作者Can Polat, Mustafa Kurban, Erchin Serpedin, Hasan Kurban
Large language models confabulate chemical objects (molecular formulas, space groups, formation energies) in fluent reasoning traces, concentrated on long-tail entities where confidence is least trustworthy. Deterministic, database-grounded verification can catch and repair such errors without the coverage cost of blanket retrieval; the binding constraint, we find, is detection, not repair. Our tiered verifier extracts each checkable claim, checks it against authoritative databases and physics, and feeds the reference into a gated correction loop. Across four models and 528 condition-pinned prompts, gated correction cuts committed-formula error from 22% to 4% at $3.2\times$ fewer retrievals than blanket augmentation, beating a conversational oracle. Repair succeeds wherever a flag fires (80--97%); the bottleneck is in-loop detection recall. Grounding improves the final answer only when the verifier's scope reaches the deliverable (83% to 90%), and the lift appears only where extractable long-tail error exists: absent on near-ceiling physical constants, large on isotope half-lives (11% to 0%).
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Large language models confabulate chemical objects (molecular formulas, space groups, formation energies) in fluent reasoning traces, concentrated on long-tail entities where confidence is least trustworthy. Deterministic, database-grounded verification can catch and repair such errors without the coverage cost of blanket retrieval; the binding constraint, we find, is detection, not repair. Our tiered verifier extracts each checkable claim, checks it against authoritative databases and physics, and feeds the reference into a gated correction loop. Across four models and 528 condition-pinned prompts, gated correction cuts committed-formula error from 22% to 4% at $3.2\times$ fewer retrievals than blanket augmentation, beating a conversational oracle. Repair succeeds wherever a flag fires (80--97%); the bottleneck is in-loop detection recall. Grounding improves the final answer only when the verifier's scope reaches the deliverable (83% to 90%), and the lift appears only where extractable long-tail error exists: absent on near-ceiling physical constants, large on isotope half-lives (11% to 0%).
We present a continuous geometric framework that models the discrete algebraic operations of the Transformer architecture as an integro-differential equation (IDE) on a semantic fiber bundle $\calE = \calM \times \R^d$. Beginning from a single geometric axiom — that the token sequence forms a discrete $1$-manifold equipped with a canonical measure lattice — we translate every core component of the modern Transformer (RMSNorm, RoPE, Softmax Attention, FFN, Residual Stream, SGD, Weight Decay) into a cohesive vocabulary of differential geometry, measure theory, and stochastic calculus. The resulting framework yields quantitative predictions spanning entropic optimal transport (Attention as a Schrödinger bridge) and non-equilibrium thermodynamics (SGD as Itô diffusion violating detailed balance). We conduct a six-part experimental campaign across five architectures (Qwen3, LLaMA\nobreakdash-3.1, Gemma\nobreakdash-3, GPT-2, Mistral) spanning $124$M to $8$B parameters. The empirical observables are quantitatively consistent with the geometric predictions: the $ε^{-1/2}$ Lipschitz scaling calibration at machine precision ($R^2 = 1.000$), the Lie--Trotter operator-splitting torsion, the symmetric ablation instability confirming the Dual-Law of Topological Stability, the $\calO(1/\sqrt{k})$ thermodynamic suppression of Poincaré recurrence on the RoPE torus, the thermodynamic context-limit phase transition, and the Non-Equilibrium Steady State parameter vortex — verified across two optimizers (AdamW and Pure SGD) to exclude momentum artifacts. The results demonstrate that analyzing Transformers through the lens of continuous stochastic differential geometry provides a predictive descriptive vocabulary for the stability limits, context bounds, and optimization dynamics of Large Language Models.
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We present a continuous geometric framework that models the discrete algebraic operations of the Transformer architecture as an integro-differential equation (IDE) on a semantic fiber bundle $\calE = \calM \times \R^d$. Beginning from a single geometric axiom — that the token sequence forms a discrete $1$-manifold equipped with a canonical measure lattice — we translate every core component of the modern Transformer (RMSNorm, RoPE, Softmax Attention, FFN, Residual Stream, SGD, Weight Decay) into a cohesive vocabulary of differential geometry, measure theory, and stochastic calculus. The resulting framework yields quantitative predictions spanning entropic optimal transport (Attention as a Schrödinger bridge) and non-equilibrium thermodynamics (SGD as Itô diffusion violating detailed balance). We conduct a six-part experimental campaign across five architectures (Qwen3, LLaMA\nobreakdash-3.1, Gemma\nobreakdash-3, GPT-2, Mistral) spanning $124$M to $8$B parameters. The empirical observables are quantitatively consistent with the geometric predictions: the $ε^{-1/2}$ Lipschitz scaling calibration at machine precision ($R^2 = 1.000$), the Lie--Trotter operator-splitting torsion, the symmetric ablation instability confirming the Dual-Law of Topological Stability, the $\calO(1/\sqrt{k})$ thermodynamic suppression of Poincaré recurrence on the RoPE torus, the thermodynamic context-limit phase transition, and the Non-Equilibrium Steady State parameter vortex — verified across two optimizers (AdamW and Pure SGD) to exclude momentum artifacts. The results demonstrate that analyzing Transformers through the lens of continuous stochastic differential geometry provides a predictive descriptive vocabulary for the stability limits, context bounds, and optimization dynamics of Large Language Models.
Analytical placers rely on differentiable objective functions to guide placement, typically combining intermediate surrogate metrics such as half-perimeter wirelength (HPWL) and cell-density penalties. However, these placement-stage surrogates remain misaligned with downstream routed and timing quality. Prior work reduces this gap with human-designed terms or learned black-box surrogates, but the former requires expert retuning and the latter is difficult to explain, debug, or deploy in analytical placement flows. CoEvoP&R addresses these limitations with a large language model (LLM)-based framework that automatically evolves analytical placement objectives. At each generation, the prompt combines the restricted objective interface, baseline context, and archived prior candidates with routing-related feedback from placement, timing proxy, and routing tools. The LLM proposes readable differentiable objectives, which are embedded and validated in DREAMPlace, evaluated through a timing proxy and an actual router, and stored with their feedback to guide later generations. Across eight ChiP-Bench Nangate45 designs and three seeds, CoEvoP&R reduces post-route routed wirelength and congestion by 16.9% and 36.7%, with gains of 0.70 ns in worst negative slack and a 912 ns reduction in total negative slack magnitude over native DREAMPlace. Across eight ICCAD 2015 Superblue designs, it reduces post-route routed wirelength and congestion by 5.4% and 23.2%. Code is available at https://github.com/FCHXWH823/CoEvoP-R.git.
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Analytical placers rely on differentiable objective functions to guide placement, typically combining intermediate surrogate metrics such as half-perimeter wirelength (HPWL) and cell-density penalties. However, these placement-stage surrogates remain misaligned with downstream routed and timing quality. Prior work reduces this gap with human-designed terms or learned black-box surrogates, but the former requires expert retuning and the latter is difficult to explain, debug, or deploy in analytical placement flows. CoEvoP&R addresses these limitations with a large language model (LLM)-based framework that automatically evolves analytical placement objectives. At each generation, the prompt combines the restricted objective interface, baseline context, and archived prior candidates with routing-related feedback from placement, timing proxy, and routing tools. The LLM proposes readable differentiable objectives, which are embedded and validated in DREAMPlace, evaluated through a timing proxy and an actual router, and stored with their feedback to guide later generations. Across eight ChiP-Bench Nangate45 designs and three seeds, CoEvoP&R reduces post-route routed wirelength and congestion by 16.9% and 36.7%, with gains of 0.70 ns in worst negative slack and a 912 ns reduction in total negative slack magnitude over native DREAMPlace. Across eight ICCAD 2015 Superblue designs, it reduces post-route routed wirelength and congestion by 5.4% and 23.2%. Code is available at https://github.com/FCHXWH823/CoEvoP-R.git.
