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Received — 2 April 2026 ⏭

InCoder-32B: Code Foundation Model for Industrial Scenarios

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jian Yang · Wei Zhang · Jiajun Wu · Junhang Cheng · Shawn Guo · Haowen Wang · Weicheng Gu · Yaxin Du · Joseph Li · Fanglin Xu · Yizhi Li · Lin Jing · Yuanbo Wang · Yuhan Gao · Ruihao Gong · Chuan Hao · Ran Tao · Aishan Liu · Tuney Zheng · Ganqu Cui · Zhoujun Li · Mingjie Tang · Chenghua Lin · Wayne Xin Zhao · Xianglong Liu · Ming Zhou · Bryan Dai · Weifeng Lv
1 April 2026 at 12:00
arXiv:2603.16790v3 Announce Type: replace-cross Abstract: Recent code large language models have achieved remarkable progress on general programming tasks. Nevertheless, their performance degrades significantly in industrial scenarios that require reasoning about hardware semantics, specialized language constructs, and strict resource constraints. To address these challenges, we introduce InCoder-32B (Industrial-Coder-32B), the first 32B-parameter code foundation model unifying code intelligence across chip design, GPU kernel optimization, embedded systems, compiler optimization, and 3D modeling. By adopting an efficient architecture, we train InCoder-32B from scratch with general code pre-training, curated industrial code annealing, mid-training that progressively extends context from 8K to 128K tokens with synthetic industrial reasoning data, and post-training with execution-grounded verification. We conduct extensive evaluation on 14 mainstream general code benchmarks and 9 industrial benchmarks spanning 4 specialized domains. Results show InCoder-32B achieves highly competitive performance on general tasks while establishing strong open-source baselines across industrial domains.

Integrative Multi-omics Analysis of Buti Huatan Tang in Chronic Obstructive Pulmonary Disease

✇Omics In Lung
By: Xin Zha · Wen-Wei Gong · Xue-Ying Li · Qing Xia · Jing-Hua Ruan · Rong Tan · Zhu-Sheng Zhu · Shao-Bo Liu
30 March 2026 at 18:00

J Vis Exp. 2026 Mar 13;(229). doi: 10.3791/70383.

ABSTRACT

This study utilized a multi-omics and computational biology framework to investigate the therapeutic potential of the Traditional Chinese Medicine (TCM) formula Buti Huatan Tang (BTHTT) against chronic obstructive pulmonary disease (COPD). Significant physiological improvements were observed in a rat model following BTHTT intervention. Histological analysis showed a reversal of lung pathological damage, while biochemical assays, and transcriptomics confirmed the normalization of IL-1β and IL-1R2 levels. Additionally, metabolic profiling revealed that BTHTT corrected disruptions in T3 and T4 thyroid hormone levels. A negative correlation was observed between the IL-1β/IL-1R2 axis and these thyroid hormones, indicating that their regulation is associated with the formula's therapeutic effect. Beyond direct measurements, machine learning algorithms identified ten COPD signature genes from clinical databases. Pathway enrichment analysis suggests that BTHTT may act through cytokine-cytokine-receptor interactions and thyroid hormone synthesis pathways. Furthermore, while 283 components were identified in vivo, compounds such as tanshinone IIA and cryptotanshinone are currently considered candidate active substances. Their role as primary drivers is supported by a model in which they stably bind to IL-1R2; this inference is based on molecular docking and molecular dynamics (MD) simulations rather than direct experimental isolation. Overall, the data support a model in which BTHTT exerts a multi-target effect on COPD by modulating inflammation and metabolic homeostasis. This integrated approach provides a refined scientific basis for the clinical application of BTHTT and highlights specific pathways for future experimental validation.

PMID:41911070 | DOI:10.3791/70383

Integrative Multi-omics Analysis of Buti Huatan Tang in Chronic Obstructive Pulmonary Disease

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Xin Zha · Wen-Wei Gong · Xue-Ying Li · Qing Xia · Jing-Hua Ruan · Rong Tan · Zhu-Sheng Zhu · Shao-Bo Liu
30 March 2026 at 18:00

J Vis Exp. 2026 Mar 13;(229). doi: 10.3791/70383.

