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Normal view

Received — 27 May 2026 ⏭

Cascade-KDE: Robust Time-Series Restoration under Out-of-Distribution Impulse Corruptions

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yuefeng Liu · Ning Yang · Ziyu Yang
26 May 2026 at 12:00
arXiv:2605.24055v1 Announce Type: cross Abstract: Real-world time-series data in industrial sensing, healthcare, and energy systems is often corrupted by a mixture of Gaussian noise and occasional large-magnitude impulse outliers. For tasks that depend on local shape, such as ECG morphology analysis and battery degradation monitoring, the main requirement is not only low reconstruction error but also preservation of derivative peaks and task-critical features. We propose Cascade-KDE, a training-free restoration framework for corrupted time series. The method first estimates a two-dimensional temporal-amplitude density, then applies a Density-Truncated Robust Expectation to limit the influence of distant abnormal points, and finally refines the sequence through an exponential cascade with adaptive stopping. This design aims to improve robustness under out-of-distribution impulse corruptions while keeping the restored trajectory close to the original local structure. Across several benchmark datasets, the proposed method shows consistent gains over classical filters and representative learning-based baselines on curve fidelity, derivative preservation, downstream classification, and runtime efficiency. These results suggest that bounded density-based restoration is a practical option for feature-preserving preprocessing in noisy time-series pipelines.

CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection

✇(Multiomics OR Omics) AND (Pancreatic)
By: Zhengjian Wang · Zhe Wang · Xuda Ji · Liping Zhao · Kai Zheng · Wen Yu · Hanzhe Zhang · Hong Chang · Fangfeng Liu
25 May 2026 at 18:00

J Transl Med. 2026 May 25. doi: 10.1186/s12967-026-08301-z. Online ahead of print.

ABSTRACT

BACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an integrative genetic and multi-omics framework, we investigated complement receptor 1 (CR1) as a candidate regulator of this immunosuppressive niche.

METHODS: We combined Mendelian randomization (MR) and metabolite mediation analyses with bulk, single-cell, and spatial transcriptomics to define the role of CR1 in HCC. Public datasets included the TCGA-HCC cohort, a single-cell RNA-sequencing dataset comprising 53,474 high-quality cells from 21 samples, and two spatially profiled HCC sections. Clinical validation was performed in 30 paired HCC and adjacent liver tissues. Functional assays were conducted in THP-1-derived macrophages using CR1 gain- and loss-of-function approaches, phagocytosis assays, and macrophage-CD8+ T-cell co-culture experiments.

RESULTS: MR analyses implicated CR1 in HCC susceptibility at both the protein and transcript levels. pQTL analysis linked genetically predicted circulating CR1 levels to HCC risk (IVW OR = 1.403, p = 0.017), and mediation analysis identified specific metabolites as candidate intermediates. Integrative multi-omics analyses showed that CR1 was preferentially enriched in TAMs, spatially co-localized with the M2 marker CD206, and associated with reduced CD8+ T-cell infiltration, enhanced T-cell exhaustion signatures, advanced clinicopathological features, and poorer survival. In 30 paired clinical samples, CR1-high tumors exhibited increased M2-like macrophage accumulation and reduced CD8+ T-cell infiltration. Functionally, CR1 overexpression drove macrophages toward an M2-like phenotype, enhanced phagocytic activity, increased PD-L1 expression, and suppressed CD8+ T-cell proliferation as well as IFN-gamma and granzyme B production, whereas CR1 knockdown produced the opposite phenotype.

CONCLUSIONS: Our study provides the first integrated genetic, spatial, and functional evidence that CR1+ TAMs constitute a clinically relevant immunoregulatory axis in HCC. These findings extend current understanding of complement-associated immunosuppression beyond canonical complement cascade activity and support CR1 as a candidate biomarker and therapeutic target for macrophage reprogramming, with potential translational relevance for combination strategies involving immune checkpoint blockade.