作者Cheng Yan, Guangyang Ye, Wuyang Zhang, Fan Xu, Zhijun Fan, Xiang Xia, Yanyong Zhang
Test-time scaling empowers Large Reasoning Models (LRMs) to tackle complex tasks via extensive Chain-of-Thought (CoT). However, this often induces the "overthinking" paradox, where redundant reasoning increases computational overhead without guaranteeing accuracy. Existing test-time efficiency optimization methods primarily fall into two categories: information-theoretic approaches, which are prone to "deceptive convergence" where low uncertainty masks hallucinations, and latent representation analyses, which are often post-hoc, lacking the real-time sensitivity for dynamic reasoning. To bridge this gap, we first posit the Phase-Momentum Alignment Hypothesis, asserting that reasoning correctness hinges on the temporal synchronization between geometric momentum and uncertainty resolution. We then theoretically formulate the Cognitive-Energy Model to characterize these dynamics through two orthogonal dimensions: Geometric Cognitive Effort, quantified by latent velocity and tortuosity, and Entropic Cognitive Uncertainty. To operationalize this, we introduce PUMA (Phase-Uncertainty Momentum Alignment), a training-free framework employing a tiered diagnostic architecture. By coupling lightweight phase monitoring with event-triggered geometric analysis, PUMA effectively distinguishes active exploration from passive stagnation, enabling precise interventions through adaptive truncation or corrective measures. Extensive experiments on LRMs spanning 1.5B to 32B demonstrate that PUMA consistently outperforms state-of-the-art baselines across diverse benchmarks, achieving a superior accuracy-efficiency trade-off and robust cross-domain generalization.
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Test-time scaling empowers Large Reasoning Models (LRMs) to tackle complex tasks via extensive Chain-of-Thought (CoT). However, this often induces the "overthinking" paradox, where redundant reasoning increases computational overhead without guaranteeing accuracy. Existing test-time efficiency optimization methods primarily fall into two categories: information-theoretic approaches, which are prone to "deceptive convergence" where low uncertainty masks hallucinations, and latent representation analyses, which are often post-hoc, lacking the real-time sensitivity for dynamic reasoning. To bridge this gap, we first posit the Phase-Momentum Alignment Hypothesis, asserting that reasoning correctness hinges on the temporal synchronization between geometric momentum and uncertainty resolution. We then theoretically formulate the Cognitive-Energy Model to characterize these dynamics through two orthogonal dimensions: Geometric Cognitive Effort, quantified by latent velocity and tortuosity, and Entropic Cognitive Uncertainty. To operationalize this, we introduce PUMA (Phase-Uncertainty Momentum Alignment), a training-free framework employing a tiered diagnostic architecture. By coupling lightweight phase monitoring with event-triggered geometric analysis, PUMA effectively distinguishes active exploration from passive stagnation, enabling precise interventions through adaptive truncation or corrective measures. Extensive experiments on LRMs spanning 1.5B to 32B demonstrate that PUMA consistently outperforms state-of-the-art baselines across diverse benchmarks, achieving a superior accuracy-efficiency trade-off and robust cross-domain generalization.
Large language models (LLMs) and agentic AI are shifting software engineering from manual coding toward intent specification, architecture, and governance. Two paradigms have emerged: vibe coding, an intuition-driven approach accepting AI artifacts via observed behavior, and Specification-Driven Development (SDD), which uses structured specifications as the authoritative source of truth. This article makes three contributions. First, based on a verified literature corpus, it identifies failure modes of ungoverned conversational generation: the productivity-reliability paradox, architectural erosion from limited context, security exposure, and technical debt. Second, it introduces the Specification Governance Reference Model (SGRM). This tool-independent framework defines four-component specification contracts, constrains stochastic generation via deterministic validation, formalizes three rigor levels, and integrates generation, verification, and governance into a closed-loop architecture. Third, it evaluates SGRM against ISO/IEC 25010, mapping quality characteristics to governance mechanisms. Empirical evidence supports this, reporting a 73% reduction in security defects under constitutional constraints and a 50% reduction in time-to-market through specification-governed agentic delivery. The analysis concludes that while vibe coding is valuable for ideation and rapid prototyping, enterprise software requires specification governance to transform probabilistic AI generation into deterministic, auditable engineering. Boundary conditions, threats to validity, and future research directions are discussed.
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Large language models (LLMs) and agentic AI are shifting software engineering from manual coding toward intent specification, architecture, and governance. Two paradigms have emerged: vibe coding, an intuition-driven approach accepting AI artifacts via observed behavior, and Specification-Driven Development (SDD), which uses structured specifications as the authoritative source of truth. This article makes three contributions. First, based on a verified literature corpus, it identifies failure modes of ungoverned conversational generation: the productivity-reliability paradox, architectural erosion from limited context, security exposure, and technical debt. Second, it introduces the Specification Governance Reference Model (SGRM). This tool-independent framework defines four-component specification contracts, constrains stochastic generation via deterministic validation, formalizes three rigor levels, and integrates generation, verification, and governance into a closed-loop architecture. Third, it evaluates SGRM against ISO/IEC 25010, mapping quality characteristics to governance mechanisms. Empirical evidence supports this, reporting a 73% reduction in security defects under constitutional constraints and a 50% reduction in time-to-market through specification-governed agentic delivery. The analysis concludes that while vibe coding is valuable for ideation and rapid prototyping, enterprise software requires specification governance to transform probabilistic AI generation into deterministic, auditable engineering. Boundary conditions, threats to validity, and future research directions are discussed.
作者Nadine Chang, Maying Shen, Shizhe Diao, Jialiang Wang, Jingde Chen, Thomas Breuel, Pavlo Molchanov, Rafid Mahmood, Jose M. Alvarez
We propose a language representation for multimodal data in which any observation, whether image, video, or text, is expressed as a bag of atomic propositions, simple statements about the entities, actions, and relations in a scene. A global semantic codebook unifies these into a shared vocabulary of canonical atomic propositions, placing every modality and observation into one interpretable space that spans fine grained facts to high level concepts and composes into richer ones. This brings interpretability with reasoning, cross-modal understanding and retrieval, and compositionality that enables complex multimodal understanding, rich data curation and complex structured retrieval. We demonstrate the framework on autonomous driving and open-world data.
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We propose a language representation for multimodal data in which any observation, whether image, video, or text, is expressed as a bag of atomic propositions, simple statements about the entities, actions, and relations in a scene. A global semantic codebook unifies these into a shared vocabulary of canonical atomic propositions, placing every modality and observation into one interpretable space that spans fine grained facts to high level concepts and composes into richer ones. This brings interpretability with reasoning, cross-modal understanding and retrieval, and compositionality that enables complex multimodal understanding, rich data curation and complex structured retrieval. We demonstrate the framework on autonomous driving and open-world data.
Bürger et al. (2024) demonstrated that truth representations in large language models are universal across statement polarity but reside within a multidimensional subspace. We extend this framework along three questions: how the dimensionality of the subspace depends on the model's knowledge, which architectural component builds the truth direction, and what the direction is a mixture of. In Part I, a training-free directional probe derived from the SVD of hidden-state minimal pairs shows that the dimensionality of truth is knowledge-dependent: the signal concentrates on a single axis for known facts and diffuses as knowledge decreases. In Part II, a relational law emerges across multiple model families: attention propagates truth frames, the feed-forward network opposes the current block's frame, and post-peak decay is causally attributed to the SwiGLU value stream. Furthermore, per-category truth axes form a semantically signed arrangement that converges across families. Stress tests expose a sign instability in this orientation, which we repair with a spectral consensus gauge to sharpen the convergence into a knowledge-gated law. Finally, a replication campaign on Gemma-2-2b, extending our decomposition tools to accommodate its sandwich normalization, confirms these laws and attributions. We quantify the knowledge gate as classical attenuation and isolate a stable, model-specific private geometry.
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Bürger et al. (2024) demonstrated that truth representations in large language models are universal across statement polarity but reside within a multidimensional subspace. We extend this framework along three questions: how the dimensionality of the subspace depends on the model's knowledge, which architectural component builds the truth direction, and what the direction is a mixture of. In Part I, a training-free directional probe derived from the SVD of hidden-state minimal pairs shows that the dimensionality of truth is knowledge-dependent: the signal concentrates on a single axis for known facts and diffuses as knowledge decreases. In Part II, a relational law emerges across multiple model families: attention propagates truth frames, the feed-forward network opposes the current block's frame, and post-peak decay is causally attributed to the SwiGLU value stream. Furthermore, per-category truth axes form a semantically signed arrangement that converges across families. Stress tests expose a sign instability in this orientation, which we repair with a spectral consensus gauge to sharpen the convergence into a knowledge-gated law. Finally, a replication campaign on Gemma-2-2b, extending our decomposition tools to accommodate its sandwich normalization, confirms these laws and attributions. We quantify the knowledge gate as classical attenuation and isolate a stable, model-specific private geometry.
