Daily Papers

The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures (scaffolds) that include the motif and maintain its geometry. Significant recent progress on motif-scaffolding has been made due to computational evaluation with reliable protein structure prediction and fixed-backbone sequence design methods. However, significant variability in evaluation strategies across publications has hindered comparability of results, challenged reproducibility, and impeded robust progress. In response we introduce MotifBench, comprising (1) a precisely specified pipeline and evaluation metrics, (2) a collection of 30 benchmark problems, and (3) an implementation of this benchmark and leaderboard at github.com/blt2114/MotifBench. The MotifBench test cases are more difficult compared to earlier benchmarks, and include protein design problems for which solutions are known but on which, to the best of our knowledge, state-of-the-art methods fail to identify any solution.

Multi-agent reinforcement learning (MARL) methods struggle with the non-stationarity of multi-agent systems and fail to adaptively learn online when tested with novel agents. Here, we leverage large language models (LLMs) to create an autonomous agent that can handle these challenges. Our agent, Hypothetical Minds, consists of a cognitively-inspired architecture, featuring modular components for perception, memory, and hierarchical planning over two levels of abstraction. We introduce the Theory of Mind module that scaffolds the high-level planning process by generating hypotheses about other agents' strategies in natural language. It then evaluates and iteratively refines these hypotheses by reinforcing hypotheses that make correct predictions about the other agents' behavior. Hypothetical Minds significantly improves performance over previous LLM-agent and RL baselines on a range of competitive, mixed motive, and collaborative domains in the Melting Pot benchmark, including both dyadic and population-based environments. Additionally, comparisons against LLM-agent baselines and ablations reveal the importance of hypothesis evaluation and refinement for succeeding on complex scenarios.

We introduce a novel sketch-to-image tool that aligns with the iterative refinement process of artists. Our tool lets users sketch blocking strokes to coarsely represent the placement and form of objects and detail strokes to refine their shape and silhouettes. We develop a two-pass algorithm for generating high-fidelity images from such sketches at any point in the iterative process. In the first pass we use a ControlNet to generate an image that strictly follows all the strokes (blocking and detail) and in the second pass we add variation by renoising regions surrounding blocking strokes. We also present a dataset generation scheme that, when used to train a ControlNet architecture, allows regions that do not contain strokes to be interpreted as not-yet-specified regions rather than empty space. We show that this partial-sketch-aware ControlNet can generate coherent elements from partial sketches that only contain a small number of strokes. The high-fidelity images produced by our approach serve as scaffolds that can help the user adjust the shape and proportions of objects or add additional elements to the composition. We demonstrate the effectiveness of our approach with a variety of examples and evaluative comparisons. Quantitatively, evaluative user feedback indicates that novice viewers prefer the quality of images from our algorithm over a baseline Scribble ControlNet for 84% of the pairs and found our images had less distortion in 81% of the pairs.

We introduce meta-prompting, an effective scaffolding technique designed to enhance the functionality of language models (LMs). This approach transforms a single LM into a multi-faceted conductor, adept at managing and integrating multiple independent LM queries. By employing high-level instructions, meta-prompting guides the LM to break down complex tasks into smaller, more manageable subtasks. These subtasks are then handled by distinct "expert" instances of the same LM, each operating under specific, tailored instructions. Central to this process is the LM itself, in its role as the conductor, which ensures seamless communication and effective integration of the outputs from these expert models. It additionally employs its inherent critical thinking and robust verification processes to refine and authenticate the end result. This collaborative prompting approach empowers a single LM to simultaneously act as a comprehensive orchestrator and a panel of diverse experts, significantly enhancing its performance across a wide array of tasks. The zero-shot, task-agnostic nature of meta-prompting greatly simplifies user interaction by obviating the need for detailed, task-specific instructions. Furthermore, our research demonstrates the seamless integration of external tools, such as a Python interpreter, into the meta-prompting framework, thereby broadening its applicability and utility. Through rigorous experimentation with GPT-4, we establish the superiority of meta-prompting over conventional scaffolding methods: When averaged across all tasks, including the Game of 24, Checkmate-in-One, and Python Programming Puzzles, meta-prompting, augmented with a Python interpreter functionality, surpasses standard prompting by 17.1%, expert (dynamic) prompting by 17.3%, and multipersona prompting by 15.2%.

Reinforcement learning with verifiable rewards (RLVR) has achieved remarkable success in enhancing the reasoning capabilities of large language models (LLMs). However, existing RLVR methods often suffer from exploration inefficiency due to mismatches between the training data's difficulty and the model's capability. LLMs fail to discover viable reasoning paths when problems are overly difficult, while learning little new capability when problems are too simple. In this work, we formalize the impact of problem difficulty by quantifying the relationship between loss descent speed and rollout accuracy. Building on this analysis, we propose SEELE, a novel supervision-aided RLVR framework that dynamically adjusts problem difficulty to stay within the high-efficiency region. SEELE augments each training sample by appending a hint (part of a full solution) after the original problem. Unlike previous hint-based approaches, SEELE deliberately and adaptively adjusts the hint length for each problem to achieve an optimal difficulty. To determine the optimal hint length, SEELE employs a multi-round rollout sampling strategy. In each round, it fits an item response theory model to the accuracy-hint pairs collected in preceding rounds to predict the required hint length for the next round. This instance-level, real-time difficulty adjustment aligns problem difficulty with the evolving model capability, thereby improving exploration efficiency. Experimental results show that SEELE outperforms Group Relative Policy Optimization (GRPO) and Supervised Fine-tuning (SFT) by +11.8 and +10.5 points, respectively, and surpasses the best previous supervision-aided approach by +3.6 points on average across six math reasoning benchmarks.

Scaffolding Large Language Models (LLMs) into multi-agent systems often improves performance on complex tasks, but the safety impact of such scaffolds has not been as thoroughly explored. In this paper, we introduce AGENTBREEDER a framework for multi-objective evolutionary search over scaffolds. Our REDAGENTBREEDER evolves scaffolds towards jailbreaking the base LLM while achieving high task success, while BLUEAGENTBREEDER instead aims to combine safety with task reward. We evaluate the systems discovered by the different instances of AGENTBREEDER and popular baselines using widely recognized reasoning, mathematics, and safety benchmarks. Our work highlights and mitigates the safety risks due to multi-agent scaffolding.