PMID:42185899 | DOI:10.1186/s12967-026-08301-z

CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection

✇Omics in Hepatocellular
By: Zhengjian Wang · Zhe Wang · Xuda Ji · Liping Zhao · Kai Zheng · Wen Yu · Hanzhe Zhang · Hong Chang · Fangfeng Liu
25 May 2026 at 18:00

J Transl Med. 2026 May 25. doi: 10.1186/s12967-026-08301-z. Online ahead of print.

ABSTRACT

BACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an integrative genetic and multi-omics framework, we investigated complement receptor 1 (CR1) as a candidate regulator of this immunosuppressive niche.

METHODS: We combined Mendelian randomization (MR) and metabolite mediation analyses with bulk, single-cell, and spatial transcriptomics to define the role of CR1 in HCC. Public datasets included the TCGA-HCC cohort, a single-cell RNA-sequencing dataset comprising 53,474 high-quality cells from 21 samples, and two spatially profiled HCC sections. Clinical validation was performed in 30 paired HCC and adjacent liver tissues. Functional assays were conducted in THP-1-derived macrophages using CR1 gain- and loss-of-function approaches, phagocytosis assays, and macrophage-CD8+ T-cell co-culture experiments.

RESULTS: MR analyses implicated CR1 in HCC susceptibility at both the protein and transcript levels. pQTL analysis linked genetically predicted circulating CR1 levels to HCC risk (IVW OR = 1.403, p = 0.017), and mediation analysis identified specific metabolites as candidate intermediates. Integrative multi-omics analyses showed that CR1 was preferentially enriched in TAMs, spatially co-localized with the M2 marker CD206, and associated with reduced CD8+ T-cell infiltration, enhanced T-cell exhaustion signatures, advanced clinicopathological features, and poorer survival. In 30 paired clinical samples, CR1-high tumors exhibited increased M2-like macrophage accumulation and reduced CD8+ T-cell infiltration. Functionally, CR1 overexpression drove macrophages toward an M2-like phenotype, enhanced phagocytic activity, increased PD-L1 expression, and suppressed CD8+ T-cell proliferation as well as IFN-gamma and granzyme B production, whereas CR1 knockdown produced the opposite phenotype.

CONCLUSIONS: Our study provides the first integrated genetic, spatial, and functional evidence that CR1+ TAMs constitute a clinically relevant immunoregulatory axis in HCC. These findings extend current understanding of complement-associated immunosuppression beyond canonical complement cascade activity and support CR1 as a candidate biomarker and therapeutic target for macrophage reprogramming, with potential translational relevance for combination strategies involving immune checkpoint blockade.

PMID:42185899 | DOI:10.1186/s12967-026-08301-z

CR1(+) tumor-associated macrophages orchestrate an immunosuppressive niche in hepatocellular carcinoma: a genetic and multi-omics dissection

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Zhengjian Wang · Zhe Wang · Xuda Ji · Liping Zhao · Kai Zheng · Wen Yu · Hanzhe Zhang · Hong Chang · Fangfeng Liu
25 May 2026 at 18:00

J Transl Med. 2026 May 25. doi: 10.1186/s12967-026-08301-z. Online ahead of print.

ABSTRACT

BACKGROUND: Hepatocellular carcinoma (HCC) remains a major global health burden and a leading cause of cancer-related mortality. Advanced disease is characterized by a profoundly immunosuppressive tumor microenvironment (TME) and limited durable responses to therapy. However, the upstream genetic determinants that drive tumor-associated macrophage (TAM) dysfunction in HCC remain poorly defined. Using an integrative genetic and multi-omics framework, we investigated complement receptor 1 (CR1) as a candidate regulator of this immunosuppressive niche.

METHODS: We combined Mendelian randomization (MR) and metabolite mediation analyses with bulk, single-cell, and spatial transcriptomics to define the role of CR1 in HCC. Public datasets included the TCGA-HCC cohort, a single-cell RNA-sequencing dataset comprising 53,474 high-quality cells from 21 samples, and two spatially profiled HCC sections. Clinical validation was performed in 30 paired HCC and adjacent liver tissues. Functional assays were conducted in THP-1-derived macrophages using CR1 gain- and loss-of-function approaches, phagocytosis assays, and macrophage-CD8+ T-cell co-culture experiments.

