simultaneously following multiple threads without significant loss in performance. Still, for many models, we find the effective context limit is significantly shorter than the supported context length, with accuracy decreasing as the context window grows. Our study also highlights the important point that token counts from different tokenizers should not be directly compared -- they often correspond to substantially different numbers of written characters. We release our code and long-context experimental data.

In day-to-day communication, people often approximate the truth - for example, rounding the time or omitting details - in order to be maximally helpful to the listener. How do large language models (LLMs) handle such nuanced trade-offs? To address this question, we use psychological models and experiments designed to characterize human behavior to analyze LLMs. We test a range of LLMs and explore how optimization for human preferences or inference-time reasoning affects these trade-offs. We find that reinforcement learning from human feedback improves both honesty and helpfulness, while chain-of-thought prompting skews LLMs towards helpfulness over honesty. Finally, GPT-4 Turbo demonstrates human-like response patterns including sensitivity to the conversational framing and listener's decision context. Our findings reveal the conversational values internalized by LLMs and suggest that even these abstract values can, to a degree, be steered by zero-shot prompting.

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

Inverse design refers to the problem of optimizing the input of an objective function in order to enact a target outcome. For many real-world engineering problems, the objective function takes the form of a simulator that predicts how the system state will evolve over time, and the design challenge is to optimize the initial conditions that lead to a target outcome. Recent developments in learned simulation have shown that graph neural networks (GNNs) can be used for accurate, efficient, differentiable estimation of simulator dynamics, and support high-quality design optimization with gradient- or sampling-based optimization procedures. However, optimizing designs from scratch requires many expensive model queries, and these procedures exhibit basic failures on either non-convex or high-dimensional problems.In this work, we show how denoising diffusion models (DDMs) can be used to solve inverse design problems efficiently and propose a particle sampling algorithm for further improving their efficiency. We perform experiments on a number of fluid dynamics design challenges, and find that our approach substantially reduces the number of calls to the simulator compared to standard techniques.

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

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

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

Code Large Language Models (LLMs) demonstrate great versatility in adapting to various downstream tasks, including code generation and completion, as well as bug detection and fixing. However, Code LLMs often fail to capture existing coding standards, leading to the generation of code that conflicts with the required design patterns for a given project. As a result, developers must post-process to adapt the generated code to the project's design norms. In this work, we empirically investigate the biases of Code LLMs in software development. Through carefully designed experiments, we assess the models' understanding of design patterns across recognition, comprehension, and generation. Our findings reveal that biases in Code LLMs significantly affect the reliability of downstream tasks.

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

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of folding into a target structure, little attention has been given to the identification of undesignable structures according to the minimum free energy (MFE) criterion under the Turner model. In this paper, we address this gap by first introducing mathematical theorems outlining sufficient conditions for recognizing undesignable structures, then proposing efficient algorithms, guided by these theorems, to verify the undesignability of RNA structures. Through the application of these theorems and algorithms to the Eterna100 puzzles, we demonstrate the ability to efficiently establish that 15 of the puzzles indeed fall within the category of undesignable structures. In addition, we provide specific insights from the study of undesignability, in the hope that it will enable more understanding of RNA folding and RNA design.

In molecular research, simulation \& design of molecules are key areas with significant implications for drug development, material science, and other fields. Current classical computational power falls inadequate to simulate any more than small molecules, let alone protein chains on hundreds of peptide. Therefore these experiment are done physically in wet-lab, but it takes a lot of time \& not possible to examine every molecule due to the size of the search area, tens of billions of dollars are spent every year in these research experiments. Molecule simulation \& design has lately advanced significantly by machine learning models, A fresh perspective on the issue of chemical synthesis is provided by deep generative models for graph-structured data. By optimising differentiable models that produce molecular graphs directly, it is feasible to avoid costly search techniques in the discrete and huge space of chemical structures. But these models also suffer from computational limitations when dimensions become huge and consume huge amount of resources. Quantum Generative machine learning in recent years have shown some empirical results promising significant advantages over classical counterparts.

