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A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development

Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.

ABSTRACT

Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.

PMID:42189071 | DOI:10.1002/advs.75839

Multi-Omics Identification of Biomarkers for High-Altitude Pulmonary Hypertension

J Cardiovasc Dev Dis. 2026 Apr 30;13(5):195. doi: 10.3390/jcdd13050195.

ABSTRACT

(1) Aim: The incidence of high-altitude pulmonary hypertension (HAPH) has risen in recent years and is expected to continue increasing; however, its diagnosis remains challenging. In this study, we employed proteomics and metabolomics to identify the proteins and metabolic biomarkers that contribute to the development of HAPH. (2) Methods: We applied integrated proteomics and metabolomics to match blood samples from 40 HAPH patients and 40 healthy controls in Yunnan's high-altitude regions to characterize molecular profiles, identify biomarkers, and develop a predictive model. (3) Results: Proteomic analysis identified four proteins (A2IPH7, K1C14, PSME2, SERPINE2) commonly dysregulated in HAPH patients from two high-altitude regions. SERPINE2 was notably downregulated and showed a negative correlation with clinical severity, which was further validated in HAPH rat lung tissues and supported by UK Biobank data for idiopathic PAH. Concurrent metabolomics uncovered 11 shared metabolites, largely acyl fatty acids, enriched in pathways such as unsaturated fatty acid synthesis. Integration of these multi-omics data enabled the development of a robust predictive model. (4) Conclusion: Our study identified key protein and metabolic biomarkers involved in HAPH development, which were validated in animal models. Based on these findings, a predictive model was developed, highlighting SERPINE2 and 11 metabolites as promising targets for the prediction and prevention of HAPH.

PMID:42188081 | DOI:10.3390/jcdd13050195

A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development

Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.

ABSTRACT

Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.

PMID:42189071 | DOI:10.1002/advs.75839

Multi-Omics Identification of Biomarkers for High-Altitude Pulmonary Hypertension

J Cardiovasc Dev Dis. 2026 Apr 30;13(5):195. doi: 10.3390/jcdd13050195.

ABSTRACT

(1) Aim: The incidence of high-altitude pulmonary hypertension (HAPH) has risen in recent years and is expected to continue increasing; however, its diagnosis remains challenging. In this study, we employed proteomics and metabolomics to identify the proteins and metabolic biomarkers that contribute to the development of HAPH. (2) Methods: We applied integrated proteomics and metabolomics to match blood samples from 40 HAPH patients and 40 healthy controls in Yunnan's high-altitude regions to characterize molecular profiles, identify biomarkers, and develop a predictive model. (3) Results: Proteomic analysis identified four proteins (A2IPH7, K1C14, PSME2, SERPINE2) commonly dysregulated in HAPH patients from two high-altitude regions. SERPINE2 was notably downregulated and showed a negative correlation with clinical severity, which was further validated in HAPH rat lung tissues and supported by UK Biobank data for idiopathic PAH. Concurrent metabolomics uncovered 11 shared metabolites, largely acyl fatty acids, enriched in pathways such as unsaturated fatty acid synthesis. Integration of these multi-omics data enabled the development of a robust predictive model. (4) Conclusion: Our study identified key protein and metabolic biomarkers involved in HAPH development, which were validated in animal models. Based on these findings, a predictive model was developed, highlighting SERPINE2 and 11 metabolites as promising targets for the prediction and prevention of HAPH.

PMID:42188081 | DOI:10.3390/jcdd13050195

Summoning the Oracle to Slay It: Mitigating Look-Ahead Bias in Financial Backtesting with Large Language Models

arXiv:2605.24564v1 Announce Type: new Abstract: Backtesting large language models (LLMs) on historical financial data is unreliable because pre-training cuts off after the events happened. An LLM trained in 2024 already "knows" which way 2018-2020 stocks moved. We name this failure parametric look-ahead bias and propose FinCAD, an inference-time adaptation of Context-Aware Decoding that suppresses an LLM's memory of historical outcomes without retraining. FinCAD pairs an adversarial bias-discovery pipeline that learns a model-specific memory-activating prior prompt with an entity- and date-adaptive rule that scales the CAD strength to per-(entity, date) memorisation, so the penalty fires on memorised in-sample dates and decays to zero out-of-sample. Across five 7-14B LLMs and five mega-cap equities, FinCAD cuts in-sample backtest returns by up to -67.1% on memorised dates while leaving 2025 out-of-sample returns within $8K and Sharpe within 0.10 of baseline, and preserves general-purpose reasoning within 1.7 pts. On an eleven-model leaderboard, it raises the in-sample / out-of-sample Spearman correlation from +0.779 to +0.846, recovering rankings that genuinely predict out-of-sample performance.