Despite the impressive generative capabilities of text-to-image diffusion models, they remain vulnerable to implicit sexual prompts, where subtle cues disguised as benign terms or adversarial tokens unexpectedly generate the inappropriate content due to model biases or latent correlations in training data. Existing safety mechanisms face fundamental limitations: detection methods primarily identify explicit content and fail to capture implicit malicious intent, while mitigation approaches rely on static negative prompts inadequate for diverse implicit scenarios. To address these challenges, we propose UniNDM, a unified noise-driven framework that rethinks safety mechanisms through the lens of noise dynamics in diffusion processes. Our key insight is that early-stage predicted noise exhibits inherent separability between normal and sexually explicit content, which we theoretically demonstrates quadratically increasing semantic concentration with timestep. Leveraging this property, we develop a lightweight noise-based detector achieving superior accuracy with virtually no computational overhead. For mitigation, we introduce noise-enhanced adaptive negative guidance: dynamically generating context-specific negative prompts via large language models to handle diverse implicit content, while optimizing initial noise by suppressing attention concentration on explicit tokens to provide comprehensive protection. Besides the U-Net-based diffusion models, we further extend our framework to emerging Diffusion Transformer architectures through region-constrained semantic guidance tailored for their unified multimodal attention. Comprehensive experiments across U-Net models and DiT models on both natural and adversarial datasets demonstrate substantial improvements over state-of-the-art methods, including SLD, UCE, Safree, etc. Our code is publicly available at https://github.com/Aries-iai/UniNDM.
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Despite the impressive generative capabilities of text-to-image diffusion models, they remain vulnerable to implicit sexual prompts, where subtle cues disguised as benign terms or adversarial tokens unexpectedly generate the inappropriate content due to model biases or latent correlations in training data. Existing safety mechanisms face fundamental limitations: detection methods primarily identify explicit content and fail to capture implicit malicious intent, while mitigation approaches rely on static negative prompts inadequate for diverse implicit scenarios. To address these challenges, we propose UniNDM, a unified noise-driven framework that rethinks safety mechanisms through the lens of noise dynamics in diffusion processes. Our key insight is that early-stage predicted noise exhibits inherent separability between normal and sexually explicit content, which we theoretically demonstrates quadratically increasing semantic concentration with timestep. Leveraging this property, we develop a lightweight noise-based detector achieving superior accuracy with virtually no computational overhead. For mitigation, we introduce noise-enhanced adaptive negative guidance: dynamically generating context-specific negative prompts via large language models to handle diverse implicit content, while optimizing initial noise by suppressing attention concentration on explicit tokens to provide comprehensive protection. Besides the U-Net-based diffusion models, we further extend our framework to emerging Diffusion Transformer architectures through region-constrained semantic guidance tailored for their unified multimodal attention. Comprehensive experiments across U-Net models and DiT models on both natural and adversarial datasets demonstrate substantial improvements over state-of-the-art methods, including SLD, UCE, Safree, etc. Our code is publicly available at https://github.com/Aries-iai/UniNDM.
作者Sharath Naganna, Tanvir Ahmed Sijan, Uddipta Kalita
Large language models often succeed on one formulation of a problem while failing on an equivalent formulation. Whether these failures arise from distinct internal circuits or different activation states of a shared circuit remains unknown. Recent mechanistic interpretability studies suggest that arithmetic in LLMs emerges from a "bag of heuristics," encoded by a sparse set of MLP neurons that represent distinct arithmetic strategies. We investigate whether arithmetic heuristic neurons are form-invariant across symbolic arithmetic, natural language word problems, and Python code in three Llama-3 models. In each format, we identify arithmetic heuristic neurons using a two-stage pipeline combining attribution patching and activation patching. A compact set of neurons is shared across all three formats, and targeted interventions show this shared circuit is both necessary and sufficient for late-layer arithmetic computation. Transferring the shared neurons' activations from a successful execution in one format to a failed execution in another recovers most incorrect predictions, exceeding 97% for addition and subtraction, indicating that cross-format failures arise from activation states rather than distinct circuits. Moreover, shared neurons consistently belong to the same heuristic families across formats, demonstrating that arithmetic computation in LLMs is largely form-invariant at the neuron level.
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Large language models often succeed on one formulation of a problem while failing on an equivalent formulation. Whether these failures arise from distinct internal circuits or different activation states of a shared circuit remains unknown. Recent mechanistic interpretability studies suggest that arithmetic in LLMs emerges from a "bag of heuristics," encoded by a sparse set of MLP neurons that represent distinct arithmetic strategies. We investigate whether arithmetic heuristic neurons are form-invariant across symbolic arithmetic, natural language word problems, and Python code in three Llama-3 models. In each format, we identify arithmetic heuristic neurons using a two-stage pipeline combining attribution patching and activation patching. A compact set of neurons is shared across all three formats, and targeted interventions show this shared circuit is both necessary and sufficient for late-layer arithmetic computation. Transferring the shared neurons' activations from a successful execution in one format to a failed execution in another recovers most incorrect predictions, exceeding 97% for addition and subtraction, indicating that cross-format failures arise from activation states rather than distinct circuits. Moreover, shared neurons consistently belong to the same heuristic families across formats, demonstrating that arithmetic computation in LLMs is largely form-invariant at the neuron level.
Large language models frequently violate fundamental scientific principles when generating technical content, undermining their reliability in scientific applications. We introduce Scientific Feasibility Control SFC, a graph-structured conformal prediction framework that provides statistical guarantees for scientific reasoning validity through progressive absolute-coherent-factuality validation. Our approach decomposes scientific reasoning into atomic absolute-coherent-factuality units requiring both individual correctness against physical laws and logical substantiation from preceding context, addressing the cascade effect where early scientific errors contaminate subsequent reasoning steps. Unlike independence-based methods that treat claims in isolation, SFC models logical dependencies as approximate deducibility graphs and operates through real-time validation with dynamic branching when scientific violations are detected, the system branches to alternative generation paths using verified context as foundation. We demonstrate SFC across established scientific reasoning benchmarks including PhyX multimodal physics, MATH, ScienceQA, and ARC Challenge, achieving 50.1 percent accuracy on PhyX physics reasoning, substantially outperforming recent reasoning models including DeepSeek-R1 49.8 percent and GPT-4 45.8 percent while providing 91.7 percent scientific validity with formal conformal coverage guarantees at alpha equals 0.10 confidence level and reducing scientific law violations by 73 percent across multiple model architectures.
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Large language models frequently violate fundamental scientific principles when generating technical content, undermining their reliability in scientific applications. We introduce Scientific Feasibility Control SFC, a graph-structured conformal prediction framework that provides statistical guarantees for scientific reasoning validity through progressive absolute-coherent-factuality validation. Our approach decomposes scientific reasoning into atomic absolute-coherent-factuality units requiring both individual correctness against physical laws and logical substantiation from preceding context, addressing the cascade effect where early scientific errors contaminate subsequent reasoning steps. Unlike independence-based methods that treat claims in isolation, SFC models logical dependencies as approximate deducibility graphs and operates through real-time validation with dynamic branching when scientific violations are detected, the system branches to alternative generation paths using verified context as foundation. We demonstrate SFC across established scientific reasoning benchmarks including PhyX multimodal physics, MATH, ScienceQA, and ARC Challenge, achieving 50.1 percent accuracy on PhyX physics reasoning, substantially outperforming recent reasoning models including DeepSeek-R1 49.8 percent and GPT-4 45.8 percent while providing 91.7 percent scientific validity with formal conformal coverage guarantees at alpha equals 0.10 confidence level and reducing scientific law violations by 73 percent across multiple model architectures.
作者Gilchan Park, Guang Zhao, Byung-Jun Yoon, Shinjae Yoo
High-content morphological profiling (Cell Painting) yields sensitive, high-dimensional signatures of cellular state, but translating longitudinal morphology trajectories into interpretable biology remains difficult, especially for weak, chronic perturbations such as low-dose-rate ionizing radiation. Large language models (LLMs) can synthesize heterogeneous evidence into biological narratives, yet their scientific use requires quantitative auditing. We present an evaluation-first, retrieval-augmented interpretation framework for longitudinal Cell Painting morphology, applied to a 9-week RPE-1 time course across five dose rates (0.003--6.0 mGy/hr). Week-matched treated-control morphology deltas are combined with retrieved perturbation neighbors, pathway context, and literature evidence through stable evidence identifiers, enabling an LLM to generate structured, evidence-linked hypotheses that are hierarchically summarized while preserving provenance. We introduce two quantitative auditing tests: V1 citation validity, which verifies that cited evidence identifiers exist in the prompt, and V2 proxy-based morphology compatibility, which evaluates consistency between predicted biological processes and the most altered morphology features. In our experiments, V1 detected no invalid evidence references, while V2 showed meaningful morphology compatibility that increased with perturbation strength and was positively associated with an independent morphology drift summary. The framework produces auditable, falsifiable biological hypotheses, including an adaptive phenotype involving metabolic reprogramming and proteostatic stress at lower dose rates (0.003--0.3 mGy/hr). Current limitations include proxy-based evaluation and the lack of ground-truth mechanism labels.