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

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

Science and Engineering fairs offer K-12 students opportunities to engage with authentic STEM practices. Particularly, students are given the chance to experience authentic and open inquiry processes, by defining which themes, questions and approaches will guide their scientific endeavors. In this study, we analyzed data from over 5,000 projects presented at a nationwide science fair in Brazil over the past 20 years using topic modeling to identify the main topics that have driven students' inquiry and design. Our analysis identified a broad range of topics being explored, with significant variations over time, region, and school setting. We argue those results and proposed methodology can not only support further research in the context of science fairs, but also inform instruction and design of contexts-specific resources to support students in open inquiry experiences in different settings.

Inverse design, where we seek to design input variables in order to optimize an underlying objective function, is an important problem that arises across fields such as mechanical engineering to aerospace engineering. Inverse design is typically formulated as an optimization problem, with recent works leveraging optimization across learned dynamics models. However, as models are optimized they tend to fall into adversarial modes, preventing effective sampling. We illustrate that by instead optimizing over the learned energy function captured by the diffusion model, we can avoid such adversarial examples and significantly improve design performance. We further illustrate how such a design system is compositional, enabling us to combine multiple different diffusion models representing subcomponents of our desired system to design systems with every specified component. In an N-body interaction task and a challenging 2D multi-airfoil design task, we demonstrate that by composing the learned diffusion model at test time, our method allows us to design initial states and boundary shapes that are more complex than those in the training data. Our method generalizes to more objects for N-body dataset and discovers formation flying to minimize drag in the multi-airfoil design task. Project website and code can be found at https://github.com/AI4Science-WestlakeU/cindm.

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

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

In this report, we survey Bayesian Optimization methods focussed on the Multi-Armed Bandit Problem. We take the help of the paper "Portfolio Allocation for Bayesian Optimization". We report a small literature survey on the acquisition functions and the types of portfolio strategies used in papers discussing Bayesian Optimization. We also replicate the experiments and report our findings and compare them to the results in the paper. Code link: https://colab.research.google.com/drive/1GZ14klEDoe3dcBeZKo5l8qqrKf_GmBDn?usp=sharing#scrollTo=XgIBau3O45_V.

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

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

To effectively optimize and personalize treatments, it is necessary to investigate the heterogeneity of treatment effects. With the wide range of users being treated over many online controlled experiments, the typical approach of manually investigating each dimension of heterogeneity becomes overly cumbersome and prone to subjective human biases. We need an efficient way to search through thousands of experiments with hundreds of target covariates and hundreds of breakdown dimensions. In this paper, we propose a systematic paradigm for detecting, surfacing and characterizing heterogeneous treatment effects. First, we detect if treatment effect variation is present in an experiment, prior to specifying any breakdowns. Second, we surface the most relevant dimensions for heterogeneity. Finally, we characterize the heterogeneity beyond just the conditional average treatment effects (CATE) by studying the conditional distributions of the estimated individual treatment effects. We show the effectiveness of our methods using simulated data and empirical studies.

We introduce Multi-Objective Counterfactuals for Design (MCD), a novel method for counterfactual optimization in design problems. Counterfactuals are hypothetical situations that can lead to a different decision or choice. In this paper, the authors frame the counterfactual search problem as a design recommendation tool that can help identify modifications to a design, leading to better functional performance. MCD improves upon existing counterfactual search methods by supporting multi-objective queries, which are crucial in design problems, and by decoupling the counterfactual search and sampling processes, thus enhancing efficiency and facilitating objective tradeoff visualization. The paper demonstrates MCD's core functionality using a two-dimensional test case, followed by three case studies of bicycle design that showcase MCD's effectiveness in real-world design problems. In the first case study, MCD excels at recommending modifications to query designs that can significantly enhance functional performance, such as weight savings and improvements to the structural safety factor. The second case study demonstrates that MCD can work with a pre-trained language model to suggest design changes based on a subjective text prompt effectively. Lastly, the authors task MCD with increasing a query design's similarity to a target image and text prompt while simultaneously reducing weight and improving structural performance, demonstrating MCD's performance on a complex multimodal query. Overall, MCD has the potential to provide valuable recommendations for practitioners and design automation researchers looking for answers to their ``What if'' questions by exploring hypothetical design modifications and their impact on multiple design objectives. The code, test problems, and datasets used in the paper are available to the public at decode.mit.edu/projects/counterfactuals/.

