Normal view
-
cs.AI, q-bio.NC updates on arXiv.org
-
Group Representational Position Encoding
arXiv:2512.07805v5 Announce Type: replace-cross Abstract: We present GRAPE (Group Representational Position Encoding), a unified framework for positional encoding based on group actions. GRAPE unifies two families of mechanisms: (i) multiplicative rotations (Multiplicative GRAPE) in $\operatorname{SO}(d)$ and (ii) additive logit biases (Additive GRAPE) arising from unipotent actions in the general linear group $\mathrm{GL}$. In Multiplicative GRAPE, a position $n \in \mathbb{Z}$ (or $t \in \mat
-
Cell
-
Metabolite-gated vascular contractility switch: OXGR1 activation mechanism enables agonist therapy for rosacea erythema
Xiao et al. identify α-KG as a rosacea-associated metabolite that activates the OXGR1-Gq-MYL9 axis in the vascular smooth muscle cells to boost contractility and suppress pathological vasodilation underlying erythema. Cryo-EM reveals a bipartite-acid pocket of OXGR1 that enables structure-guided development of A-1, a selective agonist that alleviates erythema in rosacea-like models.
Metabolite-gated vascular contractility switch: OXGR1 activation mechanism enables agonist therapy for rosacea erythema
-
cs.AI, q-bio.NC updates on arXiv.org
-
Dynamic Cogeneration of Bug Reproduction Test in Agentic Program Repair
arXiv:2601.19066v2 Announce Type: replace-cross Abstract: Bug Reproduction Tests (BRTs) have been used in many Automated Program Repair (APR) systems, primarily for validating promising fixes and aiding fix generation. In practice, when developers submit a patch, they often implement the BRT alongside the fix. Our experience deploying agentic APR reveals that developers similarly desire a BRT within AI-generated patches to increase their confidence. However, canonical APR systems tend to genera
Dynamic Cogeneration of Bug Reproduction Test in Agentic Program Repair
-
Oncogene - Issue - nature.com science feeds
-
Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis
Oncogene, Published online: 01 April 2026; doi:10.1038/s41388-026-03754-4Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis
Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis
Oncogene, Published online: 01 April 2026; doi:10.1038/s41388-026-03754-4
Targeting FTO shows therapeutic potential in esophageal squamous cell carcinoma by modulating microRNA biogenesis-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
-
CircRNA-encoded RIPK1-98 protein drives lung adenocarcinoma progression
Dev Cell. 2026 Mar 12:S1534-5807(26)00079-1. doi: 10.1016/j.devcel.2026.02.014. Online ahead of print.ABSTRACTUnexplored biological matter-including uncharacterized genetic elements, molecular entities, and microbial components-remains poorly understood. Here, we use integrated multi-omics approaches to identify and characterize previously unrecognized protein products encoded by circular RNAs (circRNAs) in human tissue specimens and to delineate their roles in the progression of lung adenocarci
CircRNA-encoded RIPK1-98 protein drives lung adenocarcinoma progression
Dev Cell. 2026 Mar 12:S1534-5807(26)00079-1. doi: 10.1016/j.devcel.2026.02.014. Online ahead of print.
ABSTRACT
Unexplored biological matter-including uncharacterized genetic elements, molecular entities, and microbial components-remains poorly understood. Here, we use integrated multi-omics approaches to identify and characterize previously unrecognized protein products encoded by circular RNAs (circRNAs) in human tissue specimens and to delineate their roles in the progression of lung adenocarcinoma (LUAD). The transcription of precursor mRNA by RNA polymerase Ⅱ subunit A (RPB1) is crucial for the biogenesis of these potential circRNA-encoded proteins. Functional and translational analyses link their expression to distinct pathological stages of LUAD in patients. The protein RIPK1-98, encoded by circRIPK1, was identified as functionally distinct from its parental gene product, receptor-interacting serine/threonine kinase 1 (RIPK1). RIPK1-98 modulates cyclin-dependent kinase 2 (CDK2)-dependent cell-cycle regulation, thereby facilitating tumor proliferation in cellular and animal models. Together, these findings suggest that RIPK1-98 serves as a biomarker for cell-cycle progression in LUAD and highlight its potential as a therapeutic target to counteract resistance to first-line treatments, such as osimertinib.
PMID:41825439 | DOI:10.1016/j.devcel.2026.02.014
-
Omics In Lung
-
CircRNA-encoded RIPK1-98 protein drives lung adenocarcinoma progression
Dev Cell. 2026 Mar 12:S1534-5807(26)00079-1. doi: 10.1016/j.devcel.2026.02.014. Online ahead of print.ABSTRACTUnexplored biological matter-including uncharacterized genetic elements, molecular entities, and microbial components-remains poorly understood. Here, we use integrated multi-omics approaches to identify and characterize previously unrecognized protein products encoded by circular RNAs (circRNAs) in human tissue specimens and to delineate their roles in the progression of lung adenocarci
CircRNA-encoded RIPK1-98 protein drives lung adenocarcinoma progression
Dev Cell. 2026 Mar 12:S1534-5807(26)00079-1. doi: 10.1016/j.devcel.2026.02.014. Online ahead of print.