RESULTS: MR analyses implicated CR1 in HCC susceptibility at both the protein and transcript levels. pQTL analysis linked genetically predicted circulating CR1 levels to HCC risk (IVW OR = 1.403, p = 0.017), and mediation analysis identified specific metabolites as candidate intermediates. Integrative multi-omics analyses showed that CR1 was preferentially enriched in TAMs, spatially co-localized with the M2 marker CD206, and associated with reduced CD8+ T-cell infiltration, enhanced T-cell exhaustion signatures, advanced clinicopathological features, and poorer survival. In 30 paired clinical samples, CR1-high tumors exhibited increased M2-like macrophage accumulation and reduced CD8+ T-cell infiltration. Functionally, CR1 overexpression drove macrophages toward an M2-like phenotype, enhanced phagocytic activity, increased PD-L1 expression, and suppressed CD8+ T-cell proliferation as well as IFN-gamma and granzyme B production, whereas CR1 knockdown produced the opposite phenotype.

CONCLUSIONS: Our study provides the first integrated genetic, spatial, and functional evidence that CR1+ TAMs constitute a clinically relevant immunoregulatory axis in HCC. These findings extend current understanding of complement-associated immunosuppression beyond canonical complement cascade activity and support CR1 as a candidate biomarker and therapeutic target for macrophage reprogramming, with potential translational relevance for combination strategies involving immune checkpoint blockade.

PMID:42185899 | DOI:10.1186/s12967-026-08301-z

Received — 4 April 2026 ⏭
  • ✇cs.AI, q-bio.NC updates on arXiv.org
  • Combating Data Laundering in LLM Training Muxing Li · Zesheng Ye · Sharon Li · Feng Liu
    arXiv:2604.01904v1 Announce Type: cross Abstract: Data rights owners can detect unauthorized data use in large language model (LLM) training by querying with proprietary samples. Often, superior performance (e.g., higher confidence or lower loss) on a sample relative to the untrained data implies it was part of the training corpus, as LLMs tend to perform better on data they have seen during training. However, this detection becomes fragile under data laundering, a practice of transforming the
     
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Combating Data Laundering in LLM Training

✇cs.AI, q-bio.NC updates on arXiv.org
By: Muxing Li · Zesheng Ye · Sharon Li · Feng Liu
3 April 2026 at 12:00
arXiv:2604.01904v1 Announce Type: cross Abstract: Data rights owners can detect unauthorized data use in large language model (LLM) training by querying with proprietary samples. Often, superior performance (e.g., higher confidence or lower loss) on a sample relative to the untrained data implies it was part of the training corpus, as LLMs tend to perform better on data they have seen during training. However, this detection becomes fragile under data laundering, a practice of transforming the stylistic form of proprietary data, while preserving critical information to obfuscate data provenance. When an LLM is trained exclusively on such laundered variants, it no longer performs better on originals, erasing the signals that standard detections rely on. We counter this by inferring the unknown laundering transformation from black-box access to the target LLM and, via an auxiliary LLM, synthesizing queries that mimic the laundered data, even if rights owners have only the originals. As the search space of finding true laundering transformations is infinite, we abstract such a process into a high-level transformation goal (e.g., "lyrical rewriting") and concrete details (e.g., "with vivid imagery"), and introduce synthesis data reversion (SDR) that instantiates this abstraction. SDR first identifies the most probable goal for synthesis to narrow the search; it then iteratively refines details so that synthesized queries gradually elicit stronger detection signals from the target LLM. Evaluated on the MIMIR benchmark against diverse laundering practices and target LLM families (Pythia, Llama2, and Falcon), SDR consistently strengthens data misuse detection, providing a practical countermeasure to data laundering.