AI-driven discovery can greatly reduce design time and enhance new therapeutics' effectiveness. Models using simulators explore broad design spaces but risk violating implicit constraints due to a lack of experimental priors. For example, in a new analysis we performed on a diverse set of models on the GuacaMol benchmark using supervised classifiers, over 60\% of molecules proposed had high probability of being mutagenic. In this work, we introduce \ourdataset, a dataset of priors for design problems extracted from literature describing compounds used in lab settings. It is constructed with LLM pipelines for discovering therapeutic entities in relevant paragraphs and summarizing information in concise fair-use facts. \ourdataset~ consists of 32.3 million pairs of natural language facts, and appropriate entity representations (i.e. SMILES or refseq IDs). To demonstrate the potential of the data, we train LLM, CLIP, and LLava architectures to reason jointly about text and design targets and evaluate on tasks from the Therapeutic Data Commons (TDC). \ourdataset~is highly effective for creating models with strong priors: in supervised prediction problems that use our data as pretraining, our best models with 15M learnable parameters outperform larger 2B TxGemma on both regression and classification TDC tasks, and perform comparably to 9B models on average. Models built with \ourdataset~can be used as constraints while optimizing for novel molecules in GuacaMol, resulting in proposals that are safer and nearly as effective. We release our dataset at https://huggingface.co/datasets/medexanon/Medex{huggingface.co/datasets/medexanon/Medex}, and will provide expanded versions as available literature grows.

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

Large Language Models (LLMs) have shown promise in accelerating the scientific research pipeline. A key capability for this process is the ability to generate novel research ideas, and prior studies have found settings in which LLM-generated research ideas were judged as more novel than human-expert ideas. However, a good idea should not simply appear to be novel, it should also result in better research after being executed. To test whether AI-generated ideas lead to better research outcomes, we conduct an execution study by recruiting 43 expert researchers to execute randomly-assigned ideas, either written by experts or generated by an LLM. Each expert spent over 100 hours implementing the idea and wrote a 4-page short paper to document the experiments. All the executed projects are then reviewed blindly by expert NLP researchers. Comparing the review scores of the same ideas before and after execution, the scores of the LLM-generated ideas decrease significantly more than expert-written ideas on all evaluation metrics (novelty, excitement, effectiveness, and overall; p < 0.05), closing the gap between LLM and human ideas observed at the ideation stage. When comparing the aggregated review scores from the execution study, we even observe that for many metrics there is a flip in rankings where human ideas score higher than LLM ideas. This ideation-execution gap highlights the limitations of current LLMs in generating truly effective research ideas and the challenge of evaluating research ideas in the absence of execution outcomes.

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

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

We introduce a gradient-free framework for Bayesian Optimal Experimental Design (BOED) in sequential settings, aimed at complex systems where gradient information is unavailable. Our method combines Ensemble Kalman Inversion (EKI) for design optimization with the Affine-Invariant Langevin Dynamics (ALDI) sampler for efficient posterior sampling-both of which are derivative-free and ensemble-based. To address the computational challenges posed by nested expectations in BOED, we propose variational Gaussian and parametrized Laplace approximations that provide tractable upper and lower bounds on the Expected Information Gain (EIG). These approximations enable scalable utility estimation in high-dimensional spaces and PDE-constrained inverse problems. We demonstrate the performance of our framework through numerical experiments ranging from linear Gaussian models to PDE-based inference tasks, highlighting the method's robustness, accuracy, and efficiency in information-driven experimental design.

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

Machine learning models, such as neural networks, decision trees, random forests, and gradient boosting machines, accept a feature vector, and provide a prediction. These models learn in a supervised fashion where we provide feature vectors mapped to the expected output. It is common practice to engineer new features from the provided feature set. Such engineered features will either augment or replace portions of the existing feature vector. These engineered features are essentially calculated fields based on the values of the other features. Engineering such features is primarily a manual, time-consuming task. Additionally, each type of model will respond differently to different kinds of engineered features. This paper reports empirical research to demonstrate what kinds of engineered features are best suited to various machine learning model types. We provide this recommendation by generating several datasets that we designed to benefit from a particular type of engineered feature. The experiment demonstrates to what degree the machine learning model can synthesize the needed feature on its own. If a model can synthesize a planned feature, it is not necessary to provide that feature. The research demonstrated that the studied models do indeed perform differently with various types of engineered features.