Several recent advances in AI systems (e.g., Tree-of-Thoughts and Program-Aided Language Models) solve problems by providing a "scaffolding" program that structures multiple calls to language models to generate better outputs. A scaffolding program is written in a programming language such as Python. In this work, we use a language-model-infused scaffolding program to improve itself. We start with a seed "improver" that improves an input program according to a given utility function by querying a language model several times and returning the best solution. We then run this seed improver to improve itself. Across a small set of downstream tasks, the resulting improved improver generates programs with significantly better performance than its seed improver. Afterward, we analyze the variety of self-improvement strategies proposed by the language model, including beam search, genetic algorithms, and simulated annealing. Since the language models themselves are not altered, this is not full recursive self-improvement. Nonetheless, it demonstrates that a modern language model, GPT-4 in our proof-of-concept experiments, is capable of writing code that can call itself to improve itself. We critically consider concerns around the development of self-improving technologies and evaluate the frequency with which the generated code bypasses a sandbox.

Outdoor-to-indoor (OtI) signal propagation further challenges the already tight link budgets at millimeter-wave (mmWave). To gain insight into OtI mmWave scenarios at 28 GHz, we conducted an extensive measurement campaign consisting of over 2,200 link measurements. In total, 43 OtI scenarios were measured in West Harlem, New York City, covering seven highly diverse buildings. The measured OtI path gain can vary by up to 40 dB for a given link distance, and the empirical path gain model for all data shows an average of 30 dB excess loss over free space at distances beyond 50 m, with an RMS fitting error of 11.7 dB. The type of glass is found to be the single dominant feature for OtI loss, with 20 dB observed difference between empirical path gain models for scenarios with low-loss and high-loss glass. The presence of scaffolding, tree foliage, or elevated subway tracks, as well as difference in floor height are each found to have an impact between 5-10 dB. We show that for urban buildings with high-loss glass, OtI coverage can support 500 Mbps for 90% of indoor user equipment (UEs) with a base station (BS) antenna placed up to 49 m away. For buildings with low-loss glass, such as our case study covering multiple classrooms of a public school, data rates over 2.5/1.2 Gbps are possible from a BS 68/175 m away from the school building, when a line-of-sight path is available. We expect these results to be useful for the deployment of mmWave networks in dense urban environments as well as the development of relevant scheduling and beam management algorithms.

We introduce Geo-R1, a reasoning-centric post-training framework that unlocks geospatial reasoning in vision-language models by combining thinking scaffolding and elevating. In the scaffolding stage, Geo-R1 instills a ``geospatial thinking paradigm" via supervised fine-tuning on synthetic chain-of-thought exemplars, enabling models to connect visual cues with geographic priors without costly human reasoning annotations. In the elevating stage, it uses GRPO-based reinforcement learning on a weakly-supervised cross-view pairing proxy. This design supplies a verifiable and scalable reward signal: teaching models to capture and reconcile features across modalities, and harnessing reasoning for accurate prediction. Geo-R1 extends geospatial modeling from domain pretraining / supervised finetuning to reasoning-first post-training, and achieves state-of-the-art performance across various geospatial reasoning benchmarks. Our model is available at https://huggingface.co/miniHui/Geo-R1.

Retrieval-Augmented Generation (RAG) has proven to be an effective method for mitigating hallucination issues inherent in large language models (LLMs). Previous approaches typically train retrievers based on semantic similarity, lacking optimization for RAG. More recent works have proposed aligning retrievers with the preference signals of LLMs. However, these preference signals are often difficult for dense retrievers, which typically have weaker language capabilities, to understand and learn effectively. Drawing inspiration from pedagogical theories like Guided Discovery Learning, we propose a novel framework, FiGRet (Fine-grained Guidance for Retrievers), which leverages the language capabilities of LLMs to construct examples from a more granular, information-centric perspective to guide the learning of retrievers. Specifically, our method utilizes LLMs to construct easy-to-understand examples from samples where the retriever performs poorly, focusing on three learning objectives highly relevant to the RAG scenario: relevance, comprehensiveness, and purity. These examples serve as scaffolding to ultimately align the retriever with the LLM's preferences. Furthermore, we employ a dual curriculum learning strategy and leverage the reciprocal feedback between LLM and retriever to further enhance the performance of the RAG system. A series of experiments demonstrate that our proposed framework enhances the performance of RAG systems equipped with different retrievers and is applicable to various LLMs.

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

Can Vision Language Models (VLMs) imagine the full scene from just a few views, like humans do? Humans form spatial mental models, internal representations of unseen space, to reason about layout, perspective, and motion. Our new MindCube benchmark with 21,154 questions across 3,268 images exposes this critical gap, where existing VLMs exhibit near-random performance. Using MindCube, we systematically evaluate how well VLMs build robust spatial mental models through representing positions (cognitive mapping), orientations (perspective-taking), and dynamics (mental simulation for "what-if" movements). We then explore three approaches to help VLMs approximate spatial mental models, including unseen intermediate views, natural language reasoning chains, and cognitive maps. The significant improvement comes from a synergistic approach, "map-then-reason", that jointly trains the model to first generate a cognitive map and then reason upon it. By training models to reason over these internal maps, we boosted accuracy from 37.8% to 60.8% (+23.0%). Adding reinforcement learning pushed performance even further to 70.7% (+32.9%). Our key insight is that such scaffolding of spatial mental models, actively constructing and utilizing internal structured spatial representations with flexible reasoning processes, significantly improves understanding of unobservable space.

Large language models (LLMs) are increasingly used across society, including in domains like business, engineering, and medicine. These fields often grapple with decision-making under uncertainty, a critical yet challenging task. In this paper, we show that directly prompting LLMs on these types of decision-making problems yields poor results, especially as the problem complexity increases. To overcome this limitation, we propose DeLLMa (Decision-making Large Language Model assistant), a framework designed to enhance decision-making accuracy in uncertain environments. DeLLMa involves a multi-step scaffolding procedure, drawing upon principles from decision theory and utility theory, to provide an optimal and human-auditable decision-making process. We validate our framework on decision-making environments involving real agriculture and finance data. Our results show that DeLLMa can significantly improve LLM decision-making performance, achieving up to a 40% increase in accuracy over competing methods.