ABSTRACT

This study utilized a multi-omics and computational biology framework to investigate the therapeutic potential of the Traditional Chinese Medicine (TCM) formula Buti Huatan Tang (BTHTT) against chronic obstructive pulmonary disease (COPD). Significant physiological improvements were observed in a rat model following BTHTT intervention. Histological analysis showed a reversal of lung pathological damage, while biochemical assays, and transcriptomics confirmed the normalization of IL-1β and IL-1R2 levels. Additionally, metabolic profiling revealed that BTHTT corrected disruptions in T3 and T4 thyroid hormone levels. A negative correlation was observed between the IL-1β/IL-1R2 axis and these thyroid hormones, indicating that their regulation is associated with the formula's therapeutic effect. Beyond direct measurements, machine learning algorithms identified ten COPD signature genes from clinical databases. Pathway enrichment analysis suggests that BTHTT may act through cytokine-cytokine-receptor interactions and thyroid hormone synthesis pathways. Furthermore, while 283 components were identified in vivo, compounds such as tanshinone IIA and cryptotanshinone are currently considered candidate active substances. Their role as primary drivers is supported by a model in which they stably bind to IL-1R2; this inference is based on molecular docking and molecular dynamics (MD) simulations rather than direct experimental isolation. Overall, the data support a model in which BTHTT exerts a multi-target effect on COPD by modulating inflammation and metabolic homeostasis. This integrated approach provides a refined scientific basis for the clinical application of BTHTT and highlights specific pathways for future experimental validation.

PMID:41911070 | DOI:10.3791/70383

Received — 26 March 2026 ⏭

VLM-CAD: VLM-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing

✇cs.AI, q-bio.NC updates on arXiv.org
By: Guanyuan Pan · Shuai Wang · Yugui Lin · Tiansheng Zhou · Pietro Li\`o · Zhenxin Zhao · Yaqi Wang
25 March 2026 at 12:00
arXiv:2601.07315v4 Announce Type: replace-cross Abstract: Vision Language Models (VLMs) have demonstrated remarkable potential in multimodal reasoning, yet they inherently suffer from spatial blindness and logical hallucinations when interpreting densely structured engineering content, such as analog circuit schematics. To address these challenges, we propose a Vision Language Model-Optimized Collaborative Agent Design Workflow for Analog Circuit Sizing (VLM-CAD) designed for robust, step-by-step reasoning over multimodal evidence. VLM-CAD bridges the modality gap by integrating a neuro-symbolic structural parsing module, Image2Net, which transforms raw pixels into explicit topological graphs and structured JSON representations to anchor VLM interpretation in deterministic facts. To ensure the reliability required for engineering decisions, we further propose ExTuRBO, an Explainable Trust Region Bayesian Optimization method. ExTuRBO serves as an explainable grounding engine, employing agent-generated semantic seeds to warm-start local searches and utilizing Automatic Relevance Determination to provide quantified evidence for the VLM's decisions. Experimental results on two complex circuit benchmarks demonstrate that VLM-CAD significantly enhances spatial reasoning accuracy and maintains physics-based explainability. VLM-CAD consistently satisfies complex specification requirements while achieving low power consumption, with a total runtime under 66 minutes, marking a significant step toward robust, explainable multimodal reasoning in specialized technical domains.

Inactivating <i>SnRK1β1A</i> promotes broad-spectrum disease resistance in rice

✇Nature - Issue - nature.com science feeds
By: Guixin Yuan · Xunli Lu · Xingbin Wang · Mengfei Li · Shiwei Wang · Zhaoxiang Huang · Zhigang Li · Fengrui Zhang · Xin Zhang · Jun Yang · Hailong Guo · Vijai Bhadauria · Wang-Sheng Zhu · Wensheng Zhao · Meng Yuan · Jian-Min Zhou · You-Liang Peng
25 March 2026 at 08:00

Nature, Published online: 25 March 2026; doi:10.1038/s41586-026-10273-5

SnRK1β1A in rice promotes susceptibility to multiple fungal diseases, and disrupting this infection-inducible gene confers broad-spectrum resistance without compromising growth or yield under normal field conditions.