Group Representational Position Encoding

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yifan Zhang · Zixiang Chen · Yifeng Liu · Zhen Qin · Huizhuo Yuan · Kangping Xu · Yang Yuan · Quanquan Gu · Andrew Chi-Chih Yao
3 April 2026 at 12:00
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 $t \in \mathbb{R}$) acts as $\mathbf{G}(n) = \exp(n \, \omega \, \mathbf{L})$ with a rank-2 skew-symmetric generator $\mathbf{L} \in \mathbb{R}^{d \times d}$, yielding a relative, compositional, norm-preserving map with a closed-form matrix exponential. RoPE is recovered exactly when the $d/2$ planes correspond to canonical coordinate pairs with a log-uniform spectrum. Learned commuting subspaces and compact non-commuting mixtures strictly extend this geometry to capture cross-subspace feature coupling at $O(d)$ and $O(r d)$ cost per head, respectively. In Additive GRAPE, additive logits arise from rank-1 (or low-rank) unipotent actions, recovering ALiBi and the Forgetting Transformer (FoX) as exact special cases while preserving an exact relative law and streaming cacheability. Overall, GRAPE provides a principled design space for positional geometry in long-context models, subsuming RoPE and ALiBi as special cases. Project page: https://github.com/model-architectures/GRAPE.

NeuroNarrator: A Generalist EEG-to-Text Foundation Model for Clinical Interpretation via Spectro-Spatial Grounding and Temporal State-Space Reasoning

✇cs.AI, q-bio.NC updates on arXiv.org
By: Guoan Wang · Shihao Yang · Jun-en Ding · Hao Zhu · Feng Liu
3 April 2026 at 12:00
arXiv:2603.16880v2 Announce Type: replace-cross Abstract: Electroencephalography (EEG) provides a non-invasive window into neural dynamics at high temporal resolution and plays a pivotal role in clinical neuroscience research. Despite this potential, prevailing computational approaches to EEG analysis remain largely confined to task-specific classification objectives or coarse-grained pattern recognition, offering limited support for clinically meaningful interpretation. To address these limitations, we introduce NeuroNarrator, the first generalist EEG-to-text foundation model designed to translate electrophysiological segments into precise clinical narratives. A cornerstone of this framework is the curation of NeuroCorpus-160K, the first harmonized large-scale resource pairing over 160,000 EEG segments with structured, clinically grounded natural-language descriptions. Our architecture first aligns temporal EEG waveforms with spatial topographic maps via a rigorous contrastive objective, establishing spectro-spatially grounded representations. Building on this grounding, we condition a Large Language Model through a state-space-inspired formulation that integrates historical temporal and spectral context to support coherent clinical narrative generation. This approach establishes a principled bridge between continuous signal dynamics and discrete clinical language, enabling interpretable narrative generation that facilitates expert interpretation and supports clinical reporting workflows. Extensive evaluations across diverse benchmarks and zero-shot transfer tasks highlight NeuroNarrator's capacity to integrate temporal, spectral, and spatial dynamics, positioning it as a foundational framework for time-frequency-aware, open-ended clinical interpretation of electrophysiological data.
Received — 2 April 2026 ⏭

Correction: Integrative multi-omics and machine learning reveals the spatial niche distribution and role of CYP27A1+TAMs in immunotherapy response in non-small cell lung cancer

✇Omics In Lung
By: Qingsheng Liu · Xufeng Liu · Han Zhang · Yuhang Jiang · Ying Shi · Qiuqiao Mu · Yuhao Jing · Daqiang Sun
1 April 2026 at 18:00

Front Immunol. 2026 Mar 16;17:1822612. doi: 10.3389/fimmu.2026.1822612. eCollection 2026.

ABSTRACT

[This corrects the article DOI: 10.3389/fimmu.2026.1782545.].

PMID:41918731 | PMC:PMC13033988 | DOI:10.3389/fimmu.2026.1822612

Correction: Integrative multi-omics and machine learning reveals the spatial niche distribution and role of CYP27A1+TAMs in immunotherapy response in non-small cell lung cancer

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Qingsheng Liu · Xufeng Liu · Han Zhang · Yuhang Jiang · Ying Shi · Qiuqiao Mu · Yuhao Jing · Daqiang Sun
1 April 2026 at 18:00

Front Immunol. 2026 Mar 16;17:1822612. doi: 10.3389/fimmu.2026.1822612. eCollection 2026.