Self-regulated learning (SRL) is crucial for college students navigating increased academic demands and independence. Insufficient SRL skills can lead to disorganized study habits, low motivation, and poor time management, undermining learners ability to thrive in challenging environments. Through a formative study involving 59 college students, we identified key challenges students face in developing SRL skills, including difficulties with goal-setting, time management, and reflective learning. To address these challenges, we introduce SRLAgent, an LLM-assisted system that fosters SRL skills through gamification and adaptive support from large language models (LLMs). Grounded in Zimmermans three-phase SRL framework, SRLAgent enables students to engage in goal-setting, strategy execution, and self-reflection within an interactive game-based environment. The system offers real-time feedback and scaffolding powered by LLMs to support students independent study efforts. We evaluated SRLAgent using a between-subjects design, comparing it to a baseline system (SRL without Agent features) and a traditional multimedia learning condition. Results showed significant improvements in SRL skills within the SRLAgent group (p < .001, Cohens d = 0.234) and higher engagement compared to the baselines. This work highlights the value of embedding SRL scaffolding and real-time AI support within gamified environments, offering design implications for educational technologies that aim to promote deeper learning and metacognitive skill development.

We stress test monitoring systems for detecting covert misbehavior in autonomous LLM agents (e.g., secretly sharing private information). To this end, we systematize a monitor red teaming (MRT) workflow that incorporates: (1) varying levels of agent and monitor situational awareness; (2) distinct adversarial strategies to evade the monitor, such as prompt injection; and (3) two datasets and environments -- SHADE-Arena for tool-calling agents and our new CUA-SHADE-Arena, which extends TheAgentCompany, for computer-use agents. We run MRT on existing LLM monitor scaffoldings, which orchestrate LLMs and parse agent trajectories, alongside a new hybrid hierarchical-sequential scaffolding proposed in this work. Our empirical results yield three key findings. First, agent awareness dominates monitor awareness: an agent's knowledge that it is being monitored substantially degrades the monitor's reliability. On the contrary, providing the monitor with more information about the agent is less helpful than expected. Second, monitor scaffolding matters more than monitor awareness: the hybrid scaffolding consistently outperforms baseline monitor scaffolding, and can enable weaker models to reliably monitor stronger agents -- a weak-to-strong scaling effect. Third, in a human-in-the-loop setting where humans discuss with the LLM monitor to get an updated judgment for the agent's behavior, targeted human oversight is most effective; escalating only pre-flagged cases to human reviewers improved the TPR by approximately 15% at FPR = 0.01. Our work establishes a standard workflow for MRT, highlighting the lack of adversarial robustness for LLMs and humans when monitoring and detecting agent misbehavior. We release code, data, and logs to spur further research.

Diffusion models have been successful on a range of conditional generation tasks including molecular design and text-to-image generation. However, these achievements have primarily depended on task-specific conditional training or error-prone heuristic approximations. Ideally, a conditional generation method should provide exact samples for a broad range of conditional distributions without requiring task-specific training. To this end, we introduce the Twisted Diffusion Sampler, or TDS. TDS is a sequential Monte Carlo (SMC) algorithm that targets the conditional distributions of diffusion models through simulating a set of weighted particles. The main idea is to use twisting, an SMC technique that enjoys good computational efficiency, to incorporate heuristic approximations without compromising asymptotic exactness. We first find in simulation and in conditional image generation tasks that TDS provides a computational statistical trade-off, yielding more accurate approximations with many particles but with empirical improvements over heuristics with as few as two particles. We then turn to motif-scaffolding, a core task in protein design, using a TDS extension to Riemannian diffusion models. On benchmark test cases, TDS allows flexible conditioning criteria and often outperforms the state of the art.

Recent advances in Large Language Models (LLMs) have underscored the potential of Reinforcement Learning (RL) to facilitate the emergence of reasoning capabilities. Despite the encouraging results, a fundamental dilemma persists as RL improvement relies on learning from high-quality samples, yet the exploration for such samples remains bounded by the inherent limitations of LLMs. This, in effect, creates an undesirable cycle in which what cannot be explored cannot be learned. In this work, we propose Rubric-Scaffolded Reinforcement Learning (RuscaRL), a novel instructional scaffolding framework designed to break the exploration bottleneck for general LLM reasoning. Specifically, RuscaRL introduces checklist-style rubrics as (1) explicit scaffolding for exploration during rollout generation, where different rubrics are provided as external guidance within task instructions to steer diverse high-quality responses. This guidance is gradually decayed over time, encouraging the model to internalize the underlying reasoning patterns; (2) verifiable rewards for exploitation during model training, where we can obtain robust LLM-as-a-Judge scores using rubrics as references, enabling effective RL on general reasoning tasks. Extensive experiments demonstrate the superiority of the proposed RuscaRL across various benchmarks, effectively expanding reasoning boundaries under the best-of-N evaluation. Notably, RuscaRL significantly boosts Qwen-2.5-7B-Instruct from 23.6 to 50.3 on HealthBench-500, surpassing GPT-4.1. Furthermore, our fine-tuned variant on Qwen3-30B-A3B-Instruct achieves 61.1 on HealthBench-500, outperforming leading LLMs including OpenAI-o3.

Solving algebraic word problems requires executing a series of arithmetic operations---a program---to obtain a final answer. However, since programs can be arbitrarily complicated, inducing them directly from question-answer pairs is a formidable challenge. To make this task more feasible, we solve these problems by generating answer rationales, sequences of natural language and human-readable mathematical expressions that derive the final answer through a series of small steps. Although rationales do not explicitly specify programs, they provide a scaffolding for their structure via intermediate milestones. To evaluate our approach, we have created a new 100,000-sample dataset of questions, answers and rationales. Experimental results show that indirect supervision of program learning via answer rationales is a promising strategy for inducing arithmetic programs.