Single-cell multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis

✇Omics In Lung
By: Lanlan Zhang · Xuezhen Gui · Ruijie Hou · Liping Jia · Shu Xia · Xin Zhang · Yingyun Fu · Qian-Fang Meng · Qun Luo · Xing Shi · Bingxin Guo · Ruifang Liang · Ludan Yue · Xue Chen · Haizhao Xu · Pengbo Wang · Xia Tong · Lujie Liu · Lingwei Wang · Baicun Li · Zi Chen · Linfu Zhou · Linshu Zhang · Rongchang Chen · Changbin Sun · Wei Xu · Lang Rao · Haibo Zhou · Bi-Sen Ding · Shanze Chen
21 March 2026 at 18:00

Nat Commun. 2026 Mar 20;17(1):2655. doi: 10.1038/s41467-026-70193-w.

ABSTRACT

Pulmonary fibrosis represents a progressive interstitial lung disease marked by excessive extracellular matrix deposition and architectural distortion. Vascular endothelial cells critically contribute to fibrogenesis through paracrine secretion of pro-fibrotic mediators, yet their mechanobiological regulation remains elusive. Using integrated single-cell multi-omics profiling of human pulmonary fibrosis specimens and experimental fibrosis models induced by bleomycin or silica, we identify mechanosensitive Piezo1 upregulation in Endothelial cells as a hallmark of fibrotic progression. Endothelial-specific Piezo1 knockout significantly attenuates Bleomycin-induced fibrotic remodeling in male mice, establishing its pathogenic necessity. Mechanistically, PIEZO1 activation promotes pulmonary fibrosis development via CAPN2-mediated STAT3 phosphorylation, which may regulate the secretion of the pro-fibrotic molecule interleukin-33. These findings suggest that the endothelial PIEZO1-CAPN2-STAT3-IL33 axis is a potential therapeutic target for PF intervention.

PMID:41862476 | PMC:PMC13004862 | DOI:10.1038/s41467-026-70193-w

A multiomics Mendelian randomization study on PANoptosis-related genes and gastric cancer risk

✇Omics in Gastric
By: Yunliang Wang · Yujian Xia · Lin Weng · Jin Wang · Wenzi Meng · Jiahui Zhu · Xin Zhao · Xinguo Zhu
17 March 2026 at 18:00

J Int Med Res. 2026 Mar;54(3):3000605261430163. doi: 10.1177/03000605261430163. Epub 2026 Mar 16.

ABSTRACT

ObjectiveTo explore the potential involvement of PANoptosis-related genes in gastric cancer susceptibility through multiomics analyses.MethodsSummary-data-based Mendelian randomization was performed by integrating blood-derived methylation, gene expression, and protein quantitative trait loci data with genome-wide association study results. The findings were further evaluated in The Cancer Genome Atlas cohort, followed by protein-protein interaction analysis, drug prediction, and molecular docking.ResultsSummary-data-based Mendelian randomization and colocalization analyses identified several traits suggestively associated with gastric cancer risk. Genetically predicted higher expression of apoptosis and caspase activation inhibitor (AVEN) and hepatocyte growth factor (HGF) as well as higher HGF protein levels were associated with increased risk, whereas higher levels of protein phosphatase 2 regulatory subunit B beta (PPP2R2B) appeared to be protective. Multiomics integration suggested epigenetic regulation of HGF and PPP2R2B. The Cancer Genome Atlas analysis corroborated the dysregulation of these candidates, with high AVEN expression associated with poorer survival. Protein-protein interaction and drug prediction analyses highlighted functional networks and potential therapeutics, supported by molecular docking demonstrating strong HGF-binding affinities. However, these associations did not reach statistical significance in the independent validation cohort, possibly due to limited statistical power.ConclusionsThis study identified AVEN, HGF, and PPP2R2B as potential candidate genes for gastric cancer. These findings require further validation in larger cohorts.