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

We provide a distillation scaling law that estimates distilled model performance based on a compute budget and its allocation between the student and teacher. Our findings reduce the risks associated with using distillation at scale; compute allocation for both the teacher and student models can now be done to maximize student performance. We provide compute optimal distillation recipes for when 1) a teacher exists, or 2) a teacher needs training. If many students are to be distilled, or a teacher already exists, distillation outperforms supervised pretraining until a compute level which grows predictably with student size. If one student is to be distilled and a teacher also needs training, supervised learning should be done instead. Additionally, we provide insights across our large scale study of distillation, which increase our understanding of distillation and inform experimental design.

Model-Based Reinforcement Learning (RL) is widely believed to have the potential to improve sample efficiency by allowing an agent to synthesize large amounts of imagined experience. Experience Replay (ER) can be considered a simple kind of model, which has proved extremely effective at improving the stability and efficiency of deep RL. In principle, a learned parametric model could improve on ER by generalizing from real experience to augment the dataset with additional plausible experience. However, owing to the many design choices involved in empirically successful algorithms, it can be very hard to establish where the benefits are actually coming from. Here, we provide theoretical and empirical insight into when, and how, we can expect data generated by a learned model to be useful. First, we provide a general theorem motivating how learning a model as an intermediate step can narrow down the set of possible value functions more than learning a value function directly from data using the Bellman equation. Second, we provide an illustrative example showing empirically how a similar effect occurs in a more concrete setting with neural network function approximation. Finally, we provide extensive experiments showing the benefit of model-based learning for online RL in environments with combinatorial complexity, but factored structure that allows a learned model to generalize. In these experiments, we take care to control for other factors in order to isolate, insofar as possible, the benefit of using experience generated by a learned model relative to ER alone.

In computer-aided engineering design, the goal of a designer is to find an optimal design on a given requirement using the numerical simulator in loop with an optimization method. In this design optimization process, a good design optimization process is one that can reduce the time from inception to design. In this work, we take a class of design problem, that is computationally cheap to evaluate but has high dimensional design space. In such cases, traditional surrogate-based optimization does not offer any benefits. In this work, we propose an alternative way to use ML model to surrogate the design process that formulates the search problem as an inverse problem and can save time by finding the optimal design or at least a good initial seed design for optimization. By using this trained surrogate model with the traditional optimization method, we can get the best of both worlds. We call this as Surrogate Assisted Optimization (SAO)- a hybrid approach by mixing ML surrogate with the traditional optimization method. Empirical evaluations of propeller design problems show that a better efficient design can be found in fewer evaluations using SAO.

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

Social scientists are now using large language models to create "silicon samples" - synthetic datasets intended to stand in for human respondents, aimed at revolutionising human subjects research. However, there are many analytic choices which must be made to produce these samples. Though many of these choices are defensible, their impact on sample quality is poorly understood. I map out these analytic choices and demonstrate how a very small number of decisions can dramatically change the correspondence between silicon samples and human data. Configurations (N = 252) varied substantially in their capacity to estimate (i) rank ordering of participants, (ii) response distributions, and (iii) between-scale correlations. Most critically, configurations were not consistent in quality: those that performed well on one dimension often performed poorly on another, implying that there is no "one-size-fits-all" configuration that optimises the accuracy of these samples. I call for greater attention to the threat of analytic flexibility in using silicon samples.

This paper presents a modeling effort to explore the underlying physics of temperature evolution during additive friction stir deposition (AFSD) by a human-AI teaming approach. AFSD is an emerging solid-state additive manufacturing technology that deposits materials without melting. However, both process modeling and modeling of the AFSD tool are at an early stage. In this paper, a human-AI teaming approach is proposed to combine models based on first principles with AI. The resulting human-informed machine learning method, denoted as AFSD-Physics, can effectively learn the governing equations of temperature evolution at the tool and the build from in-process measurements. Experiments are designed and conducted to collect in-process measurements for the deposition of aluminum 7075 with a total of 30 layers. The acquired governing equations are physically interpretable models with low computational cost and high accuracy. Model predictions show good agreement with the measurements. Experimental validation with new process parameters demonstrates the model's generalizability and potential for use in tool temperature control and process optimization.