In this paper, we introduce the novel concept of pedagogically aligned Large Language Models (LLMs) that signifies a transformative shift in the application of LLMs within educational contexts. Rather than providing direct responses to user queries, pedagogically-aligned LLMs function as scaffolding tools, breaking complex problems into manageable subproblems and guiding students towards the final answer through constructive feedback and hints. The objective is to equip learners with problem-solving strategies that deepen their understanding and internalization of the subject matter. Previous research in this field has primarily applied the supervised finetuning approach without framing the objective as an alignment problem, hence not employing reinforcement learning through human feedback (RLHF) methods. This study reinterprets the narrative by viewing the task through the lens of alignment and demonstrates how RLHF methods emerge naturally as a superior alternative for aligning LLM behaviour. Building on this perspective, we propose a novel approach for constructing a reward dataset specifically designed for the pedagogical alignment of LLMs. We apply three state-of-the-art RLHF algorithms and find that they outperform SFT significantly. Our qualitative analyses across model differences and hyperparameter sensitivity further validate the superiority of RLHF over SFT. Also, our study sheds light on the potential of online feedback for enhancing the performance of pedagogically-aligned LLMs, thus providing valuable insights for the advancement of these models in educational settings.

While LLMs can effectively help prototype single ML functionalities, many real-world applications involve complex tasks that cannot be easily handled via a single run of an LLM. Recent work has found that chaining multiple LLM runs together (with the output of one step being the input to the next) can help users accomplish these more complex tasks, and in a way that is perceived to be more transparent and controllable. However, it remains unknown what users need when authoring their own LLM chains -- a key step for lowering the barriers for non-AI-experts to prototype AI-infused applications. In this work, we explore the LLM chain authoring process. We conclude from pilot studies find that chaining requires careful scaffolding for transforming intermediate node outputs, as well as debugging the chain at multiple granularities; to help with these needs, we designed PromptChainer, an interactive interface for visually programming chains. Through case studies with four people, we show that PromptChainer supports building prototypes for a range of applications, and conclude with open questions on scaling chains to complex tasks, and supporting low-fi chain prototyping.

Large language models (LLMs) are increasingly being applied to programming tasks, ranging from single-turn code completion to autonomous agents. Current code agent designs frequently depend on complex, hand-crafted workflows and tool sets. However, this reliance on elaborate scaffolding presents several challenges: agent performance becomes overly dependent on prompt tuning and custom design choices, heavy human intervention obscures a model's true underlying capabilities, and intricate pipelines are costly to build and maintain. Furthermore, optimizing complex task prompts increases the risk of data leakage. Currently, when introducing new models, LLM providers like OpenAI and Anthropic often publish benchmark scores to demonstrate their models' coding proficiency, but keep their proprietary evaluation frameworks confidential. To address these limitations, we introduce Lita (Lite Agent), which operationalizes liteness, a principle of minimizing manual design while retaining the essential elements of a fully autonomous agent. Lita enables a more faithful and unified evaluation without elaborate scaffolding. Experiments on the Aider Polyglot and SWE-Bench with frontier models demonstrate that Lita achieves competitive or superior performance compared to workflow-based and agentic baselines. Crucially, Lita also consumes fewer tokens and requires significantly less design effort. Our results suggest that Lita is sufficient to reveal the underlying coding competence of modern LLMs. Finally, we propose the Agent Complexity Law: the performance gap between agents of varying complexity, from simple to sophisticated designs, will shrink as the core model improves, ultimately converging to a negligible difference.

Large language model (LLM) powered chatbots are primarily text-based today, and impose a large interactional cognitive load, especially for exploratory or sensemaking tasks such as planning a trip or learning about a new city. Because the interaction is textual, users have little scaffolding in the way of structure, informational "scent", or ability to specify high-level preferences or goals. We introduce ExploreLLM that allows users to structure thoughts, help explore different options, navigate through the choices and recommendations, and to more easily steer models to generate more personalized responses. We conduct a user study and show that users find it helpful to use ExploreLLM for exploratory or planning tasks, because it provides a useful schema-like structure to the task, and guides users in planning. The study also suggests that users can more easily personalize responses with high-level preferences with ExploreLLM. Together, ExploreLLM points to a future where users interact with LLMs beyond the form of chatbots, and instead designed to support complex user tasks with a tighter integration between natural language and graphical user interfaces.

Large language models exhibit systematic deficiencies in creative writing, particularly in non-English contexts where training data is scarce and lacks process-level supervision. We present COIG-Writer, a novel Chinese creative writing dataset that captures both diverse outputs and their underlying thought processes through systematic reverse-engineering of high-quality texts. Unlike existing datasets that provide only input-output pairs, COIG-Writer comprises 1,665 meticulously curated triplets spanning 51 genres, each containing: (1) a reverse-engineered prompt, (2) detailed creative reasoning documenting decision-making processes, and (3) the final text. Through comprehensive experiments, we identify a two-component model of creative writing: narrative logic (provided by process supervision) and linguistic expression (maintained by general-purpose data). Our findings reveal three critical insights: (1) Process supervision is highly effective but requires stabilization with general data. A ratio of at least one creative sample to twelve general samples is needed to achieve optimal performance; below this threshold, the win rate progressively degrades (from 62.75% down to 35.78%)., (2) creative capabilities are culturally-bound with no cross-lingual transfer (89.26pp gap between Chinese and English performance), and (3) lexical diversity inversely correlates with creative quality (TTR paradox), suggesting high diversity signals compensatory behavior for logical deficiencies. These findings establish that creative excellence emerges from the interaction between logical scaffolding and linguistic grounding, analogous to how mathematical reasoning enhances but cannot replace linguistic competence in foundation models.