LipoAgent: Coordinating Fine-Tuned LLM Agents for Safer Lipid Design

arXiv:2605.25250v1 Announce Type: new Abstract: Lipid nanoparticles (LNPs) are among the most clinically mature platforms for nucleic acid delivery, yet designing lipids that are both effective and biologically safe remains a major bottleneck. In practical screening, toxicity is a decision-level constraint: if a lipid is toxic, its efficiency prediction is clinically irrelevant. We propose LipoAgent, a safety-aware multi-agent LLM framework for lipid discovery. LipoAgent combines domain-specific finetuning with a conditional prediction objective that enforces toxicity as a prerequisite for efficiency prediction, and further improves reliability via multi-agent verification with lightweight human oversight when disagreement persists. Across multiple foundation models, LipoAgent achieves an average 32% relative improvement in mRNA transfection efficiency prediction compared with other reported models for lipid design. Wet-lab validation confirms that virtual screening rankings reliably translate to biological transfection outcomes. The code is publicly available at https://github.com/SAI-Lab-NYU/LipoAgent.git.

IPR-1: Interactive Physical Reasoner

arXiv:2511.15407v4 Announce Type: replace Abstract: Humans learn by observing, interacting with environments, and internalizing physics and causality. Here, we aim to ask whether an agent can similarly acquire human-like reasoning from interaction and keep improving with more experience. To study this, we introduce a Game-to-Unseen (G2U) benchmark of 1,000+ heterogeneous games that exhibit significant visual domain gaps. Existing approaches, including VLMs and world models, struggle to capture underlying physics and causality since they are not focused on core mechanisms and overfit to visual details. VLM/VLA agents reason but lack look-ahead in interactive settings, while world models imagine but imitate visual patterns rather than analyze physics and causality. We therefore propose IPR (Interactive Physical Reasoner), using world-model rollouts to score and reinforce a VLM's policy, and introduce PhysCode, a physics-centric action code aligning semantic intent with dynamics to provide a shared action space for prediction and reasoning. Pretrained on 1,000+ games, our IPR performs robustly on levels from primitive intuition to goal-driven reasoning, and even surpasses GPT-5 overall. We find that performance improves with more training games and interaction steps, and that the model also zero-shot transfers to unseen games. These results support physics-centric interaction as a path to steadily improving physical reasoning. Further demos and project details can be found at https://mybearyzhang.github.io/ipr-1.

Prism: Spectral-Aware Block-Sparse Attention

arXiv:2602.08426v2 Announce Type: replace-cross Abstract: Block-sparse attention is promising for accelerating long-context LLM pre-filling, yet identifying relevant blocks efficiently remains a bottleneck. Existing methods typically employ coarse-grained attention as a proxy for block importance estimation, but often resort to expensive token-level searching or scoring, resulting in significant selection overhead. In this work, we trace the inaccuracy of standard coarse-grained attention via mean pooling to a theoretical root cause: the interaction between mean pooling and Rotary Positional Embeddings (RoPE). We prove that mean pooling acts as a low-pass filter that induces destructive interference in high-frequency dimensions, effectively creating a "blind spot" for local positional information (e.g., slash patterns). To address this, we introduce Prism, a training-free spectral-aware approach that decomposes block selection into high-frequency and low-frequency branches. By applying energy-based temperature calibration, Prism restores the attenuated positional signals directly from pooled representations, enabling block importance estimation using purely block-level operations, thereby improving efficiency. Extensive evaluations confirm that Prism maintains accuracy parity with full attention while delivering up to $\mathbf{5.1\times}$ speedup.