ABSTRACT

[This corrects the article DOI: 10.3389/fimmu.2026.1782545.].

PMID:41918731 | PMC:PMC13033988 | DOI:10.3389/fimmu.2026.1822612

AI-guided multi-omics analysis identifies NPC1-modulated susceptibility to SARS-CoV-2 infection under PM(2.5) exposure

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Guoqing Feng · Zheng Dong · Limei Ke · Weilai Zhou · Yu Tian · Xingtian Li · Wenxin Xiang · Yanjun Li · Qi Huang · Linfeng Liu · Bo Yin · Shouyi Yan · Jianxiu Liu · Xindong Ma · Huaiyong Chen · Miao He · Ke Hao · Sijin Liu · Qian Di
30 March 2026 at 18:00

Nat Commun. 2026 Mar 30. doi: 10.1038/s41467-026-71196-3. Online ahead of print.

ABSTRACT

Exposure to airborne fine particulate matter (PM2.5) has been linked to increased risk of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, yet the underlying mechanisms remain unclear. Here, by leveraging a fine-tuned foundation model of single-cell transcriptomics, we uncover shared transcriptional signatures between PM2.5 exposure and SARS-CoV-2 infection. We further validate this association using population-level epidemiological analyses and perform genome-wide association studies (GWAS) to identify genetic variants that modulate infection risk under PM2.5 exposure. In addition, we identify NPC1 as a key modulator involved in SARS-CoV-2 infection efficiency under virus-laden PM2.5 exposure through integrative functional genomic analyses and in vitro experiments. Our findings suggest that PM2.5 facilitates viral entry through an NPC1-modulated endo-lysosomal pathway, providing a mechanistic explanation for observed pollution-related susceptibility. By integrating artificial intelligence (AI)-guided transcriptomics, epidemiology, GWAS, functional genomics, and in vitro verification, our study elucidates how environmental and genetic factors jointly influence SARS-CoV-2 susceptibility. This work highlights how AI-assisted multi-omics integration systematically decodes the health impacts of environmental exposures from molecular to population levels and informs air quality policy and infectious disease preparedness.

PMID:41912520 | DOI:10.1038/s41467-026-71196-3

Received — 26 March 2026 ⏭

TRACE: A Multi-Agent System for Autonomous Physical Reasoning in Seismological

✇cs.AI, q-bio.NC updates on arXiv.org
By: Feng Liu · Jian Xu · Xin Cui · Xinghao Wang · Zijie Guo · Jiong Wang · S. Mostafa Mousavi · Xinyu Gu · Hao Chen · Ben Fei · Lihua Fang · Fenghua Ling · Zefeng Li · Lei Bai
25 March 2026 at 12:00
arXiv:2603.21152v2 Announce Type: replace-cross Abstract: Inferring the physical mechanisms that govern earthquake sequences from indirect geophysical observations remains difficult, particularly across tectonically distinct environments where similar seismic patterns can reflect different underlying processes. Current interpretations rely heavily on the expert synthesis of catalogs, spatiotemporal statistics, and candidate physical models, limiting reproducibility and the systematic transfer of insight across settings. Here we present TRACE (Trans-perspective Reasoning and Automated Comprehensive Evaluator), a multi-agent system that combines large language model planning with formal seismological constraints to derive auditable, physically grounded mechanistic inference from raw observations. Applied to the 2019 Ridgecrest sequence, TRACE autonomously identifies stress-perturbation-induced delayed triggering, resolving the cascading interaction between the Mw 6.4 and Mw 7.1 mainshocks; in the Santorini-Kolumbo case, the system identifies a structurally guided intrusion model, distinguishing fault-channeled episodic migration from the continuous propagation expected in homogeneous crustal failure. By providing a generalizable logical infrastructure for interpreting heterogeneous seismic phenomena, TRACE advances the field from expert-dependent analysis toward knowledge-guided autonomous discovery in Earth sciences.
Received — 11 March 2026 ⏭