PMID:41840829 | DOI:10.1177/03000605261430163

Received — 17 March 2026 ⏭

Partially Recentralization Softmax Loss for Vision-Language Models Robustness

✇cs.AI, q-bio.NC updates on arXiv.org
By: Hao Wang · Jinzhe Jiang · Xin Zhang · Chen Li
16 March 2026 at 12:00
arXiv:2402.03627v4 Announce Type: replace-cross Abstract: As Large Language Models make a breakthrough in natural language processing tasks (NLP), multimodal technique becomes extremely popular. However, it has been shown that multimodal NLP are vulnerable to adversarial attacks, where the outputs of a model can be dramatically changed by a perturbation to the input. While several defense techniques have been proposed both in computer vision and NLP models, the multimodal robustness of models have not been fully explored. In this paper, we study the adversarial robustness provided by modifying loss function of pre-trained multimodal models, by restricting top K softmax outputs. Based on the evaluation and scoring, our experiments show that after a fine-tuning, adversarial robustness of pre-trained models can be significantly improved, against popular attacks. Further research should be studying, such as output diversity, generalization and the robustness-performance trade-off of this kind of loss functions. Our code will be available after this paper is accepted

How to Build a Quantum Supercomputer: Scaling from Hundreds to Millions of Qubits

✇cs.AI, q-bio.NC updates on arXiv.org
By: Masoud Mohseni · Artur Scherer · K. Grace Johnson · Oded Wertheim · Matthew Otten · Namit Anand · Navid Anjum Aadit · Yuri Alexeev · Gilad Ben-Shach · Kirk M. Bresniker · Kerem Y. Camsari · Barbara Chapman · Soumitra Chatterjee · Shuvro Chowdhury · Gebremedhin A. Dagnew · Tom Dvir · Aniello Esposito · Farah Fahim · Michael Ferguson · Marco Fiorentino · Archit Gajjar · Katerina Gratsea · Gaurav Gyawali · Christian Heiter · Ali H. Z. Kavaki · Abdullah Khalid · Xiangzhou Kong · Bohdan Kulchytskyy · Elica Kyoseva · Ruoyu Li · P. Aaron Lott · Igor L. Markov · Robert F. McDermott · Lucas Morais · Giacomo Pedretti · Pooja Rao · Eleanor Rieffel · Allyson Silva · John Sorebo · Panagiotis Spentzouris · Ziv Steiner · Boyan Torosov · Davide Venturelli · Robert J. Visser · Zak Webb · Xin Zhan · Yonatan Cohen · Pooya Ronagh · Alan Ho · Raymond G. Beausoleil · John M. Martinis
16 March 2026 at 12:00
arXiv:2411.10406v3 Announce Type: replace-cross Abstract: In the span of four decades, quantum computation has evolved from an intellectual curiosity to a potentially realizable technology. Today, small-scale demonstrations have become possible for quantum algorithmic primitives on hundreds of physical qubits. Nevertheless, there are significant outstanding challenges in quantum hardware, fabrication, software architecture, and algorithms on the path towards a full-stack scalable quantum computing technology. Here, we provide a comprehensive review of these scaling challenges. We show how to facilitate scaling by adopting existing semiconductor technology to build much higher-quality qubits, employing systems engineering approaches, and performing distributed heterogeneous quantum-classical computing. We provide a detailed resource and sensitivity analysis for quantum applications on surface-code error-corrected quantum computers given current, target, and desired hardware specifications based on superconducting qubits, accounting for a realistic distribution of errors. We provide comprehensive resource estimates for several utility-scale applications including quantum chemistry calculations, catalyst design, NMR spectroscopy, and Fermi-Hubbard simulation. We show that orders of magnitude enhancement in performance could be obtained by a combination of hardware improvements and tight quantum-HPC integration. Furthermore, we introduce high-performance architectures for quantum-probabilistic computing with custom-designed accelerators to tackle today's industry-scale classical optimization, machine learning, and quantum simulation tasks in a cost-effective manner.
Received — 14 March 2026 ⏭
Received — 11 March 2026 ⏭

Contact-Guided 3D Genome Structure Generation of E. coli via Diffusion Transformers

