arXiv:2609.10055v1 Announce Type: new Abstract: Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at https://github.com/zhelishisongjie/OntologyAligner.

arXiv:2609.10142v1 Announce Type: cross Abstract: Large language models remain fragile against malicious fine-tuning, motivating training-time defenses against harmful persona drift. Preventative Steering injects undesirable-trait persona vectors during fine-tuning and removes them at evaluation time, yet the mechanism behind its lasting protection remains unclear. Analyzing its temporal optimization dynamics, we find that the defense emerges from an early compensatory adaptation phase followed by a steady-state phase where the corrective signal decays; in parameter space, attention output projections emerge as the dominant residual-write route for defensive updates. Through Intervention Delta Preservation (IDP) and IDP Continuation experiments, we further show that preserving or reinjecting the weight offset fails to maintain protection, indicating that preventative steering relies on active adaptation rather than a static defense. Motivated by this finding, we propose Progressive Intensity Scheduling (PIS), which starts with a moderate injection strength and increases it after static-strength alignment begins to decay. Across the evaluated Qwen2.5 and Gemma-3 models, PIS improves safety robustness over static-strength steering while reducing harmful trait expression.

arXiv:2608.15877v3 Announce Type: replace Abstract: Search and recommendation serve a shared discovery objective but encode intent differently. We study this boundary through Dear Algo on Threads, a deployed product where open-ended requests such as \emph{more NBA news} or \emph{less politics} steer subsequent feed recommendations rather than return a one-shot result list. Its agentic intent layer compiles explicit, inferred, negative, and compound intent into a grounded executable plan, then invokes conventional retrieval and optional semantic or multimodal reranking. The layer shares an intent-to-retrieval contract without requiring one model or serving path across search-like and recommendation-like modes. We evaluate Dear Algo under a precision-first objective. In a blinded audit of 300 public request-item pairs (296 evaluable), a strict categorical LLM-as-a-judge gate achieved 94.4\% exact-Relevant precision [88.8\%, 98.9\%]. Across 72 normalized request clusters, the full configuration produced 7.73 judge-qualified candidates per 20 slots versus 6.61 for an LLM-derived-query baseline, a gain of 1.11 [0.12, 2.12]. In a candidate-randomized serving-path study restricted to the reranker path's first 72 eligible hours, the user-weighted judge-Irrelevant share among judged admissions was 2.80\% versus 4.78\% off (-1.97 points [-3.02, -0.94]), while Exact-Relevant share was 2.24 points higher [0.08, 4.41]. Together, these studies show how explicit natural-language intent can be carried into feed recommendation under a precision-first evaluation framework

arXiv:2609.08977v2 Announce Type: replace-cross Abstract: In this work, we present Gander, an end-to-end model that unifies omni perception, realtime interaction, and agentic capabilities within a single framework. In contrast to turn-based conventional paradigms, Gander continuously receives streaming inputs across multiple modalities, including video, speech, and text, enabling natural full-duplex interaction in both everyday conversations and complex workflow-oriented agent scenarios. Users can interrupt the model at any time, while the model can also proactively provide intermediate feedback or ask follow up questions. To natively support these capabilities, Gander adopts two key architectural designs: 1) It employs a Cerebellum-Brain collaborative framework, in which the Cerebellum is responsible for realtime interaction and omni conversational capabilities, while the Brain handles complex reasoning and higher-level agentic tasks. The two components interact continuously through tool calling and the agent orchestration runtime. 2) The Cerebellum is built upon a streaming Thinker-Talker architecture, user inputs and model outputs are further flattened into an ordered token stream at the chunk level, providing a unified representation for low latency, continuous interaction. We conduct comprehensive evaluations of Gander across four dimensions: conversational ability, omni understanding, interactive capability, and agentic intelligence. Internal human evaluations demonstrate that Gander maintains the natural and expressive spoken dialogue capabilities of SOTA open source models while achieving competitive performance in omni interaction. Gander also demonstrates robustness in challenging real-world scenarios, including background noise interference, multi-party interactions, and backchannel communication. We release Gander together with its models, code, and data to facilitate further research and development in the community.

arXiv:2605.23904v2 Announce Type: replace Abstract: Agent skills today are hand-crafted, generated one-shot, or evolved through loosely controlled self-revision, none of which behaves like a deep-learning optimizer for the skill, and none of which reliably improves over its starting point under feedback. We argue the skill should instead be trained as the external state of a frozen agent, with the same discipline that makes weight-space optimization reproducible. SkillOpt is, to our knowledge, the first systematic controllable text-space optimizer for agent skills: a separate optimizer model turns scored rollouts into bounded add/delete/replace edits on a single skill document, and an edit is accepted only when it strictly improves a held-out validation score. A textual learning-rate budget, rejected-edit buffer, and epoch-wise slow/meta update make skill training stable while adding zero inference-time model calls at deployment. Across six benchmarks, seven target models, and three execution harnesses (direct chat, Codex, Claude Code), SkillOpt is best or tied on all 52 evaluated (model, benchmark, harness) cells and beats every per-cell competitor among human, one-shot LLM, Trace2Skill, TextGrad, GEPA, and EvoSkill skills. On GPT-5.5 it lifts the average no-skill accuracy by +23.5 points in direct chat, by +24.8 inside the Codex agentic loop, and by +19.1 inside Claude Code. Transfer experiments further show that optimized skill artifacts retain value when moved across model scales, between Codex and Claude Code execution environments, and to a nearby math benchmark without further optimization. Code: https://aka.ms/skillopt