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High-content morphological profiling (Cell Painting) yields sensitive, high-dimensional signatures of cellular state, but translating longitudinal morphology trajectories into interpretable biology remains difficult, especially for weak, chronic perturbations such as low-dose-rate ionizing radiation. Large language models (LLMs) can synthesize heterogeneous evidence into biological narratives, yet their scientific use requires quantitative auditing. We present an evaluation-first, retrieval-augmented interpretation framework for longitudinal Cell Painting morphology, applied to a 9-week RPE-1 time course across five dose rates (0.003--6.0 mGy/hr). Week-matched treated-control morphology deltas are combined with retrieved perturbation neighbors, pathway context, and literature evidence through stable evidence identifiers, enabling an LLM to generate structured, evidence-linked hypotheses that are hierarchically summarized while preserving provenance. We introduce two quantitative auditing tests: V1 citation validity, which verifies that cited evidence identifiers exist in the prompt, and V2 proxy-based morphology compatibility, which evaluates consistency between predicted biological processes and the most altered morphology features. In our experiments, V1 detected no invalid evidence references, while V2 showed meaningful morphology compatibility that increased with perturbation strength and was positively associated with an independent morphology drift summary. The framework produces auditable, falsifiable biological hypotheses, including an adaptive phenotype involving metabolic reprogramming and proteostatic stress at lower dose rates (0.003--0.3 mGy/hr). Current limitations include proxy-based evaluation and the lack of ground-truth mechanism labels.
Autoregressive language models are least accurate at the beginning of a sequence, where little context forces reliance on a generic pretraining prior. We show that this cold-start penalty is domain dependent and reduce it with a domain-conditional position offset: a single learned vector added to the embedding activation at the first sequence positions while all model weights remain frozen. The offset trains in minutes on roughly one hundred documents, switches between domains without added sequence state, and has no measurable latency overhead. Across eight Mamba, GPT-NeoX, and Llama models spanning 410M to 8B parameters, it reduces held-out in-domain perplexity by up to 27%; the effect persists at 70B, and one position captures most of the benefit. A matched, converged direct logit-bias correction reaches at most only 7.9% and leaves later-token loss unchanged, showing that the offset propagates through model state rather than merely recalibrating the output prior. A tuned LoRA reaches lower perplexity but uses two to three orders of magnitude more parameters and an active low-rank weight path, while soft prompts add sequence positions. With wrong-domain controls, offsets improve retrieval reranking and domain classification when decisions depend on early in-domain tokens, For the few-shot reasoning whose signal occurs later, the results maintains unchanged. Position-aware prefill application also help generation tasks, whereas naive application at every cached decoding step causes repetition. The offset is therefore not the strongest adapter, but a lightweight, hot switchable tool for short in-domain scoring and calibration.
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Autoregressive language models are least accurate at the beginning of a sequence, where little context forces reliance on a generic pretraining prior. We show that this cold-start penalty is domain dependent and reduce it with a domain-conditional position offset: a single learned vector added to the embedding activation at the first sequence positions while all model weights remain frozen. The offset trains in minutes on roughly one hundred documents, switches between domains without added sequence state, and has no measurable latency overhead. Across eight Mamba, GPT-NeoX, and Llama models spanning 410M to 8B parameters, it reduces held-out in-domain perplexity by up to 27%; the effect persists at 70B, and one position captures most of the benefit. A matched, converged direct logit-bias correction reaches at most only 7.9% and leaves later-token loss unchanged, showing that the offset propagates through model state rather than merely recalibrating the output prior. A tuned LoRA reaches lower perplexity but uses two to three orders of magnitude more parameters and an active low-rank weight path, while soft prompts add sequence positions. With wrong-domain controls, offsets improve retrieval reranking and domain classification when decisions depend on early in-domain tokens, For the few-shot reasoning whose signal occurs later, the results maintains unchanged. Position-aware prefill application also help generation tasks, whereas naive application at every cached decoding step causes repetition. The offset is therefore not the strongest adapter, but a lightweight, hot switchable tool for short in-domain scoring and calibration.
作者Shuhan Huang, Naifan Zhang, Yuanbo Tang, Yang Li, Wai Kin Victor Chan
Mixture-of-Experts (MoE) enables efficient scaling of Transformer models by routing tokens to a small subset of experts. However, existing routers typically condition expert selection on shallow or isolated token representations, which often produce unstable and semantically inconsistent routing decisions across layers. In this work, we revisit expert selection from a representation perspective and identify context incompleteness as a key bottleneck limiting effective expert specialization. To address this issue, we propose Multi-level Context Fusion MOE (MCF-MOE), a framework that constructs context-aware representations by integrating complementary signals from cross-layer semantic aggregation and local token-level interactions, enabling more informative and consistent expert selection. Experiments on language modeling and understanding benchmarks demonstrate that MCF-MOE consistently improves routing consistency and downstream performance over strong MoE baselines, highlighting the importance of contextual completeness in expert routing. The code is available at https://anonymous.4open.science/r/MCFMOE.
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Mixture-of-Experts (MoE) enables efficient scaling of Transformer models by routing tokens to a small subset of experts. However, existing routers typically condition expert selection on shallow or isolated token representations, which often produce unstable and semantically inconsistent routing decisions across layers. In this work, we revisit expert selection from a representation perspective and identify context incompleteness as a key bottleneck limiting effective expert specialization. To address this issue, we propose Multi-level Context Fusion MOE (MCF-MOE), a framework that constructs context-aware representations by integrating complementary signals from cross-layer semantic aggregation and local token-level interactions, enabling more informative and consistent expert selection. Experiments on language modeling and understanding benchmarks demonstrate that MCF-MOE consistently improves routing consistency and downstream performance over strong MoE baselines, highlighting the importance of contextual completeness in expert routing. The code is available at https://anonymous.4open.science/r/MCFMOE.
作者Boi Mai Quach, Binh T. Nguyen, Cathal Gurrin, Graham Healy
Language models (LMs) are trained to excel at predicting the next word in the sequence given prior context, and humans also share this predictability in reading comprehension. Neuroscience research reveals that next-word predictability influences brain response, as recorded at millisecond resolution using electroencephalography (EEG). While our evidence indicates that advanced LMs achieve accuracies closely aligned with human performance at the next-word prediction task, this raises the question: Does higher prediction accuracy necessarily mean that these models adequately capture the cognitive signals associated with human reading comprehension? Here, we generate regressors for both humans and LMs based on two information measures, including top-1 prediction and surprisal, to predict event-related potential (ERP) elicited from EEG recordings which reflect different stages of cognitive processing during reading. We argue that modelling ERP patterns offers fine-grained analysis of the cognitive plausibility of various LMs during reading. Our results indicate that only surprisal potentially correlates with language-processing ERPs, especially for open-class words with high semantic content. Moreover, our findings challenge the assumption that scaling LMs with increased parameters and computational budgets will consistently lead to improved convergence with human-like linguistic processing.
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Language models (LMs) are trained to excel at predicting the next word in the sequence given prior context, and humans also share this predictability in reading comprehension. Neuroscience research reveals that next-word predictability influences brain response, as recorded at millisecond resolution using electroencephalography (EEG). While our evidence indicates that advanced LMs achieve accuracies closely aligned with human performance at the next-word prediction task, this raises the question: Does higher prediction accuracy necessarily mean that these models adequately capture the cognitive signals associated with human reading comprehension? Here, we generate regressors for both humans and LMs based on two information measures, including top-1 prediction and surprisal, to predict event-related potential (ERP) elicited from EEG recordings which reflect different stages of cognitive processing during reading. We argue that modelling ERP patterns offers fine-grained analysis of the cognitive plausibility of various LMs during reading. Our results indicate that only surprisal potentially correlates with language-processing ERPs, especially for open-class words with high semantic content. Moreover, our findings challenge the assumption that scaling LMs with increased parameters and computational budgets will consistently lead to improved convergence with human-like linguistic processing.