TABQAWORLD: Optimizing Multimodal Reasoning for Multi-Turn Table Question Answering

arXiv:2604.03393v1 Announce Type: new Abstract: Multimodal reasoning has emerged as a powerful framework for enhancing reasoning capabilities of reasoning models. While multi-turn table reasoning methods have improved reasoning accuracy through tool use and reward modeling, they rely on fixed text serialization for table state readouts. This introduces representation errors in table encoding that significantly accumulate over multiple turns. Such accumulation is alleviated by tabular grounding methods in the expense of inference compute and cost, rendering real world deployment impractical. To address this, we introduce TABQAWORLD, a table reasoning framework that jointly optimizes tabular action through representation and estimation. For representation, TABQAWORLD employs an action-conditioned multimodal selection policy, which dynamically switches between visual and textual representations to maximize table state readout reliability. For estimation, TABQAWORLD optimizes stepwise reasoning trajectory through table metadata including dimension, data types and key values, safely planning trajectory and compressing low-complexity actions to reduce conversation turns and latency. Designed as a training-free framework, empirical evaluations show that TABQAWORLD achieves state-of-the-art performance with 4.87% accuracy improvements over baselines, with 5.42% accuracy gain and 33.35% inference latency reduction over static settings, establishing a new standard for reliable and efficient table reasoning.

FeynmanBench: Benchmarking Multimodal LLMs on Diagrammatic Physics Reasoning

arXiv:2604.03893v1 Announce Type: new Abstract: Breakthroughs in frontier theory often depend on the combination of concrete diagrammatic notations with rigorous logic. While multimodal large language models (MLLMs) show promise in general scientific tasks, current benchmarks often focus on local information extraction rather than the global structural logic inherent in formal scientific notations. In this work, we introduce FeynmanBench, the first benchmark centered on Feynman diagram tasks. It is designed to evaluate AI's capacity for multistep diagrammatic reasoning, which requires satisfying conservation laws and symmetry constraints, identifying graph topology, converting between diagrammatic and algebraic representations, and constructing scattering amplitudes under specific conventions and gauges. To support large-scale and reproducible evaluation, we developed an automated pipeline producing diverse Feynman diagrams along with verifiable topological annotations and amplitude results. Our database spans the electromagnetic, weak, and strong interactions of the Standard Model, encompasses over 100 distinct types and includes more than 2000 tasks. Experiments on state-of-the-art MLLMs reveal systematic failure modes, including unstable enforcement of physical constraints and violations of global topological conditions, highlighting the need for physics-grounded benchmarks for visual reasoning over scientific notation. FeynmanBench provides a logically rigorous test of whether AI can effectively engage in scientific discovery, particularly within theoretical physics.

RDEx-CMOP: Feasibility-Aware Indicator-Guided Differential Evolution for Fixed-Budget Constrained Multiobjective Optimization

arXiv:2604.03708v1 Announce Type: cross Abstract: Constrained multiobjective optimisation requires fast feasibility attainment together with stable convergence and diversity preservation under strict evaluation budgets. This report documents RDEx-CMOP, the differential evolution variant used in the IEEE CEC 2025 numerical optimisation competition (C06 special session) constrained multiobjective track. RDEx-CMOP integrates an {\epsilon}-level feasibility schedule, a SPEA2-style indicator-driven fitness assignment, and a fitness-oriented current-to-pbest/1 mutation operator. We evaluate RDEx-CMOP on the official CEC 2025 CMOP benchmark using the median-target U-score framework and the released trace data. Experimental results show that RDEx-CMOP achieves the highest total score and the best overall average rank among all released comparison algorithms, with strong target-attainment behaviour and near-zero final violation on most problems.

CREBench: Evaluating Large Language Models in Cryptographic Binary Reverse Engineering

arXiv:2604.03750v1 Announce Type: cross Abstract: Reverse engineering (RE) is central to software security, particularly for cryptographic programs that handle sensitive data and are highly prone to vulnerabilities. It supports critical tasks such as vulnerability discovery and malware analysis. Despite its importance, RE remains labor-intensive and requires substantial expertise, making large language models (LLMs) a potential solution for automating the process. However, their capabilities for RE remain systematically underexplored. To address this gap, we study the cryptographic binary RE capabilities of LLMs and introduce \textbf{CREBench}, a benchmark comprising 432 challenges built from 48 standard cryptographic algorithms, 3 insecure crypto key usage scenarios, and 3 difficulty levels. Each challenge follows a Capture-the-Flag (CTF) RE challenge, requiring the model to analyze the underlying cryptographic logic and recover the correct input. We design an evaluation framework comprising four sub-tasks, from algorithm identification to correct flag recovery. We evaluate eight frontier LLMs on CREBench. GPT-5.4, the best-performing model, achieves 64.03 out of 100 and recovers the flag in 59\% of challenges. We also establish a strong human expert baseline of 92.19 points, showing that humans maintain an advantage in cryptographic RE tasks. Our code and dataset are available at https://github.com/wangyu-ovo/CREBench.