✇cs.AI, q-bio.NC updates on arXiv.org
By: Mingxin Zhang · Xiaofeng Dai · Yu Yao · Ziqi Yin
10 March 2026 at 12:00
arXiv:2603.07472v1 Announce Type: cross Abstract: In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure, we formulate genome reconstruction as a conditional generative modeling problem that samples heterogeneous conformations whose ensemble-averaged contacts are consistent with the input Hi-C data. A synthetic dataset is constructed using coarse-grained molecular dynamics simulations to generate chromatin ensembles and corresponding Hi-C maps under circular topology. Our models operate in a latent diffusion setting with a variational autoencoder that preserves per-bin alignment and supports replication-aware representations. Hi-C information is injected through a transformer-based encoder and cross-attention, enforcing a physically interpretable one-way constraint from Hi-C to structure. The model is trained using a flow-matching objective for stable optimization. On held-out ensembles, generated structures reproduce the input Hi-C distance-decay and structural correlation metrics while maintaining substantial conformational diversity, demonstrating the effectiveness of diffusion-based generative modeling for ensemble-level 3D genome reconstruction.

CrystaL: Spontaneous Emergence of Visual Latents in MLLMs

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yang Zhang · Danyang Li · Yuxuan Li · Xin Zhang · Tianyu Xie · Mingming Cheng · Xiang Li
10 March 2026 at 12:00
arXiv:2602.20980v2 Announce Type: replace-cross Abstract: Multimodal Large Language Models (MLLMs) have achieved remarkable performance by integrating powerful language backbones with large-scale visual encoders. Among these, latent Chain-of-Thought (CoT) methods enable implicit reasoning in continuous hidden states, facilitating seamless vision-language integration and faster inference. However, existing heuristically predefined supervision signals in latent CoT provide limited guidance for preserving critical visual information in intermediate latent states. To address this limitation, we propose CrystaL (Crystallized Latent Reasoning), a single-stage framework with two paths to process intact and corrupted images, respectively. By explicitly aligning the attention patterns and prediction distributions across the two paths, CrystaL crystallizes latent representations into task-relevant visual semantics, without relying on auxiliary annotations or external modules. Extensive experiments on perception-intensive benchmarks demonstrate that CrystaL consistently outperforms state-of-the-art baselines, achieving substantial gains in fine-grained visual understanding while maintaining robust reasoning capabilities.
Received — 5 March 2026 ⏭

IntPro: A Proxy Agent for Context-Aware Intent Understanding via Retrieval-conditioned Inference

✇cs.AI, q-bio.NC updates on arXiv.org
By: Guanming Liu · Meng Wu · Peng Zhang · Yu Zhang · Yubo Shu · Xianliang Huang · Kainan Tu · Ning Gu · Liuxin Zhang · Qianying Wang · Tun Lu
5 March 2026 at 13:00
arXiv:2603.03325v1 Announce Type: cross Abstract: Large language models (LLMs) have become integral to modern Human-AI collaboration workflows, where accurately understanding user intent serves as a crucial step for generating satisfactory responses. Context-aware intent understanding, which involves inferring user intentions from situational environments, is inherently challenging because it requires reasoning over both the immediate context and the user's underlying motivations that drive their behavior. Moreover, existing approaches often treat intent understanding as a static recognition task, overlooking users' accumulated intent patterns that could provide valuable references for more accurate and generalizable understanding. To address this gap, we propose IntPro, a proxy agent that learns to adapt to individual users via retrieval-conditioned intent inference. We design intent explanations that abstract how contextual signals connect to expressed intents, and store them in an individual intent history library for retrieval. We train IntPro through supervised fine-tuning on retrieval-conditioned trajectories and multi-turn Group Relative Policy Optimization (GRPO) with tool-aware reward functions, enabling the agent to learn when to leverage historical intent patterns and when to infer directly. Experiments across three diverse scenarios (Highlight-Intent, MIntRec2.0, and Weibo Post-Sync) demonstrate that IntPro achieves strong intent understanding performance with effective context-aware reasoning capabilities across different scenarios and model types.
Received — 25 February 2026 ⏭

IR$^3$: Contrastive Inverse Reinforcement Learning for Interpretable Detection and Mitigation of Reward Hacking