We present a case study on proof-driven software understanding of mature, security-critical infrastructure. While formal methods are traditionally applied during the design phase, we present our experience applying formal reasoning onto a mature industrial C++ codebase. We focus on a formal analysis of the core algorithm that implements the Stellar blockchain's SDEX order book. By combining large language models (LLMs), Prototype Verification System (PVS), and SeaHorn, we are able to prove core properties of the production codebase. Our approach also identified an inconsistency in documentation related to the reachability of an exception location. Most importantly, however, we produce artifacts that make it easy for code changes to be checked against established invariants. This work demonstrates how the strategic combination of theorem proving and model checking provides a path for delivering robust assurance to legacy systems.
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We present a case study on proof-driven software understanding of mature, security-critical infrastructure. While formal methods are traditionally applied during the design phase, we present our experience applying formal reasoning onto a mature industrial C++ codebase. We focus on a formal analysis of the core algorithm that implements the Stellar blockchain's SDEX order book. By combining large language models (LLMs), Prototype Verification System (PVS), and SeaHorn, we are able to prove core properties of the production codebase. Our approach also identified an inconsistency in documentation related to the reachability of an exception location. Most importantly, however, we produce artifacts that make it easy for code changes to be checked against established invariants. This work demonstrates how the strategic combination of theorem proving and model checking provides a path for delivering robust assurance to legacy systems.
作者Yilin Wang, Xiangxi Zheng, Dongxing Mao, Linjie Li, Zhengyuan Yang, Ping Yu, Rui Yan, Yuan Yao, Alex Jinpeng Wang
Understanding long videos with multimodal large language models (MLLMs) requires selecting a compact set of frames from thousands of candidates, yet identifying the right frames seemingly requires understanding the video first. We resolve this circular dependency with a simple observation: cross-modal attention at validation-selected extraction layers in MLLMs already provides query-relevant frame evidence without requiring autoregressive generation. We exploit this property to build DAFS (Dynamic Attention-based Budget-aware Frame Selection), a training-free frame selector. A lightweight MLLM selector, even with only 2B parameters, can extract frame-level evidence by converting selected-layer attention into relevance scores through query-conditioned aggregation. This enables cross-frame comparison without autoregressive decoding. To handle the selector's own context constraint, we formulate the joint allocation of candidate pool size and per-frame token budget as a discrete optimization problem solved by dynamic programming. Under a 32-frame budget, our selector improves over uniform sampling by up to 6.4 points on Video-MME and outperforms prior training-based selectors under matched frame budgets, while generalizing across selector and answerer backbones, and across tasks, without retraining.
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Understanding long videos with multimodal large language models (MLLMs) requires selecting a compact set of frames from thousands of candidates, yet identifying the right frames seemingly requires understanding the video first. We resolve this circular dependency with a simple observation: cross-modal attention at validation-selected extraction layers in MLLMs already provides query-relevant frame evidence without requiring autoregressive generation. We exploit this property to build DAFS (Dynamic Attention-based Budget-aware Frame Selection), a training-free frame selector. A lightweight MLLM selector, even with only 2B parameters, can extract frame-level evidence by converting selected-layer attention into relevance scores through query-conditioned aggregation. This enables cross-frame comparison without autoregressive decoding. To handle the selector's own context constraint, we formulate the joint allocation of candidate pool size and per-frame token budget as a discrete optimization problem solved by dynamic programming. Under a 32-frame budget, our selector improves over uniform sampling by up to 6.4 points on Video-MME and outperforms prior training-based selectors under matched frame budgets, while generalizing across selector and answerer backbones, and across tasks, without retraining.
Prompt optimization adapts large language models (LLMs) without updating model parameters, but many automatic prompt optimizers remain heuristic search procedures over candidate instructions. This paper studies prompt optimization as Bayesian posterior sampling over discrete prompt tokens. We define a posterior distribution by combining a task likelihood term, which rewards prompts that explain input-output examples, with a language-model prior, which favors fluent instructions. This converts prompt optimization into an energy-based posterior sampling problem, for which gradients can be used to guide discrete Markov chain Monte Carlo (MCMC) proposals over vocabulary tokens. We refer to our framework as BayesPO, short for Bayesian Prompt Optimization. In this paper, BayesPO is instantiated with Markov chain Monte Carlo: it uses a Metropolis-Hastings corrected Gibbs-with-Langevin (GwL) proposal and integrates parallel tempering for global exploration of rugged LLM-induced energy landscapes. The concrete sampler further adapts the GwL sampler to the practical constraints of non-weight-tied LLM embeddings. Experiments with Qwen2.5 models show that the sampler discovers semantically meaningful prompts on diagnostic tasks, that parallel tempering helps escape a local optimum in a poetry completion task, and that post-optimizing APE prompts on 24 instruction-induction subtasks improves average accuracy from 60.04% to 63.23%. The study also reveals two main limitations: energy minimization may overfit small optimization sets, and the current sampler remains computationally expensive. These findings position Bayesian prompt sampling as a principled post-optimization tool and point to a promising direction for probabilistic prompt optimization.
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Prompt optimization adapts large language models (LLMs) without updating model parameters, but many automatic prompt optimizers remain heuristic search procedures over candidate instructions. This paper studies prompt optimization as Bayesian posterior sampling over discrete prompt tokens. We define a posterior distribution by combining a task likelihood term, which rewards prompts that explain input-output examples, with a language-model prior, which favors fluent instructions. This converts prompt optimization into an energy-based posterior sampling problem, for which gradients can be used to guide discrete Markov chain Monte Carlo (MCMC) proposals over vocabulary tokens. We refer to our framework as BayesPO, short for Bayesian Prompt Optimization. In this paper, BayesPO is instantiated with Markov chain Monte Carlo: it uses a Metropolis-Hastings corrected Gibbs-with-Langevin (GwL) proposal and integrates parallel tempering for global exploration of rugged LLM-induced energy landscapes. The concrete sampler further adapts the GwL sampler to the practical constraints of non-weight-tied LLM embeddings. Experiments with Qwen2.5 models show that the sampler discovers semantically meaningful prompts on diagnostic tasks, that parallel tempering helps escape a local optimum in a poetry completion task, and that post-optimizing APE prompts on 24 instruction-induction subtasks improves average accuracy from 60.04% to 63.23%. The study also reveals two main limitations: energy minimization may overfit small optimization sets, and the current sampler remains computationally expensive. These findings position Bayesian prompt sampling as a principled post-optimization tool and point to a promising direction for probabilistic prompt optimization.
Data-driven pre-fault dynamic security assessment (DSA) rapidly evaluates the dynamic risk of credible contingencies on a power system using machine learning. Existing approaches face two limitations. First, they require a large labelled database for training, with a separate model trained, tuned, and maintained for each contingency in a potentially long list of credible contingencies. Second, the trained models generalize poorly to unseen contingencies. This work addresses the limitations by using a tabular foundation model (TFM) that assesses stability through in-context learning, requiring no retraining or hyperparameter optimization. A single TFM can assess many contingencies at once, removing the need for one model per classifier. We also characterize when the use of electrical distance coordinates (EDC) as continuous features enables generalization of TFM to unseen contingencies and when they do not, demonstrating how a few labelled samples can reliably improve generalization. Through comprehensive case studies on the IEEE 68-bus system, we show that a single TFM attains an average Macro F1 score of about 90% with only 120 labelled samples per contingency, roughly two orders of magnitude fewer than conventionally assumed, without any model retraining or hyperparameter tuning. For new/unseen contingencies, we show that using just 10 labelled samples of the new contingency with EDC encoding matches the best achievable transfer learning oracle model, which requires fully labelled data and is not deployable in practice. Overall, this initial study paves the way towards developing and deploying foundation models for power system operations, with possible applications across multiple operational tasks.
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Data-driven pre-fault dynamic security assessment (DSA) rapidly evaluates the dynamic risk of credible contingencies on a power system using machine learning. Existing approaches face two limitations. First, they require a large labelled database for training, with a separate model trained, tuned, and maintained for each contingency in a potentially long list of credible contingencies. Second, the trained models generalize poorly to unseen contingencies. This work addresses the limitations by using a tabular foundation model (TFM) that assesses stability through in-context learning, requiring no retraining or hyperparameter optimization. A single TFM can assess many contingencies at once, removing the need for one model per classifier. We also characterize when the use of electrical distance coordinates (EDC) as continuous features enables generalization of TFM to unseen contingencies and when they do not, demonstrating how a few labelled samples can reliably improve generalization. Through comprehensive case studies on the IEEE 68-bus system, we show that a single TFM attains an average Macro F1 score of about 90% with only 120 labelled samples per contingency, roughly two orders of magnitude fewer than conventionally assumed, without any model retraining or hyperparameter tuning. For new/unseen contingencies, we show that using just 10 labelled samples of the new contingency with EDC encoding matches the best achievable transfer learning oracle model, which requires fully labelled data and is not deployable in practice. Overall, this initial study paves the way towards developing and deploying foundation models for power system operations, with possible applications across multiple operational tasks.