Individual and Combined Effects of English as a Second Language and Typos on LLM Performance

arXiv:2604.04723v1 Announce Type: cross Abstract: Large language models (LLMs) are used globally, and because much of their training data is in English, they typically perform best on English inputs. As a result, many non-native English speakers interact with them in English as a second language (ESL), and these inputs often contain typographical errors. Prior work has largely studied the effects of ESL variation and typographical errors separately, even though they often co-occur in real-world use. In this study, we use the Trans-EnV framework to transform standard English inputs into eight ESL variants and apply MulTypo to inject typos at three levels: low, moderate, and severe. We find that combining ESL variation and typos generally leads to larger performance drops than either factor alone, though the combined effect is not simply additive. This pattern is clearest on closed-ended tasks, where performance degradation can be characterized more consistently across ESL variants and typo levels, while results on open-ended tasks are more mixed. Overall, these findings suggest that evaluations on clean standard English may overestimate real-world model performance, and that evaluating ESL variation and typographical errors in isolation does not fully capture model behavior in realistic settings.

Enhancing Foundation VLM Robustness to Missing Modality: Scalable Diffusion for Bi-directional Feature Restoration

arXiv:2602.03151v2 Announce Type: replace Abstract: Vision Language Model (VLM) typically assume complete modality input during inference. However, their effectiveness drops sharply when certain modalities are unavailable or incomplete. Current research on missing modality primarily faces two dilemmas: Prompt-based methods struggle to restore missing yet indispensable features and degrade the generalizability of VLM. Imputation-based approaches, lacking effective guidance, are prone to generating semantically irrelevant noise. Restoring precise semantics while sustaining VLM's generalization remains challenging. Therefore, we propose a general missing modality restoration strategy in this paper. We introduce an enhanced diffusion model as a pluggable mid-stage training module to effectively restore missing features. Our strategy introduces two key innovations: (I) Dynamic Modality Gating, which adaptively leverages conditional features to guide the generation of semantically consistent features; (II) Cross-Modal Mutual Learning mechanism, which bridges the semantic spaces of the dual models to achieve bi-directional alignment. Notably, our strategy maintains the original integrity of the pre-trained VLM, requiring no fine-tuning of the backbone models while significantly boosting resilience to information loss. Zero-shot evaluations across benchmark datasets demonstrate that our approach consistently outperforms existing baselines, establishing it as a robust and scalable extension that ensures VLM reliability across diverse missing rates and conditions. Our code and models will be publicly available.

Generate Then Correct: Single Shot Global Correction for Aspect Sentiment Quad Prediction

arXiv:2603.13777v2 Announce Type: replace-cross Abstract: Aspect-based sentiment analysis (ABSA) extracts aspect-level sentiment signals from user-generated text, supports product analytics, experience monitoring, and public-opinion tracking, and is central to fine-grained opinion mining. A key challenge in ABSA is aspect sentiment quad prediction (ASQP), which requires identifying four elements: the aspect term, the aspect category, the opinion term, and the sentiment polarity. However, existing studies usually linearize the unordered quad set into a fixed-order template and decode it left-to-right. With teacher forcing training, the resulting training-inference mismatch (exposure bias) lets early prefix errors propagate to later elements. The linearization order determines which elements appear earlier in the prefix, so this propagation becomes order-sensitive and is hard to repair in a single pass. To address this, we propose a method, Generate-then-Correct (G2C): a generator drafts quads and a corrector performs a single-shot, sequence-level global correction trained on LLM-synthesized drafts with common error patterns. On the Rest15 and Rest16 datasets, G2C outperforms strong baseline models.