SFIBA: Spatial-based Full-target Invisible Backdoor Attacks

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yangxu Yin · Honglong Chen · Yudong Gao · Peng Sun · Zhishuai Li · Weifeng Liu
10 March 2026 at 12:00
arXiv:2504.21052v2 Announce Type: replace-cross Abstract: Multi-target backdoor attacks pose significant security threats to deep neural networks, as they can preset multiple target classes through a single backdoor injection. This allows attackers to control the model to misclassify poisoned samples with triggers into any desired target class during inference, exhibiting superior attack performance compared with conventional backdoor attacks. However, existing multi-target backdoor attacks fail to guarantee trigger specificity and stealthiness in black-box settings, resulting in two main issues. First, they are unable to simultaneously target all classes when only training data can be manipulated, limiting their effectiveness in realistic attack scenarios. Second, the triggers often lack visual imperceptibility, making poisoned samples easy to detect. To address these problems, we propose a Spatial-based Full-target Invisible Backdoor Attack, called SFIBA. It restricts triggers for different classes to specific local spatial regions and morphologies in the pixel space to ensure specificity, while employing a frequency-domain-based trigger injection method to guarantee stealthiness. Specifically, for injection of each trigger, we first apply fast fourier transform to obtain the amplitude spectrum of clean samples in local spatial regions. Then, we employ discrete wavelet transform to extract the features from the amplitude spectrum and use singular value decomposition to integrate the trigger. Subsequently, we selectively filter parts of the trigger in pixel space to implement trigger morphology constraints and adjust injection coefficients based on visual effects. We conduct experiments on multiple datasets and models. The results demonstrate that SFIBA can achieve excellent attack performance and stealthiness, while preserving the model's performance on benign samples, and can also bypass existing backdoor defenses.
Received — 25 February 2026 ⏭

Can Multimodal LLMs See Science Instruction? Benchmarking Pedagogical Reasoning in K-12 Classroom Videos

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yixuan Shen · Peng He · Honglu Liu · Yuyang Ji · Tingting Li · Tianlong Chen · Kaidi Xu · Feng Liu
24 February 2026 at 13:00
arXiv:2602.18466v1 Announce Type: cross Abstract: K-12 science classrooms are rich sites of inquiry where students coordinate phenomena, evidence, and explanatory models through discourse; yet, the multimodal complexity of these interactions has made automated analysis elusive. Existing benchmarks for classroom discourse focus primarily on mathematics and rely solely on transcripts, overlooking the visual artifacts and model-based reasoning emphasized by the Next Generation Science Standards (NGSS). We address this gap with SciIBI, the first video benchmark for analyzing science classroom discourse, featuring 113 NGSS-aligned clips annotated with Core Instructional Practices (CIP) and sophistication levels. By evaluating eight state-of-the-art LLMs and Multimodal LLMs, we reveal fundamental limitations: current models struggle to distinguish pedagogically similar practices, suggesting that CIP coding requires instructional reasoning beyond surface pattern matching. Furthermore, adding video input yields inconsistent gains across architectures. Crucially, our evidence-based evaluation reveals that models often succeed through surface shortcuts rather than genuine pedagogical understanding. These findings establish science classroom discourse as a challenging frontier for multimodal AI and point toward human-AI collaboration, where models retrieve evidence to accelerate expert review rather than replace it.

Foundation and Large-Scale AI Models in Neuroscience: A Comprehensive Review

✇cs.AI, q-bio.NC updates on arXiv.org
By: Shihao Yang · Xiying Huang · Danilo Bernardo · Jun-En Ding · Andrew Michael · Jingmei Yang · Patrick Kwan · Ashish Raj · Feng Liu
24 February 2026 at 13:00
arXiv:2510.16658v2 Announce Type: replace Abstract: The development of large-scale artificial intelligence (AI) models is influencing neuroscience research by enabling end-to-end learning from raw brain signals and neural data. In this paper, we review applications of large-scale AI models across five major neuroscience domains: neuroimaging and data processing, brain-computer interfaces and neural decoding, clinical decision support and translational frameworks, and disease-specific applications across neurological and psychiatric disorders. These models show potential to address major computational neuroscience challenges, including multimodal neural data integration, spatiotemporal pattern interpretation, and the development of translational frameworks for clinical research. Moreover, the interaction between neuroscience and AI has become increasingly reciprocal, as biologically informed architectural constraints are now incorporated to develop more interpretable and computationally efficient models. This review highlights both the promise of such technologies and critical implementation considerations, with particular emphasis on rigorous evaluation frameworks, effective integration of domain knowledge, prospective clinical validation, and comprehensive ethical guidelines. Finally, a systematic listing of critical neuroscience datasets used to develop and evaluate large-scale AI models across diverse research applications is provided.