Recent advancements in large language models (LLMs) have sparked optimism about their potential to accelerate scientific discovery, with a growing number of works proposing research agents that autonomously generate and validate new ideas. Despite this, no evaluations have shown that LLM systems can take the very first step of producing novel, expert-level ideas, let alone perform the entire research process. We address this by establishing an experimental design that evaluates research idea generation while controlling for confounders and performs the first head-to-head comparison between expert NLP researchers and an LLM ideation agent. By recruiting over 100 NLP researchers to write novel ideas and blind reviews of both LLM and human ideas, we obtain the first statistically significant conclusion on current LLM capabilities for research ideation: we find LLM-generated ideas are judged as more novel (p < 0.05) than human expert ideas while being judged slightly weaker on feasibility. Studying our agent baselines closely, we identify open problems in building and evaluating research agents, including failures of LLM self-evaluation and their lack of diversity in generation. Finally, we acknowledge that human judgements of novelty can be difficult, even by experts, and propose an end-to-end study design which recruits researchers to execute these ideas into full projects, enabling us to study whether these novelty and feasibility judgements result in meaningful differences in research outcome.

Transformer models cannot easily scale to long sequences due to their O(N^2) time and space complexity. This has led to Transformer variants seeking to lower computational complexity, such as Longformer and Performer. While such models have theoretically greater efficiency, their effectiveness on real NLP tasks has not been well studied. We benchmark 7 variants of Transformer models on 5 difficult NLP tasks and 7 datasets. We design experiments to isolate the effect of pretraining and hyperparameter settings, to focus on their capacity for long-range attention. Moreover, we present various methods to investigate attention behaviors to illuminate model details beyond metric scores. We find that the modified attention in long-range transformers has advantages on content selection and query-guided decoding, but they come with previously unrecognized drawbacks such as insufficient attention to distant tokens and accumulated approximation error.

De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks appeared recently and show promising results. However, the new models have not been profiled on consistent tasks, and comparative studies to well-established algorithms have only seldom been performed. To standardize the assessment of both classical and neural models for de novo molecular design, we propose an evaluation framework, GuacaMol, based on a suite of standardized benchmarks. The benchmark tasks encompass measuring the fidelity of the models to reproduce the property distribution of the training sets, the ability to generate novel molecules, the exploration and exploitation of chemical space, and a variety of single and multi-objective optimization tasks. The benchmarking open-source Python code, and a leaderboard can be found on https://benevolent.ai/guacamol

In this article, we use probing to investigate phenomena that occur during fine-tuning and knowledge distillation of a BERT-based natural language understanding (NLU) model. Our ultimate purpose was to use probing to better understand practical production problems and consequently to build better NLU models. We designed experiments to see how fine-tuning changes the linguistic capabilities of BERT, what the optimal size of the fine-tuning dataset is, and what amount of information is contained in a distilled NLU based on a tiny Transformer. The results of the experiments show that the probing paradigm in its current form is not well suited to answer such questions. Structural, Edge and Conditional probes do not take into account how easy it is to decode probed information. Consequently, we conclude that quantification of information decodability is critical for many practical applications of the probing paradigm.

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/.

Whole-Slide Image (WSI) is an important tool for evaluating the prognosis of cancer patients. Present WSI-based prognosis studies generally follow a conventional paradigm -- cancer-specific model development -- where one cancer disease corresponds to one model and this model cannot make use of the prognostic knowledge from others. Despite its notable success in recent years, this paradigm has inherent limitations and has always been struggling with practical requirements: (i) scaling to the rare tumor diseases with very limited samples and (ii) benefiting from the generalizable prognostic knowledge in other cancers. To this end, this paper presents the first systematic study on Prognostic Knowledge Transfer in Pathology, called Path-PKT. It comprises three main parts. (1) We curate a large dataset (UNI2-h-DSS) with 13 cancers and use it to evaluate the transferability of prognostic knowledge between different cancers computationally. (2) We design experiments to understand what factors affect knowledge transfer and what causes positive transfers. (3) Motivated by empirical findings, we propose a new baseline approach (MoE-PKT) with a routing mechanism to utilize the generalizable prognostic knowledge in other cancers. Finally, we show the transferability of source models to rare tumor diseases. This study could lay solid foundations for the study of knowledge transfer in WSI-based cancer prognosis. Source code is available at https://github.com/liupei101/Path-PKT.