In this time when biased information, deep fakes, and propaganda proliferate, the accessibility of reliable data sources is more important than ever. National statistical institutes provide curated data that contain quantitative information on a wide range of topics. However, that information is typically spread across many tables and the plain numbers may be arduous to process. Hence, this open data may be practically inaccessible. We ask the question "Are current Generative AI models capable of facilitating the identification of the right data and the fully-automatic creation of charts to provide information in visual form, corresponding to user queries?". We present a structured evaluation of recent large language models' (LLMs) capabilities to generate charts from complex data in response to user queries. Working with diverse public data from Statistics Netherlands, we assessed multiple LLMs on their ability to identify relevant data tables, perform necessary manipulations, and generate appropriate visualizations autonomously. We propose a new evaluation framework spanning three dimensions: data retrieval & pre-processing, code quality, and visual representation. Results indicate that locating and processing the correct data represents the most significant challenge. Additionally, LLMs rarely implement visualization best practices without explicit guidance. When supplemented with information about effective chart design, models showed marked improvement in representation scores. Furthermore, an agentic approach with iterative self-evaluation led to excellent performance across all evaluation dimensions. These findings suggest that LLMs' effectiveness for automated chart generation can be enhanced through appropriate scaffolding and feedback mechanisms, and that systems can already reach the necessary accuracy across the three evaluation dimensions.

We present APT, an advanced Large Language Model (LLM)-driven framework that enables autonomous agents to construct complex and creative structures within the Minecraft environment. Unlike previous approaches that primarily concentrate on skill-based open-world tasks or rely on image-based diffusion models for generating voxel-based structures, our method leverages the intrinsic spatial reasoning capabilities of LLMs. By employing chain-of-thought decomposition along with multimodal inputs, the framework generates detailed architectural layouts and blueprints that the agent can execute under zero-shot or few-shot learning scenarios. Our agent incorporates both memory and reflection modules to facilitate lifelong learning, adaptive refinement, and error correction throughout the building process. To rigorously evaluate the agent's performance in this emerging research area, we introduce a comprehensive benchmark consisting of diverse construction tasks designed to test creativity, spatial reasoning, adherence to in-game rules, and the effective integration of multimodal instructions. Experimental results using various GPT-based LLM backends and agent configurations demonstrate the agent's capacity to accurately interpret extensive instructions involving numerous items, their positions, and orientations. The agent successfully produces complex structures complete with internal functionalities such as Redstone-powered systems. A/B testing indicates that the inclusion of a memory module leads to a significant increase in performance, emphasizing its role in enabling continuous learning and the reuse of accumulated experience. Additionally, the agent's unexpected emergence of scaffolding behavior highlights the potential of future LLM-driven agents to utilize subroutine planning and leverage the emergence ability of LLMs to autonomously develop human-like problem-solving techniques.

Large language models (LLMs) are shaping a new user interface (UI) paradigm in writing tools by enabling users to generate text through prompts. This paradigm shifts some creative control from the user to the system, thereby diminishing the user's authorship and autonomy in the writing process. To restore autonomy, we introduce Textfocals, a UI prototype designed to investigate a human-centered approach that emphasizes the user's role in writing. Textfocals supports the writing process by providing LLM-generated summaries, questions, and advice (i.e., LLM views) in a sidebar of a text editor, encouraging reflection and self-driven revision in writing without direct text generation. Textfocals' UI affordances, including contextually adaptive views and scaffolding for prompt selection and customization, offer a novel way to interact with LLMs where users maintain full authorship of their writing. A formative user study with Textfocals showed promising evidence that this approach might help users develop underdeveloped ideas, cater to the rhetorical audience, and clarify their writing. However, the study also showed interaction design challenges related to document navigation and scoping, prompt engineering, and context management. Our work highlights the breadth of the design space of writing support interfaces powered by generative AI that maintain authorship integrity.

Can machines truly think, reason and act in domains like humans? This enduring question continues to shape the pursuit of Artificial General Intelligence (AGI). Despite the growing capabilities of models such as GPT-4.5, DeepSeek, Claude 3.5 Sonnet, Phi-4, and Grok 3, which exhibit multimodal fluency and partial reasoning, these systems remain fundamentally limited by their reliance on token-level prediction and lack of grounded agency. This paper offers a cross-disciplinary synthesis of AGI development, spanning artificial intelligence, cognitive neuroscience, psychology, generative models, and agent-based systems. We analyze the architectural and cognitive foundations of general intelligence, highlighting the role of modular reasoning, persistent memory, and multi-agent coordination. In particular, we emphasize the rise of Agentic RAG frameworks that combine retrieval, planning, and dynamic tool use to enable more adaptive behavior. We discuss generalization strategies, including information compression, test-time adaptation, and training-free methods, as critical pathways toward flexible, domain-agnostic intelligence. Vision-Language Models (VLMs) are reexamined not just as perception modules but as evolving interfaces for embodied understanding and collaborative task completion. We also argue that true intelligence arises not from scale alone but from the integration of memory and reasoning: an orchestration of modular, interactive, and self-improving components where compression enables adaptive behavior. Drawing on advances in neurosymbolic systems, reinforcement learning, and cognitive scaffolding, we explore how recent architectures begin to bridge the gap between statistical learning and goal-directed cognition. Finally, we identify key scientific, technical, and ethical challenges on the path to AGI.

Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific control, and flexibility for de novo enzyme backbone generation. To address this, we introduce EnzyBind, a dataset with 11,100 experimentally validated enzyme-substrate pairs specifically curated from PDBbind. Building on this, we propose EnzyControl, a method that enables functional and substrate-specific control in enzyme backbone generation. Our approach generates enzyme backbones conditioned on MSA-annotated catalytic sites and their corresponding substrates, which are automatically extracted from curated enzyme-substrate data. At the core of EnzyControl is EnzyAdapter, a lightweight, modular component integrated into a pretrained motif-scaffolding model, allowing it to become substrate-aware. A two-stage training paradigm further refines the model's ability to generate accurate and functional enzyme structures. Experiments show that our EnzyControl achieves the best performance across structural and functional metrics on EnzyBind and EnzyBench benchmarks, with particularly notable improvements of 13\% in designability and 13\% in catalytic efficiency compared to the baseline models. The code is released at https://github.com/Vecteur-libre/EnzyControl.