Physics-informed neural networks (PINNs) are unusually sensitive to interacting choices of architecture, activation, loss weighting, collocation, optimization, and constraint enforcement. Large language models (LLMs) can propose these choices, but independent recommendations do not accumulate experience from previously trained PINNs. We propose a closed-loop evolutionary algorithm that guides an LLM to generate complete, executable PINN configurations across generations, using measured training outcomes to determine subsequent search decisions. The algorithm maintains an evaluated population and lineage, applies parent-conditioned mutation and crossover, preserves elite and diverse solutions, rejects effective duplicates, and converts parent-relative successes and failures into the next-generation context supplied to the LLM. Every proposed configuration is executed directly under an exact optimizer-step budget. On a one-dimensional multiscale wave equation, two independent ten-generation runs trained 60 PINNs for 600,000 optimizer steps. In both runs, the best configuration appeared in the final generation, with best mean-squared error reduced by 2.97% and 95.38% relative to the initial population. The stronger run validated residual connections and increased depth on separate branches, combined them in a later generation, and then refined width and collocation density. It also revealed that low solution error can coexist with a high PDE residual. These results demonstrate the feasibility of evolutionary-algorithm-guided LLMs for PINN design on a controlled PDE while motivating broader, physics-aware evaluation.
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Physics-informed neural networks (PINNs) are unusually sensitive to interacting choices of architecture, activation, loss weighting, collocation, optimization, and constraint enforcement. Large language models (LLMs) can propose these choices, but independent recommendations do not accumulate experience from previously trained PINNs. We propose a closed-loop evolutionary algorithm that guides an LLM to generate complete, executable PINN configurations across generations, using measured training outcomes to determine subsequent search decisions. The algorithm maintains an evaluated population and lineage, applies parent-conditioned mutation and crossover, preserves elite and diverse solutions, rejects effective duplicates, and converts parent-relative successes and failures into the next-generation context supplied to the LLM. Every proposed configuration is executed directly under an exact optimizer-step budget. On a one-dimensional multiscale wave equation, two independent ten-generation runs trained 60 PINNs for 600,000 optimizer steps. In both runs, the best configuration appeared in the final generation, with best mean-squared error reduced by 2.97% and 95.38% relative to the initial population. The stronger run validated residual connections and increased depth on separate branches, combined them in a later generation, and then refined width and collocation density. It also revealed that low solution error can coexist with a high PDE residual. These results demonstrate the feasibility of evolutionary-algorithm-guided LLMs for PINN design on a controlled PDE while motivating broader, physics-aware evaluation.
作者Zhendong Li, Lei Sun, Ruibo Ming, He Zhang, Danda Pani Paudel, Luc Van Gool, Jinjin Gu
Workflow generation in visual creation systems such as ComfyUI demands not only syntactic accuracy but also expert-level reasoning over modular compositions. Existing large language model (LLM) approaches often treat this as a direct text-to-JSON generation task, struggling with structural brittleness and lacking the experiential knowledge required for effective design. We argue that successful workflow generation requires modeling knowledge itself, including its structure, hierarchy, and reasoning dynamics. To this end, we propose a knowledge-centric framework that learns to invert, inject, and infer with knowledge across multiple abstraction levels. We first perform knowledge inversion to distill hierarchical representations, ranging from full pseudo-codes and skeletons to high-level strategies, from large collections of real-world workflows. We then conduct knowledge injection through supervised fine-tuning, teaching the model to reason from task descriptions to strategies and from strategies to executable structures. During inference, the model performs reversible reasoning to synthesize executable workflows, augmented by self-refinement for structural coherence. Extensive experiments demonstrate that our method produces workflows with richer node diversity, more coherent structures, and higher execution success rates than existing systems, establishing a new foundation for knowledge-driven, agentic workflow generation.
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Workflow generation in visual creation systems such as ComfyUI demands not only syntactic accuracy but also expert-level reasoning over modular compositions. Existing large language model (LLM) approaches often treat this as a direct text-to-JSON generation task, struggling with structural brittleness and lacking the experiential knowledge required for effective design. We argue that successful workflow generation requires modeling knowledge itself, including its structure, hierarchy, and reasoning dynamics. To this end, we propose a knowledge-centric framework that learns to invert, inject, and infer with knowledge across multiple abstraction levels. We first perform knowledge inversion to distill hierarchical representations, ranging from full pseudo-codes and skeletons to high-level strategies, from large collections of real-world workflows. We then conduct knowledge injection through supervised fine-tuning, teaching the model to reason from task descriptions to strategies and from strategies to executable structures. During inference, the model performs reversible reasoning to synthesize executable workflows, augmented by self-refinement for structural coherence. Extensive experiments demonstrate that our method produces workflows with richer node diversity, more coherent structures, and higher execution success rates than existing systems, establishing a new foundation for knowledge-driven, agentic workflow generation.
Metaphor in Arabic is a culturally grounded mechanism for constructing meaning, encoding cultural knowledge that shapes interpretation. Yet current Arabic language models typically collapse lexical, cultural, and metaphorical information into a single representational space, a phenomenon we term "semantic smearing". We introduce CAMMAR (Culture-Aware Matryoshka for Metaphorical Arabic Representations), a representation learning framework that organizes meaning into nested lexical, cultural, and metaphorical embedding subspaces through a staged semantic curriculum. The design implements compositional principles of Al-Jurjani's theory of nazum, modeling figurative meaning as compositionally grounded in prior semantic relations, and yields a training-free geometric measure of metaphoricity based on the distance between lexical and metaphorical representations. Evaluated on a new span-annotated Arabic metaphor set as word-matched figurative/literal pairs, the geometric readout detects metaphor well above chance when the inter-layer geometry is shaped by paired supervision (AUC up to 0.84; figurative outscores its literal counterpart for the same word in 82.6% of pairs), but sits at chance under an unsupervised domain contrast alone, a clean separation between a legible-under-supervision regime and a non-emergent one. A controlled ablation shows that grounding the lexical layer in morphological roots gives a small but consistent gain, an effect absent from direct probing that reflects the layer's quality as a measurement anchor. We will release the datasets, cultural concept inventory, and code upon acceptance.
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Metaphor in Arabic is a culturally grounded mechanism for constructing meaning, encoding cultural knowledge that shapes interpretation. Yet current Arabic language models typically collapse lexical, cultural, and metaphorical information into a single representational space, a phenomenon we term "semantic smearing". We introduce CAMMAR (Culture-Aware Matryoshka for Metaphorical Arabic Representations), a representation learning framework that organizes meaning into nested lexical, cultural, and metaphorical embedding subspaces through a staged semantic curriculum. The design implements compositional principles of Al-Jurjani's theory of nazum, modeling figurative meaning as compositionally grounded in prior semantic relations, and yields a training-free geometric measure of metaphoricity based on the distance between lexical and metaphorical representations. Evaluated on a new span-annotated Arabic metaphor set as word-matched figurative/literal pairs, the geometric readout detects metaphor well above chance when the inter-layer geometry is shaped by paired supervision (AUC up to 0.84; figurative outscores its literal counterpart for the same word in 82.6% of pairs), but sits at chance under an unsupervised domain contrast alone, a clean separation between a legible-under-supervision regime and a non-emergent one. A controlled ablation shows that grounding the lexical layer in morphological roots gives a small but consistent gain, an effect absent from direct probing that reflects the layer's quality as a measurement anchor. We will release the datasets, cultural concept inventory, and code upon acceptance.
作者Danilo Monteiro Ribeiro, Ronnie de Souza Santos, Rodrigo Siqueira, Breno Andrade, Rafael Batista Duarte, Gilberto Hida, Julia Alencar, Gustavo Pinto
The growing adoption of Large Language Models in scientific research has created a need to understand what competencies researchers and graduate students require to use these tools critically and responsibly. This rapid review analyzed 194 articles retrieved from Elicit and Google Scholar (2022 to 2025), from which 40 were selected for competency extraction and thematic analysis following independent dual screening (Gwet AC1: 0.76 to 0.83). Eight competencies were identified. The most prevalent was domain expertise and oversight of AI outputs (n = 123), encompassing subject matter mastery, systematic skepticism, source verification, and researcher accountability. Other key competencies include metacognition and decision making about AI use (n = 55), ethics and academic integrity (n = 53), prompt engineering for research (n = 38), and reproducibility of AI use (n = 29). AI literacy and technical knowledge (n = 16) was explicitly identified as a risk factor when absent, with domain expertise treated as a prerequisite for meaningful critical evaluation. The findings suggest that preparing researchers to use LLMs goes beyond technical instruction, requiring an integrated set of epistemic, ethical, and methodological competencies centered on human accountability for the knowledge produced. These results have direct implications for the design of graduate programs and AI literacy initiatives.