SelfAI: A self-directed framework for long-horizon scientific discovery

✇cs.AI, q-bio.NC updates on arXiv.org
By: Xiao Wu · Ting-Zhu Huang · Liang-Jian Deng · Xiaobing Yu · Yu Zhong · Shangqi Deng · Ufaq Khan · Jianghao Wu · Xiaofeng Liu · Imran Razzak · Xiaojun Chang · Yutong Xie
24 February 2026 at 13:00
arXiv:2512.00403v2 Announce Type: replace-cross Abstract: Scientific discovery increasingly entails long-horizon exploration of complex hypothesis spaces, yet most existing approaches emphasize final performance while offering limited insight into how scientific exploration unfolds over time, particularly balancing efficiency-diversity trade-offs and supporting reproducible, human-in-the-loop discovery workflows. We introduce SelfAI, a self-directed, multi-agent-enabled discovery system that automates scientific exploration as a strategic, trajectory-driven decision-making process. SelfAI translates high-level research intent into executable experiments, reasons over accumulated experimental trajectories to guide subsequent exploration, and applies adaptive stopping decisions to terminate unproductive search paths within a closed-loop workflow governed by explicit efficiency-diversity trade-offs. Evaluated using real-world experiments spanning domains from machine learning to drug discovery, SelfAI consistently discovers high-quality solutions with substantially fewer redundant trials than classical optimization and recent LLM-based baselines. The proposed methods establish a general framework for organizing long-horizon scientific discovery and adaptive decision-making in complex scientific and engineering systems.

Group Representational Position Encoding

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yifan Zhang · Zixiang Chen · Yifeng Liu · Zhen Qin · Huizhuo Yuan · Kangping Xu · Yang Yuan · Quanquan Gu · Andrew Chi-Chih Yao
24 February 2026 at 13:00
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 $t \in \mathbb{R}$) acts as $\mathbf{G}(n) = \exp(n \, \omega \, \mathbf{L})$ with a rank-2 skew-symmetric generator $\mathbf{L} \in \mathbb{R}^{d \times d}$, yielding a relative, compositional, norm-preserving map with a closed-form matrix exponential. RoPE is recovered exactly when the $d/2$ planes correspond to canonical coordinate pairs with a log-uniform spectrum. Learned commuting subspaces and compact non-commuting mixtures strictly extend this geometry to capture cross-subspace feature coupling at $O(d)$ and $O(r d)$ cost per head, respectively. In Additive GRAPE, additive logits arise from rank-1 (or low-rank) unipotent actions, recovering ALiBi and the Forgetting Transformer (FoX) as exact special cases while preserving an exact relative law and streaming cacheability. Overall, GRAPE provides a principled design space for positional geometry in long-context models, subsuming RoPE and ALiBi as special cases. Project page: https://github.com/model-architectures/GRAPE.