The Latent Space: Foundation, Evolution, Mechanism, Ability, and Outlook

arXiv:2604.02029v1 Announce Type: new Abstract: Latent space is rapidly emerging as a native substrate for language-based models. While modern systems are still commonly understood through explicit token-level generation, an increasing body of work shows that many critical internal processes are more naturally carried out in continuous latent space than in human-readable verbal traces. This shift is driven by the structural limitations of explicit-space computation, including linguistic redundancy, discretization bottlenecks, sequential inefficiency, and semantic loss. This survey aims to provide a unified and up-to-date landscape of latent space in language-based models. We organize the survey into five sequential perspectives: Foundation, Evolution, Mechanism, Ability, and Outlook. We begin by delineating the scope of latent space, distinguishing it from explicit or verbal space and from the latent spaces commonly studied in generative visual models. We then trace the field's evolution from early exploratory efforts to the current large-scale expansion. To organize the technical landscape, we examine existing work through the complementary lenses of mechanism and ability. From the perspective of Mechanism, we identify four major lines of development: Architecture, Representation, Computation, and Optimization. From the perspective of Ability, we show how latent space supports a broad capability spectrum spanning Reasoning, Planning, Modeling, Perception, Memory, Collaboration, and Embodiment. Beyond consolidation, we discuss the key open challenges, and outline promising directions for future research. We hope this survey serves not only as a reference for existing work, but also as a foundation for understanding latent space as a general computational and systems paradigm for next-generation intelligence.

Do Emotions in Prompts Matter? Effects of Emotional Framing on Large Language Models

arXiv:2604.02236v1 Announce Type: new Abstract: Emotional tone is pervasive in human communication, yet its influence on large language model (LLM) behaviour remains unclear. Here, we examine how first-person emotional framing in user-side queries affect LLM performance across six benchmark domains, including mathematical reasoning, medical question answering, reading comprehension, commonsense reasoning and social inference. Across models and tasks, static emotional prefixes usually produce only small changes in accuracy, suggesting that affective phrasing is typically a mild perturbation rather than a reliable general-purpose intervention. This stability is not uniform: effects are more variable in socially grounded tasks, where emotional context more plausibly interacts with interpersonal reasoning. Additional analyses show that stronger emotional wording induces only modest extra change, and that human-written prefixes reproduce the same qualitative pattern as LLM-generated ones. We then introduce EmotionRL, an adaptive emotional prompting framework that selects emotional framing adaptively for each query. Although no single emotion is consistently beneficial, adaptive selection yields more reliable gains than fixed emotional prompting. Together, these findings show that emotional tone is neither a dominant driver of LLM performance nor irrelevant noise, but a weak and input-dependent signal that can be exploited through adaptive control.

Predicting LLM Output Length via Entropy-Guided Representations

arXiv:2602.11812v2 Announce Type: replace Abstract: The long-tailed distribution of sequence lengths in LLM serving and reinforcement learning (RL) sampling causes significant computational waste due to excessive padding in batched inference. Existing methods rely on auxiliary models for static length prediction, but they incur high overhead, generalize poorly, and fail in stochastic "one-to-many" sampling scenarios. We introduce a lightweight framework that reuses the main model's internal hidden states for efficient length prediction. Our framework features two core components: 1) Entropy-Guided Token Pooling (EGTP), which uses on-the-fly activations and token entropy for highly accurate static prediction with negligible cost, and 2) Progressive Length Prediction (PLP), which dynamically estimates the remaining length at each decoding step to handle stochastic generation. To validate our approach, we build and release ForeLen, a comprehensive benchmark with long-sequence, Chain-of-Thought, and RL data. On ForeLen, EGTP achieves state-of-the-art accuracy, reducing MAE by 29.16\% over the best baseline. Integrating our methods with a length-aware scheduler yields significant end-to-end throughput gains. Our work provides a new technical and evaluation baseline for efficient LLM inference.

GISTBench: Evaluating LLM User Understanding via Evidence-Based Interest Verification

arXiv:2603.29112v1 Announce Type: new Abstract: We introduce GISTBench, a benchmark for evaluating Large Language Models' (LLMs) ability to understand users from their interaction histories in recommendation systems. Unlike traditional RecSys benchmarks that focus on item prediction accuracy, our benchmark evaluates how well LLMs can extract and verify user interests from engagement data. We propose two novel metric families: Interest Groundedness (IG), decomposed into precision and recall components to separately penalize hallucinated interest categories and reward coverage, and Interest Specificity (IS), which assesses the distinctiveness of verified LLM-predicted user profiles. We release a synthetic dataset constructed on real user interactions on a global short-form video platform. Our dataset contains both implicit and explicit engagement signals and rich textual descriptions. We validate our dataset fidelity against user surveys, and evaluate eight open-weight LLMs spanning 7B to 120B parameters. Our findings reveal performance bottlenecks in current LLMs, particularly their limited ability to accurately count and attribute engagement signals across heterogeneous interaction types.
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