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The growing adoption of Large Language Models in scientific research has created a need to understand what competencies researchers and graduate students require to use these tools critically and responsibly. This rapid review analyzed 194 articles retrieved from Elicit and Google Scholar (2022 to 2025), from which 40 were selected for competency extraction and thematic analysis following independent dual screening (Gwet AC1: 0.76 to 0.83). Eight competencies were identified. The most prevalent was domain expertise and oversight of AI outputs (n = 123), encompassing subject matter mastery, systematic skepticism, source verification, and researcher accountability. Other key competencies include metacognition and decision making about AI use (n = 55), ethics and academic integrity (n = 53), prompt engineering for research (n = 38), and reproducibility of AI use (n = 29). AI literacy and technical knowledge (n = 16) was explicitly identified as a risk factor when absent, with domain expertise treated as a prerequisite for meaningful critical evaluation. The findings suggest that preparing researchers to use LLMs goes beyond technical instruction, requiring an integrated set of epistemic, ethical, and methodological competencies centered on human accountability for the knowledge produced. These results have direct implications for the design of graduate programs and AI literacy initiatives.
Fortunetelling is a cultural practice for navigating uncertainty, often associated with people's beliefs and decisions. Fortunetelling with recent large language models (LLMs) introduces new opportunities and risks. This paper conducts qualitative studies to understand users' practices, perceptions, and impacts of LLM fortunetelling in China. We first analyze 1,045 posts on Chinese social media, yielding a comprehensive taxonomy of the diverse foretold topics (e.g., career, romance), emotion reactions (e.g., surprise, worry), and perceived credibility (e.g., doubt, trust) of LLM fortunetelling. Then, we conduct interviews with 20 users of LLM fortunetelling. The findings indicate that users treat LLM fortunetelling as a tool less for accurate prediction but more for emotional support. While the fortunetelling results rarely change users' initial beliefs or decisions, they are associated with subtle mindset shifts, with some users reporting small behavioral adjustments. We discuss implications for gaining benefits from LLM fortunetelling.
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Fortunetelling is a cultural practice for navigating uncertainty, often associated with people's beliefs and decisions. Fortunetelling with recent large language models (LLMs) introduces new opportunities and risks. This paper conducts qualitative studies to understand users' practices, perceptions, and impacts of LLM fortunetelling in China. We first analyze 1,045 posts on Chinese social media, yielding a comprehensive taxonomy of the diverse foretold topics (e.g., career, romance), emotion reactions (e.g., surprise, worry), and perceived credibility (e.g., doubt, trust) of LLM fortunetelling. Then, we conduct interviews with 20 users of LLM fortunetelling. The findings indicate that users treat LLM fortunetelling as a tool less for accurate prediction but more for emotional support. While the fortunetelling results rarely change users' initial beliefs or decisions, they are associated with subtle mindset shifts, with some users reporting small behavioral adjustments. We discuss implications for gaining benefits from LLM fortunetelling.
In-context learning is a remarkable property of transformers and has recently received a lot of interest. In many studies of in-context learning, it has been shown that transformers are capable of implementing solver for linear and non-linear regression problems, in which the most of them implement gradient descent algorithm. However, it is still unclear whether those implementations have actually been acquired through training. In this paper, we construct a transformer with linear self-attention, which in-context learns the least squares estimate in a simple regression task. The point here is that the closed form (analytical) solution is approximately obtained by using layer normalization rather than an approximate solution based on gradient descent algorithm. Then, we show an experimental example, in which our implementation is mainly used in the transformer trained with l1 regularization when the target output is the least squares estimate.
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In-context learning is a remarkable property of transformers and has recently received a lot of interest. In many studies of in-context learning, it has been shown that transformers are capable of implementing solver for linear and non-linear regression problems, in which the most of them implement gradient descent algorithm. However, it is still unclear whether those implementations have actually been acquired through training. In this paper, we construct a transformer with linear self-attention, which in-context learns the least squares estimate in a simple regression task. The point here is that the closed form (analytical) solution is approximately obtained by using layer normalization rather than an approximate solution based on gradient descent algorithm. Then, we show an experimental example, in which our implementation is mainly used in the transformer trained with l1 regularization when the target output is the least squares estimate.
We present S1-Omni, a unified multimodal reasoning model for scientific understanding, prediction, and generation. AI for Science (AI4S) has advanced significantly through domain-specific models, tool-augmented LLMs, and scientific language models. However, model capabilities remain highly fragmented, limiting the joint modeling of heterogeneous data, scientific laws, and expert knowledge. S1-Omni addresses this gap by consolidating these capabilities into a single, coherent scientific reasoning model. The architecture of S1-Omni is built upon three core components: unified representation of scientific data, natural-world knowledge alignment, and decoding for domain-specific tasks. First, S1-Omni maps natural-language instructions and scientific objects, including CIF, SMILES, protein sequences, spectra, and scientific images, into a shared representation space. Second, it incorporates scientific laws and expert knowledge into data construction and training, enabling the model to reason from scientific evidence. Third, it performs task-specific decoding to support a broad range of applications, including property prediction, spectrum-to-molecular generation, protein site and structure prediction, and scientific image generation and editing. S1-Omni is trained on S1-Omni-Corpus, which covers 200 scientific tasks and contains millions of reasoning samples, and is evaluated on over 60 scientific benchmarks. It outperforms GPT-5.5 and Gemini-3.1-Pro on most benchmarks and matches or surpasses domain-specific models on several benchmarks. Overall, S1-Omni provides a practical path toward unified scientific modeling.
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We present S1-Omni, a unified multimodal reasoning model for scientific understanding, prediction, and generation. AI for Science (AI4S) has advanced significantly through domain-specific models, tool-augmented LLMs, and scientific language models. However, model capabilities remain highly fragmented, limiting the joint modeling of heterogeneous data, scientific laws, and expert knowledge. S1-Omni addresses this gap by consolidating these capabilities into a single, coherent scientific reasoning model. The architecture of S1-Omni is built upon three core components: unified representation of scientific data, natural-world knowledge alignment, and decoding for domain-specific tasks. First, S1-Omni maps natural-language instructions and scientific objects, including CIF, SMILES, protein sequences, spectra, and scientific images, into a shared representation space. Second, it incorporates scientific laws and expert knowledge into data construction and training, enabling the model to reason from scientific evidence. Third, it performs task-specific decoding to support a broad range of applications, including property prediction, spectrum-to-molecular generation, protein site and structure prediction, and scientific image generation and editing. S1-Omni is trained on S1-Omni-Corpus, which covers 200 scientific tasks and contains millions of reasoning samples, and is evaluated on over 60 scientific benchmarks. It outperforms GPT-5.5 and Gemini-3.1-Pro on most benchmarks and matches or surpasses domain-specific models on several benchmarks. Overall, S1-Omni provides a practical path toward unified scientific modeling.
Large Language Models (LLMs) can generate natural language explanations that rationalize their own decisions, a phenomenon commonly referred to as self-explanations.Such explanations have emerged as a promising direction for explainable artificial intelligence (XAI), particularly for interpreting LLM behavior.However, while self-explanations often appear plausible, whether they faithfully reflect a model's underlying reasoning process remains an open question. In this opinion paper, we argue that self-explanations can be highly plausible, questionably faithful, and yet highly actionable. From a traditional XAI perspective, we identify the limitations of standard evaluation protocols for LLM-generated self-explanations and propose practical guidelines for assessing their plausibility and faithfulness. Moreover, we argue that evaluation should extend beyond these criteria to actionability, highlighting applications of LLM rationalization capabilities that support informed decision-making and appropriate action across diverse stakeholders.
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Large Language Models (LLMs) can generate natural language explanations that rationalize their own decisions, a phenomenon commonly referred to as self-explanations.Such explanations have emerged as a promising direction for explainable artificial intelligence (XAI), particularly for interpreting LLM behavior.However, while self-explanations often appear plausible, whether they faithfully reflect a model's underlying reasoning process remains an open question. In this opinion paper, we argue that self-explanations can be highly plausible, questionably faithful, and yet highly actionable. From a traditional XAI perspective, we identify the limitations of standard evaluation protocols for LLM-generated self-explanations and propose practical guidelines for assessing their plausibility and faithfulness. Moreover, we argue that evaluation should extend beyond these criteria to actionability, highlighting applications of LLM rationalization capabilities that support informed decision-making and appropriate action across diverse stakeholders.