✇cs.AI, q-bio.NC updates on arXiv.org
By: Mohammad Beigi · Ming Jin · Junshan Zhang · Jiaxin Zhang · Qifan Wang · Lifu Huang
24 February 2026 at 13:00
arXiv:2602.19416v1 Announce Type: new Abstract: Reinforcement Learning from Human Feedback (RLHF) enables powerful LLM alignment but can introduce reward hacking - models exploit spurious correlations in proxy rewards without genuine alignment. Compounding this, the objectives internalized during RLHF remain opaque, making hacking behaviors difficult to detect or correct. We introduce IR3 (Interpretable Reward Reconstruction and Rectification), a framework that reverse-engineers, interprets, and surgically repairs the implicit objectives driving RLHF-tuned models. We propose Contrastive Inverse Reinforcement Learning (C-IRL), which reconstructs the implicit reward function by contrasting paired responses from post-alignment and baseline policies to explain behavioral shifts during RLHF. We then decompose the reconstructed reward via sparse autoencoders into interpretable features, enabling identification of hacking signatures through contribution analysis. Finally, we propose mitigation strategies - clean reward optimization, adversarial shaping, constrained optimization, and feature-guided distillation - that target problematic features while preserving beneficial alignment. Experiments across multiple reward model configurations show that IR3 achieves 0.89 correlation with ground-truth rewards, identifies hacking features with over 90% precision, and significantly reduces hacking behaviors while maintaining capabilities within 3% of the original model.

Feature Representation Transferring to Lightweight Models via Perception Coherence

✇cs.AI, q-bio.NC updates on arXiv.org
By: Hai-Vy Nguyen · Fabrice Gamboa · Sixin Zhang · Reda Chhaibi · Serge Gratton · Thierry Giaccone
24 February 2026 at 13:00
arXiv:2505.06595v3 Announce Type: replace-cross Abstract: In this paper, we propose a method for transferring feature representation to lightweight student models from larger teacher models. We mathematically define a new notion called \textit{perception coherence}. Based on this notion, we propose a loss function, which takes into account the dissimilarities between data points in feature space through their ranking. At a high level, by minimizing this loss function, the student model learns to mimic how the teacher model \textit{perceives} inputs. More precisely, our method is motivated by the fact that the representational capacity of the student model is weaker than the teacher model. Hence, we aim to develop a new method allowing for a better relaxation. This means that, the student model does not need to preserve the absolute geometry of the teacher one, while preserving global coherence through dissimilarity ranking. Importantly, while rankings are defined only on finite sets, our notion of \textit{perception coherence} extends them into a probabilistic form. This formulation depends on the input distribution and applies to general dissimilarity metrics. Our theoretical insights provide a probabilistic perspective on the process of feature representation transfer. Our experiments results show that our method outperforms or achieves on-par performance compared to strong baseline methods for representation transferring.
Received — 17 February 2026 ⏭

RV-Syn: Rational and Verifiable Mathematical Reasoning Data Synthesis based on Structured Function Library

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jiapeng Wang · Jinhao Jiang · Zhiqiang Zhang · Jun Zhou · Wayne Xin Zhao
17 February 2026 at 13:00
arXiv:2504.20426v3 Announce Type: replace Abstract: The advancement of reasoning capabilities in Large Language Models (LLMs) requires substantial amounts of high-quality reasoning data, particularly in mathematics. Existing data synthesis methods, such as data augmentation from annotated training sets or direct question generation based on relevant knowledge points and documents, have expanded datasets but face challenges in mastering the inner logic of the problem during generation and ensuring the verifiability of the solutions. To address these issues, we propose RV-Syn, a novel Rational and Verifiable mathematical Synthesis approach. RV-Syn constructs a structured mathematical operation function library based on initial seed problems and generates computational graphs as solutions by combining Python-formatted functions from this library. These graphs are then back-translated into complex problems. Based on the constructed computation graph, we achieve solution-guided logic-aware problem generation. Furthermore, the executability of the computational graph ensures the verifiability of the solving process. Experimental results show that RV-Syn surpasses existing synthesis methods, including those involving human-generated problems, achieving greater efficient data scaling. This approach provides a scalable framework for generating high-quality reasoning datasets.
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