One Token Is Enough: Improving Diffusion Language Models with a Sink Token

✇cs.AI, q-bio.NC updates on arXiv.org
By: Zihou Zhang · Zheyong Xie · Li Zhong · Haifeng Liu · Yao Hu · Shaosheng Cao
24 February 2026 at 13:00
arXiv:2601.19657v4 Announce Type: replace-cross Abstract: Diffusion Language Models (DLMs) have emerged as a compelling alternative to autoregressive approaches, enabling parallel text generation with competitive performance. Despite these advantages, there is a critical instability in DLMs: the moving sink phenomenon. Our analysis indicates that sink tokens exhibit low-norm representations in the Transformer's value space, and that the moving sink phenomenon serves as a protective mechanism in DLMs to prevent excessive information mixing. However, their unpredictable positions across diffusion steps undermine inference robustness. To resolve this, we propose a simple but effective extra sink token implemented via a modified attention mask. Specifically, we introduce a special token constrained to attend solely to itself, while remaining globally visible to all other tokens. Experimental results demonstrate that introducing a single extra token stabilizes attention sinks, substantially improving model performance. Crucially, further analysis confirms that the effectiveness of this token is independent of its position and characterized by negligible semantic content, validating its role as a robust and dedicated structural sink.

Step 3.5 Flash: Open Frontier-Level Intelligence with 11B Active Parameters

✇cs.AI, q-bio.NC updates on arXiv.org
By: Ailin Huang · Ang Li · Aobo Kong · Bin Wang · Binxing Jiao · Bo Dong · Bojun Wang · Boyu Chen · Brian Li · Buyun Ma · Chang Su · Changxin Miao · Changyi Wan · Chao Lou · Chen Hu · Chen Xu · Chenfeng Yu · Chengting Feng · Chengyuan Yao · Chunrui Han · Dan Ma · Dapeng Shi · Daxin Jiang · Dehua Ma · Deshan Sun · Di Qi · Enle Liu · Fajie Zhang · Fanqi Wan · Guanzhe Huang · Gulin Yan · Guoliang Cao · Guopeng Li · Han Cheng · Hangyu Guo · Hanshan Zhang · Hao Nie · Haonan Jia · Haoran Lv · Hebin Zhou · Hekun Lv · Heng Wang · Heung-Yeung Shum · Hongbo Huang · Hongbo Peng · Hongyu Zhou · Hongyuan Wang · Houyong Chen · Huangxi Zhu · Huimin Wu · Huiyong Guo · Jia Wang · Jian Zhou · Jianjian Sun · Jiaoren Wu · Jiaran Zhang · Jiashu Lv · Jiashuo Liu · Jiayi Fu · Jiayu Liu · Jie Cheng · Jie Luo · Jie Yang · Jie Zhou · Jieyi Hou · Jing Bai · Jingcheng Hu · Jingjing Xie · Jingwei Wu · Jingyang Zhang · Jishi Zhou · Junfeng Liu · Junzhe Lin · Ka Man Lo · Kai Liang · Kaibo Liu · Kaijun Tan · Kaiwen Yan · Kaixiang Li · Kang An · Kangheng Lin · Lei Yang · Liang Lv · Liang Zhao · Liangyu Chen · Lieyu Shi · Liguo T
24 February 2026 at 13:00
arXiv:2602.10604v2 Announce Type: replace-cross Abstract: We introduce Step 3.5 Flash, a sparse Mixture-of-Experts (MoE) model that bridges frontier-level agentic intelligence and computational efficiency. We focus on what matters most when building agents: sharp reasoning and fast, reliable execution. Step 3.5 Flash pairs a 196B-parameter foundation with 11B active parameters for efficient inference. It is optimized with interleaved 3:1 sliding-window/full attention and Multi-Token Prediction (MTP-3) to reduce the latency and cost of multi-round agentic interactions. To reach frontier-level intelligence, we design a scalable reinforcement learning framework that combines verifiable signals with preference feedback, while remaining stable under large-scale off-policy training, enabling consistent self-improvement across mathematics, code, and tool use. Step 3.5 Flash demonstrates strong performance across agent, coding, and math tasks, achieving 85.4% on IMO-AnswerBench, 86.4% on LiveCodeBench-v6 (2024.08-2025.05), 88.2% on tau2-Bench, 69.0% on BrowseComp (with context management), and 51.0% on Terminal-Bench 2.0, comparable to frontier models such as GPT-5.2 xHigh and Gemini 3.0 Pro. By redefining the efficiency frontier, Step 3.5 Flash provides a high-density foundation for deploying sophisticated agents in real-world industrial environments.
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