ABSTRACT
Unexplored biological matter-including uncharacterized genetic elements, molecular entities, and microbial components-remains poorly understood. Here, we use integrated multi-omics approaches to identify and characterize previously unrecognized protein products encoded by circular RNAs (circRNAs) in human tissue specimens and to delineate their roles in the progression of lung adenocarcinoma (LUAD). The transcription of precursor mRNA by RNA polymerase Ⅱ subunit A (RPB1) is crucial for the biogenesis of these potential circRNA-encoded proteins. Functional and translational analyses link their expression to distinct pathological stages of LUAD in patients. The protein RIPK1-98, encoded by circRIPK1, was identified as functionally distinct from its parental gene product, receptor-interacting serine/threonine kinase 1 (RIPK1). RIPK1-98 modulates cyclin-dependent kinase 2 (CDK2)-dependent cell-cycle regulation, thereby facilitating tumor proliferation in cellular and animal models. Together, these findings suggest that RIPK1-98 serves as a biomarker for cell-cycle progression in LUAD and highlight its potential as a therapeutic target to counteract resistance to first-line treatments, such as osimertinib.
PMID:41825439 | DOI:10.1016/j.devcel.2026.02.014
-
cs.AI, q-bio.NC updates on arXiv.org
-
FinToolBench: Evaluating LLM Agents for Real-World Financial Tool Use
arXiv:2603.08262v1 Announce Type: new Abstract: The integration of Large Language Models (LLMs) into the financial domain is driving a paradigm shift from passive information retrieval to dynamic, agentic interaction. While general-purpose tool learning has witnessed a surge in benchmarks, the financial sector, characterized by high stakes, strict compliance, and rapid data volatility, remains critically underserved. Existing financial evaluations predominantly focus on static textual analysis
FinToolBench: Evaluating LLM Agents for Real-World Financial Tool Use
-
cs.AI, q-bio.NC updates on arXiv.org
-
DARC: Disagreement-Aware Alignment via Risk-Constrained Decoding
arXiv:2603.08145v1 Announce Type: cross Abstract: Preference-based alignment methods (e.g., RLHF, DPO) typically optimize a single scalar objective, implicitly averaging over heterogeneous human preferences. In practice, systematic annotator and user-group disagreement makes mean-reward maximization brittle and susceptible to proxy over-optimization. We propose **Disagreement-Aware Alignment via Risk-Constrained Decoding (DARC)**, a retraining-free inference-time method that frames response sel
DARC: Disagreement-Aware Alignment via Risk-Constrained Decoding
-
cs.AI, q-bio.NC updates on arXiv.org
-
Prompt Optimization Via Diffusion Language Models
arXiv:2602.18449v1 Announce Type: cross Abstract: We propose a diffusion-based framework for prompt optimization that leverages Diffusion Language Models (DLMs) to iteratively refine system prompts through masked denoising. By conditioning on interaction traces, including user queries, model responses, and optional feedback, our method enables flexible, span-level prompt updates without requiring gradient access or modifying the downstream language model. Across diverse benchmarks (e.g., $\tau$
Prompt Optimization Via Diffusion Language Models
-
cs.AI, q-bio.NC updates on arXiv.org
-
Group Representational Position Encoding
arXiv:2512.07805v4 Announce Type: replace-cross Abstract: We present GRAPE (Group Representational Position Encoding), a unified framework for positional encoding based on group actions. GRAPE unifies two families of mechanisms: (i) multiplicative rotations (Multiplicative GRAPE) in $\operatorname{SO}(d)$ and (ii) additive logit biases (Additive GRAPE) arising from unipotent actions in the general linear group $\mathrm{GL}$. In Multiplicative GRAPE, a position $n \in \mathbb{Z}$ (or $t \in \mat
Group Representational Position Encoding
-
cs.AI, q-bio.NC updates on arXiv.org
-
STaRR: Spatial-Temporal Token-Dynamics-Aware Responsive Remasking for Diffusion Language Models
arXiv:2601.04205v2 Announce Type: replace-cross Abstract: Diffusion Language Models (DLMs) enable parallel decoding via iterative denoising, where remasking strategies play a critical role in balancing inference speed and output quality. Existing methods predominantly rely on static confidence thresholds, overlooking the spatial-temporal dynamics of token confidence, causing unnecessary remasking. We propose Spatial-Temporal Token-Dynamics-Aware Responsive Remasking (STaRR), a training-free fra