While the internal mechanisms of autoregressive (AR) transformers have been studied extensively, much less is known about diffusion language models (DLMs), an emerging alternative that generates text by iterative denoising. In this work, we study how DLMs implement induction, a mechanism behind in-context learning in which the model finds a repeated context and copies the token that followed it. Our analysis compares attention-only AR models and absorbing-mask DLMs with matched architectures. We find that DLMs learn a bidirectional induction circuit, where previous-token and next-token heads write local context into the residual stream and later induction heads use it to find and copy the answer from the matching source position. The circuit is direction-symmetric, working whether the source appears in the past or in the future. When only left context is visible, matching what an AR model sees, the DLM does not outperform its AR counterpart in induction capabilities. However, we observe it has stronger induction when both sides of the masked token are visible, pointing to bidirectional context access rather than a stronger one-sided mechanism. Beyond induction, we provide causal evidence that DLMs compute the global fraction of masked tokens and use it as an implicit timestep, even though they are given no explicit timestep embedding.
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While the internal mechanisms of autoregressive (AR) transformers have been studied extensively, much less is known about diffusion language models (DLMs), an emerging alternative that generates text by iterative denoising. In this work, we study how DLMs implement induction, a mechanism behind in-context learning in which the model finds a repeated context and copies the token that followed it. Our analysis compares attention-only AR models and absorbing-mask DLMs with matched architectures. We find that DLMs learn a bidirectional induction circuit, where previous-token and next-token heads write local context into the residual stream and later induction heads use it to find and copy the answer from the matching source position. The circuit is direction-symmetric, working whether the source appears in the past or in the future. When only left context is visible, matching what an AR model sees, the DLM does not outperform its AR counterpart in induction capabilities. However, we observe it has stronger induction when both sides of the masked token are visible, pointing to bidirectional context access rather than a stronger one-sided mechanism. Beyond induction, we provide causal evidence that DLMs compute the global fraction of masked tokens and use it as an implicit timestep, even though they are given no explicit timestep embedding.
While large language models (LLMs) can solve advanced reasoning problems in seconds, we show that even frontier models fail to perform a much simpler operation: exactly copying an input string that lies well within their context windows. We attribute this failure to positional encodings in Transformer architectures, whose inductive bias favors copying through a shortcut based on matching local contexts rather than carefully locating the corresponding input positions. To address this issue, we introduce 2D-RoPE, which organizes text into a 2D grid rather than a 1D sequence and assigns each token a row ID and a column ID. Under this view, copying becomes simply retrieving input tokens at a fixed column offset, which makes the task easy to learn. In synthetic copy experiments, shallow Transformers with 2D-RoPE achieve perfect copying at input lengths hundreds of times longer than those seen during training, whereas standard positional encodings fall far behind. We further show that the advantage of 2D-RoPE language models on copy tasks consistently holds in large-scale pretraining on DCLM with model sizes up to 1.4B parameters. Overall, our results suggest that viewing text in 2D can benefit language modeling, and we hope this encourages future work to further explore the potential of 2D positional encodings.
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While large language models (LLMs) can solve advanced reasoning problems in seconds, we show that even frontier models fail to perform a much simpler operation: exactly copying an input string that lies well within their context windows. We attribute this failure to positional encodings in Transformer architectures, whose inductive bias favors copying through a shortcut based on matching local contexts rather than carefully locating the corresponding input positions. To address this issue, we introduce 2D-RoPE, which organizes text into a 2D grid rather than a 1D sequence and assigns each token a row ID and a column ID. Under this view, copying becomes simply retrieving input tokens at a fixed column offset, which makes the task easy to learn. In synthetic copy experiments, shallow Transformers with 2D-RoPE achieve perfect copying at input lengths hundreds of times longer than those seen during training, whereas standard positional encodings fall far behind. We further show that the advantage of 2D-RoPE language models on copy tasks consistently holds in large-scale pretraining on DCLM with model sizes up to 1.4B parameters. Overall, our results suggest that viewing text in 2D can benefit language modeling, and we hope this encourages future work to further explore the potential of 2D positional encodings.
OWL ontologies provide a formal knowledge representation framework that enables semantic reasoning, and have been widely adopted across domains such as healthcare and bioinformatics. In practice, however, real-world ontologies are often incomplete, which pose challenges for reasoning. In this work, we focus on a fundamental subsumption reasoning problem: given an incomplete ontology and a candidate (non-entailed) subsumption, determine whether the subsumption is semantically plausible and, if so, providing a logically sound explanation containing potential missing axioms. This task unifies subsumption verification with ontology abduction, and generalizes the latter by removing the need for a predefined candidate set of missing axioms. To address this subsumption reasoning problem, we propose NeurOWL, an end-to-end neuro-symbolic framework that jointly performs verification and abduction, leveraging both formally defined semantics and textual semantics through Large Language Models and ontology embeddings. We evaluate NeurOWL on real-world ontologies across multiple domains, demonstrating strong and robust performance across different domains.
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OWL ontologies provide a formal knowledge representation framework that enables semantic reasoning, and have been widely adopted across domains such as healthcare and bioinformatics. In practice, however, real-world ontologies are often incomplete, which pose challenges for reasoning. In this work, we focus on a fundamental subsumption reasoning problem: given an incomplete ontology and a candidate (non-entailed) subsumption, determine whether the subsumption is semantically plausible and, if so, providing a logically sound explanation containing potential missing axioms. This task unifies subsumption verification with ontology abduction, and generalizes the latter by removing the need for a predefined candidate set of missing axioms. To address this subsumption reasoning problem, we propose NeurOWL, an end-to-end neuro-symbolic framework that jointly performs verification and abduction, leveraging both formally defined semantics and textual semantics through Large Language Models and ontology embeddings. We evaluate NeurOWL on real-world ontologies across multiple domains, demonstrating strong and robust performance across different domains.
作者Xingru Chen, Zelang Liang, Yongjia Ma, Jiqing Zhan, Shuling Yang, Lian Wen, Kun Zhan
Diffusion-based Large Language Models(DLLMs) enable parallel generation via Semi-Autoregressive (SAR) decoding in text generation. However, current methods suffer from severe operator-level redundancy: they recompute the entire sequence during denoising steps, ignoring that the prefix and masked suffix remain invariant within a block. We propose LaCache, a training-free acceleration framework that alleviates this redundancy through lossless caching and mixed precision. Specifically, LaCache employs Lossless State Memoization (LSM) by caching three types of intermediate results: (i) EmbedCache for embedding outputs, (ii) RoPECache for token-wise pre-attention states, and (iii) FACache for the online softmax statistics within FlashAttention. These caches allow the model to skip redundant computation on unchanged tokens without altering the output. To further alleviate memory-bandwidth bottlenecks, LaCache inegrates a per-group FP8 quantization strategy for FFN layers, tailored to step-dependent activation distributions across the diffusion process. Experiments demonstrate that LaCache alone achieves approximately 1.3X end-to-end speedup over vanilla DLLM. When combined with existing acceleration methods, LaCache reaches up to 40.2X end-to-end speedup while maintaining comparable task accuracy.
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Diffusion-based Large Language Models(DLLMs) enable parallel generation via Semi-Autoregressive (SAR) decoding in text generation. However, current methods suffer from severe operator-level redundancy: they recompute the entire sequence during denoising steps, ignoring that the prefix and masked suffix remain invariant within a block. We propose LaCache, a training-free acceleration framework that alleviates this redundancy through lossless caching and mixed precision. Specifically, LaCache employs Lossless State Memoization (LSM) by caching three types of intermediate results: (i) EmbedCache for embedding outputs, (ii) RoPECache for token-wise pre-attention states, and (iii) FACache for the online softmax statistics within FlashAttention. These caches allow the model to skip redundant computation on unchanged tokens without altering the output. To further alleviate memory-bandwidth bottlenecks, LaCache inegrates a per-group FP8 quantization strategy for FFN layers, tailored to step-dependent activation distributions across the diffusion process. Experiments demonstrate that LaCache alone achieves approximately 1.3X end-to-end speedup over vanilla DLLM. When combined with existing acceleration methods, LaCache reaches up to 40.2X end-to-end speedup while maintaining comparable task accuracy.