While automatic dialogue tutors hold great potential in making education personalized and more accessible, research on such systems has been hampered by a lack of sufficiently large and high-quality datasets. Collecting such datasets remains challenging, as recording tutoring sessions raises privacy concerns and crowdsourcing leads to insufficient data quality. To address this, we propose a framework to generate such dialogues by pairing human teachers with a Large Language Model (LLM) prompted to represent common student errors. We describe how we use this framework to collect MathDial, a dataset of 3k one-to-one teacher-student tutoring dialogues grounded in multi-step math reasoning problems. While models like GPT-3 are good problem solvers, they fail at tutoring because they generate factually incorrect feedback or are prone to revealing solutions to students too early. To overcome this, we let teachers provide learning opportunities to students by guiding them using various scaffolding questions according to a taxonomy of teacher moves. We demonstrate MathDial and its extensive annotations can be used to finetune models to be more effective tutors (and not just solvers). We confirm this by automatic and human evaluation, notably in an interactive setting that measures the trade-off between student solving success and telling solutions. The dataset is released publicly.

Large Language Models (LLMs) display striking surface fluency yet systematically fail at tasks requiring symbolic reasoning, arithmetic accuracy, and logical consistency. This paper offers a structural diagnosis of such failures, revealing a persistent gap between comprehension and competence. Through controlled experiments and architectural analysis, we demonstrate that LLMs often articulate correct principles without reliably applying them--a failure rooted not in knowledge access, but in computational execution. We term this phenomenon the computational split-brain syndrome, where instruction and action pathways are geometrically and functionally dissociated. This core limitation recurs across domains, from mathematical operations to relational inferences, and explains why model behavior remains brittle even under idealized prompting. We argue that LLMs function as powerful pattern completion engines, but lack the architectural scaffolding for principled, compositional reasoning. Our findings delineate the boundary of current LLM capabilities and motivate future models with metacognitive control, principle lifting, and structurally grounded execution. This diagnosis also clarifies why mechanistic interpretability findings may reflect training-specific pattern coordination rather than universal computational principles, and why the geometric separation between instruction and execution pathways suggests limitations in neural introspection and mechanistic analysis.

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

Research on applications of Reinforcement Learning (RL) to Large Language Models (LLMs) has mostly been focused on single-turn problems, such as mathematical reasoning or single-shot code generation. While these problems can be viewed as token-level multi-turn MDPs, this view corresponds to a degenerate case of multi-turn interaction where the environment provides no feedback. This contrasts with many real-world domains, such as software engineering (SWE), which require rich multi-turn interactions with a stateful environment that responds to each action with a non-trivial observation. To bridge this gap, we demonstrate the successful application of RL to this general regime. Using a modified Decoupled Advantage Policy Optimization (DAPO) algorithm, we train an agent based on Qwen2.5-72B-Instruct to solve real-world software engineering tasks. Our approach increases the agent's success rate on the SWE-bench Verified benchmark from a 20% rejection fine-tuned baseline to 39%, without relying on any teacher models. On SWE-rebench, our agent matches or outperforms leading open-weight models such as DeepSeek-V3-0324 and Qwen3-235B-A22B using an identical scaffolding, offering a viable path toward building more capable autonomous agents for complex real-world problems based on open models.

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

Human experts excel at fine-grained visual discrimination by leveraging domain knowledge to refine perceptual features, a capability that remains underdeveloped in current Multimodal Large Language Models (MLLMs). Despite possessing vast expert-level knowledge, MLLMs struggle to integrate reasoning into visual perception, often generating direct responses without deeper analysis. To bridge this gap, we introduce knowledge-intensive visual grounding (KVG), a novel visual grounding task that requires both fine-grained perception and domain-specific knowledge integration. To address the challenges of KVG, we propose DeepPerception, an MLLM enhanced with cognitive visual perception capabilities. Our approach consists of (1) an automated data synthesis pipeline that generates high-quality, knowledge-aligned training samples, and (2) a two-stage training framework combining supervised fine-tuning for cognitive reasoning scaffolding and reinforcement learning to optimize perception-cognition synergy. To benchmark performance, we introduce KVG-Bench a comprehensive dataset spanning 10 domains with 1.3K manually curated test cases. Experimental results demonstrate that DeepPerception significantly outperforms direct fine-tuning, achieving +8.08\% accuracy improvements on KVG-Bench and exhibiting +4.60\% superior cross-domain generalization over baseline approaches. Our findings highlight the importance of integrating cognitive processes into MLLMs for human-like visual perception and open new directions for multimodal reasoning research. The data, codes, and models are released at https://github.com/thunlp/DeepPerception.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

We introduce MLE-bench, a benchmark for measuring how well AI agents perform at machine learning engineering. To this end, we curate 75 ML engineering-related competitions from Kaggle, creating a diverse set of challenging tasks that test real-world ML engineering skills such as training models, preparing datasets, and running experiments. We establish human baselines for each competition using Kaggle's publicly available leaderboards. We use open-source agent scaffolds to evaluate several frontier language models on our benchmark, finding that the best-performing setup--OpenAI's o1-preview with AIDE scaffolding--achieves at least the level of a Kaggle bronze medal in 16.9% of competitions. In addition to our main results, we investigate various forms of resource scaling for AI agents and the impact of contamination from pre-training. We open-source our benchmark code (github.com/openai/mle-bench/) to facilitate future research in understanding the ML engineering capabilities of AI agents.

Vision-language models (VLMs) have achieved strong results on coding and math benchmarks that are challenging for humans, yet their ability to perform tasks that come naturally to humans--such as perception, spatial navigation, and memory management--remains understudied. Real video games are crafted to be intuitive for humans to learn and master by leveraging innate inductive biases, making them an ideal testbed for evaluating such capabilities in VLMs. To this end, we introduce VideoGameBench, a benchmark consisting of 10 popular video games from the 1990s that VLMs directly interact with in real-time. VideoGameBench challenges models to complete entire games with access to only raw visual inputs and a high-level description of objectives and controls, a significant departure from existing setups that rely on game-specific scaffolding and auxiliary information. We keep three of the games secret to encourage solutions that generalize to unseen environments. Our experiments show that frontier vision-language models struggle to progress beyond the beginning of each game. We find inference latency to be a major limitation of frontier models in the real-time setting; therefore, we introduce VideoGameBench Lite, a setting where the game pauses while waiting for the LM's next action. The best performing model, Gemini 2.5 Pro, completes only 0.48% of VideoGameBench and 1.6% of VideoGameBench Lite. We hope that the formalization of the human skills mentioned above into this benchmark motivates progress in these research directions.

State-of-the-art AI systems can be significantly improved without expensive retraining via "post-training enhancements"-techniques applied after initial training like fine-tuning the system to use a web browser. We review recent post-training enhancements, categorizing them into five types: tool-use, prompting methods, scaffolding, solution selection, and data generation. Different enhancements improve performance on different tasks, making it hard to compare their significance. So we translate improvements from different enhancements into a common currency, the compute-equivalent gain: how much additional training compute would be needed to improve performance by the same amount as the enhancement. Our non-experimental work shows that post-training enhancements have significant benefits: most surveyed enhancements improve benchmark performance by more than a 5x increase in training compute, some by more than 20x. Post-training enhancements are relatively cheap to develop: fine-tuning costs are typically <1% of the original training cost. Governing the development of capable post-training enhancements may be challenging because frontier models could be enhanced by a wide range of actors.

Designing antibody sequences to better resemble those observed in natural human repertoires is a key challenge in biologics development. We introduce IgCraft: a multi-purpose model for paired human antibody sequence generation, built on Bayesian Flow Networks. IgCraft presents one of the first unified generative modeling frameworks capable of addressing multiple antibody sequence design tasks with a single model, including unconditional sampling, sequence inpainting, inverse folding, and CDR motif scaffolding. Our approach achieves competitive results across the full spectrum of these tasks while constraining generation to the space of human antibody sequences, exhibiting particular strengths in CDR motif scaffolding (grafting) where we achieve state-of-the-art performance in terms of humanness and preservation of structural properties. By integrating previously separate tasks into a single scalable generative model, IgCraft provides a versatile platform for sampling human antibody sequences under a variety of contexts relevant to antibody discovery and engineering. Model code and weights are publicly available at github.com/mgreenig/IgCraft.

Recently, language models like Llama 3.1 Instruct have become increasingly capable of agentic behavior, enabling them to perform tasks requiring short-term planning and tool use. In this study, we apply refusal-vector ablation to Llama 3.1 70B and implement a simple agent scaffolding to create an unrestricted agent. Our findings imply that these refusal-vector ablated models can successfully complete harmful tasks, such as bribing officials or crafting phishing attacks, revealing significant vulnerabilities in current safety mechanisms. To further explore this, we introduce a small Safe Agent Benchmark, designed to test both harmful and benign tasks in agentic scenarios. Our results imply that safety fine-tuning in chat models does not generalize well to agentic behavior, as we find that Llama 3.1 Instruct models are willing to perform most harmful tasks without modifications. At the same time, these models will refuse to give advice on how to perform the same tasks when asked for a chat completion. This highlights the growing risk of misuse as models become more capable, underscoring the need for improved safety frameworks for language model agents.

The powerful generative capacity of Large Language Models (LLMs) has instigated a paradigm shift in recommendation. However, existing generative models (e.g., OneRec) operate as implicit predictors, critically lacking the capacity for explicit and controllable reasoning-a key advantage of LLMs. To bridge this gap, we propose OneRec-Think, a unified framework that seamlessly integrates dialogue, reasoning, and personalized recommendation. OneRec-Think incorporates: (1) Itemic Alignment: cross-modal Item-Textual Alignment for semantic grounding; (2) Reasoning Activation: Reasoning Scaffolding to activate LLM reasoning within the recommendation context; and (3) Reasoning Enhancement, where we design a recommendation-specific reward function that accounts for the multi-validity nature of user preferences. Experiments across public benchmarks show state-of-the-art performance. Moreover, our proposed "Think-Ahead" architecture enables effective industrial deployment on Kuaishou, achieving a 0.159\% gain in APP Stay Time and validating the practical efficacy of the model's explicit reasoning capability.

Vision-Language-Action (VLA) models have achieved notable success but often struggle with limited generalizations. To address this, integrating generalized Vision-Language Models (VLMs) as assistants to VLAs has emerged as a popular solution. However, current approaches often combine these models in rigid, sequential structures: using VLMs primarily for high-level scene understanding and task planning, and VLAs merely as executors of lower-level actions, leading to ineffective collaboration and poor grounding challenges. In this paper, we propose an embodied agent framework, PhysiAgent, tailored to operate effectively in physical environments. By incorporating monitor, memory, self-reflection mechanisms, and lightweight off-the-shelf toolboxes, PhysiAgent offers an autonomous scaffolding framework to prompt VLMs to organize different components based on real-time proficiency feedback from VLAs to maximally exploit VLAs' capabilities. Experimental results demonstrate significant improvements in task-solving performance on complex real-world robotic tasks, showcasing effective self-regulation of VLMs, coherent tool collaboration, and adaptive evolution of the framework during execution. PhysiAgent makes practical and pioneering efforts to integrate VLMs and VLAs, effectively grounding embodied agent frameworks in real-world settings.

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.

This paper presents a study of using large language models (LLMs) in modifying existing code. While LLMs for generating code have been widely studied, their role in code modification remains less understood. Although "prompting" serves as the primary interface for developers to communicate intents to LLMs, constructing effective prompts for code modification introduces challenges different from generation. Prior work suggests that natural language summaries may help scaffold this process, yet such approaches have been validated primarily in narrow domains like SQL rewriting. This study investigates two prompting strategies for LLM-assisted code modification: Direct Instruction Prompting, where developers describe changes explicitly in free-form language, and Summary-Mediated Prompting, where changes are made by editing the generated summaries of the code. We conducted an exploratory study with 15 developers who completed modification tasks using both techniques across multiple scenarios. Our findings suggest that developers followed an iterative workflow: understanding the code, localizing the edit, and validating outputs through execution or semantic reasoning. Each prompting strategy presented trade-offs: direct instruction prompting was more flexible and easier to specify, while summary-mediated prompting supported comprehension, prompt scaffolding, and control. Developers' choice of strategy was shaped by task goals and context, including urgency, maintainability, learning intent, and code familiarity. These findings highlight the need for more usable prompt interactions, including adjustable summary granularity, reliable summary-code traceability, and consistency in generated summaries.

If AI models can detect when they are being evaluated, the effectiveness of evaluations might be compromised. For example, models could have systematically different behavior during evaluations, leading to less reliable benchmarks for deployment and governance decisions. We investigate whether frontier language models can accurately classify transcripts based on whether they originate from evaluations or real-world deployment, a capability we call evaluation awareness. To achieve this, we construct a diverse benchmark of 1,000 prompts and transcripts from 61 distinct datasets. These span public benchmarks (e.g., MMLU, SWEBench), real-world deployment interactions, and agent trajectories from scaffolding frameworks (e.g., web-browsing agents). Frontier models clearly demonstrate above-random evaluation awareness (Gemini-2.5-Pro reaches an AUC of 0.83), but do not yet surpass our simple human baseline (AUC of 0.92). Furthermore, both AI models and humans are better at identifying evaluations in agentic settings compared to chat settings. Additionally, we test whether models can identify the purpose of the evaluation. Under multiple-choice and open-ended questioning, AI models far outperform random chance in identifying what an evaluation is testing for. Our results indicate that frontier models already exhibit a substantial, though not yet superhuman, level of evaluation-awareness. We recommend tracking this capability in future models.

Reparameterized diffusion models (RDMs) have recently matched autoregressive methods in protein generation, motivating their use for challenging tasks such as designing membrane proteins, which possess interleaved soluble and transmembrane (TM) regions. We introduce the Membrane Diffusion Language Model (MemDLM), a fine-tuned RDM-based protein language model that enables controllable membrane protein sequence design. MemDLM-generated sequences recapitulate the TM residue density and structural features of natural membrane proteins, achieving comparable biological plausibility and outperforming state-of-the-art diffusion baselines in motif scaffolding tasks by producing lower perplexity, higher BLOSUM-62 scores, and improved pLDDT confidence. To enhance controllability, we develop Per-Token Guidance (PET), a novel classifier-guided sampling strategy that selectively solubilizes residues while preserving conserved TM domains, yielding sequences with reduced TM density but intact functional cores. Importantly, MemDLM designs validated in TOXCAT beta-lactamase growth assays demonstrate successful TM insertion, distinguishing high-quality generated sequences from poor ones. Together, our framework establishes the first experimentally-validated diffusion-based model for rational membrane protein generation, integrating de novo design, motif scaffolding, and targeted property optimization.

Language models trained on internet-scale data sets have shown an impressive ability to solve problems in Natural Language Processing and Computer Vision. However, experience is showing that these models are frequently brittle in unexpected ways, and require significant scaffolding to ensure that they operate correctly in the larger systems that comprise "language-model agents." In this paper, we argue that behavior trees provide a unifying framework for combining language models with classical AI and traditional programming. We introduce Dendron, a Python library for programming language model agents using behavior trees. We demonstrate the approach embodied by Dendron in three case studies: building a chat agent, a camera-based infrastructure inspection agent for use on a mobile robot or vehicle, and an agent that has been built to satisfy safety constraints that it did not receive through instruction tuning or RLHF.

The Teacher-Student Chatroom Corpus (TSCC) is a collection of written conversations captured during one-to-one lessons between teachers and learners of English. The lessons took place in an online chatroom and therefore involve more interactive, immediate and informal language than might be found in asynchronous exchanges such as email correspondence. The fact that the lessons were one-to-one means that the teacher was able to focus exclusively on the linguistic abilities and errors of the student, and to offer personalised exercises, scaffolding and correction. The TSCC contains more than one hundred lessons between two teachers and eight students, amounting to 13.5K conversational turns and 133K words: it is freely available for research use. We describe the corpus design, data collection procedure and annotations added to the text. We perform some preliminary descriptive analyses of the data and consider possible uses of the TSCC.

We explore using T5 (Raffel et al. (2019)) to directly translate natural language questions into SQL statements. General purpose natural language that interfaces to information stored within databases requires flexibly translating natural language questions into database queries. The best performing text-to-SQL systems approach this task by first converting questions into an intermediate logical form (LF) (Lyu et al. (2020)). While LFs provide a convenient intermediate representation and simplify query generation, they introduce an additional layer of complexity and annotation requirements. However, weakly supervised modeling that directly converts questions to SQL statements has proven more difficult without the scaffolding provided by LFs (Min et al. (2019)). We approach direct conversion of questions to SQL statements using T5 (Raffel et al. (2019)), a pre-trained textto-text generation model, modified to support pointer-generator style decoding (See et al. (2017)). We explore using question augmentation with table schema information and the use of automatically generated silver training data. The resulting model achieves 90.5% execution accuracy on the WikiSQL (Zhong et al. (2017)) test data set, a new state-of-the-art on weakly supervised SQL generation. The performance improvement is 6.6% absolute over the prior state-of-the-art (Min et al. (2019)) and approaches the performance of state-ofthe-art systems making use of LFs.

In-Context Learning (ICL) enables transformer-based language models to adapt to new tasks by conditioning on demonstration examples. However, traditional example-driven in-context learning lacks explicit modules for knowledge retrieval and transfer at the abstraction level. Inspired by cognitive science, specifically schema theory, which holds that humans interpret new information by activating pre-existing mental frameworks (schemas) to structure understanding, we introduce SCHEMA ACTIVATED IN CONTEXT LEARNING (SA-ICL). This framework extracts the representation of the building blocks of cognition for the reasoning process instilled from prior examples, creating an abstracted schema, a lightweight, structured template of key inferential steps and their relationships, which is then used to augment a model's reasoning process when presented with a novel question. We demonstrate that a broad range of large language models (LLMs) lack the capacity to form and utilize internal schema-based learning representations implicitly, but instead benefit significantly from explicit schema-based scaffolding. Across chemistry and physics questions from the GPQA dataset, our experiments show that SA-ICL consistently boosts performance, up to 36.19 percent, when the single demonstration example is of high quality, which simultaneously reduces reliance on the number of demonstrations and enhances interpretability. SCHEMA ACTIVATED IN CONTEXT LEARNING not only bridges disparate ICL strategies ranging from pattern priming to Chain-of-Thought prompting, but also paves a new path for enhancing human-like reasoning in LLMs.