Oncogenesis, Published online: 13 April 2026; doi:10.1038/s41389-026-00614-4

SREBP2 regulates CCDC25 expression and promotes tumor metastasis in Triple-Negative Breast Cancer

arXiv:2604.02022v1 Announce Type: new Abstract: Evaluating the safety of LLM-based agents is increasingly important because risks in realistic deployments often emerge over multi-step interactions rather than isolated prompts or final responses. Existing trajectory-level benchmarks remain limited by insufficient interaction diversity, coarse observability of safety failures, and weak long-horizon realism. We introduce ATBench, a trajectory-level benchmark for structured, diverse, and realistic evaluation of agent safety. ATBench organizes agentic risk along three dimensions: risk source, failure mode, and real-world harm. Based on this taxonomy, we construct trajectories with heterogeneous tool pools and a long-context delayed-trigger protocol that captures realistic risk emergence across multiple stages. The benchmark contains 1,000 trajectories (503 safe and 497 unsafe), averaging 9.01 turns and 3.95k tokens, with 1,954 invoked tools drawn from pools spanning 2,084 available tools. Data quality is supported by rule-based and LLM-based filtering plus full human audit. Experiments on frontier LLMs, open-source models, and specialized guard systems show that ATBench is challenging even for strong evaluators, while enabling taxonomy-stratified analysis, cross-benchmark comparison, and diagnosis of long-horizon failure patterns.

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.

arXiv:2603.29557v1 Announce Type: new Abstract: Scientific idea generation (SIG) is critical to AI-driven autonomous research, yet existing approaches are often constrained by a static retrieval-then-generation paradigm, leading to homogeneous and insufficiently divergent ideas. In this work, we propose FlowPIE, a tightly coupled retrieval-generation framework that treats literature exploration and idea generation as a co-evolving process. FlowPIE expands literature trajectories via a flow-guided Monte Carlo Tree Search (MCTS) inspired by GFlowNets, using the quality of current ideas assessed by an LLM-based generative reward model (GRM) as a supervised signal to guide adaptive retrieval and construct a diverse, high-quality initial population. Based on this population, FlowPIE models idea generation as a test-time idea evolution process, applying selection, crossover, and mutation with the isolation island paradigm and GRM-based fitness computation to incorporate cross-domain knowledge. It effectively mitigates the information cocoons arising from over-reliance on parametric knowledge and static literature. Extensive evaluations demonstrate that FlowPIE consistently produces ideas with higher novelty, feasibility and diversity compared to strong LLM-based and agent-based frameworks, while enabling reward scaling during test time.

arXiv:2510.21356v2 Announce Type: replace-cross Abstract: Eye gaze offers valuable cues about attention, short-term intent, and future actions, making it a powerful signal for modeling egocentric behavior. In this work, we propose a gaze-regularized framework that enhances VLMs for two key egocentric understanding tasks: fine-grained future event prediction and current activity understanding. Unlike prior approaches that rely solely on visual inputs or use gaze as an auxiliary input signal , our method uses gaze only during training. We introduce a gaze-regularized attention mechanism that aligns model focus with human visual gaze. This design is flexible and modular, allowing it to generalize across multiple VLM architectures that utilize attention. Experimental results show that our approach improves semantic prediction scores by up to 11 for future event prediction and around 7 for current activity understanding, compared to the corresponding baseline models trained without gaze regularization. These results highlight the value of gaze-guided training in improving the accuracy and robustness of egocentric VLMs. Overall, this work establishes a foundation for using human gaze to enhance the predictive capabilities of VLMs in real-world scenarios like assistive robots and human-machine collaboration. Code and additional information is available at: https://github.com/anupampani/Gaze-VLM

arXiv:2503.05031v2 Announce Type: replace-cross Abstract: Alzheimer's disease (AD) is a major neurodegenerative condition that affects millions around the world. As one of the main biomarkers in the AD diagnosis procedure, brain amyloid positivity is typically identified by positron emission tomography (PET), which is costly and invasive. Brain structural magnetic resonance imaging (sMRI) may provide a safer and more convenient solution for the AD diagnosis. Recent advances in geometric deep learning have facilitated sMRI analysis and early diagnosis of AD. However, determining AD pathology, such as brain amyloid deposition, in preclinical stage remains challenging, as less significant morphological changes can be observed. As a result, few AD classification models are generalizable to the brain amyloid positivity classification task. Blood-based biomarkers (BBBMs), on the other hand, have recently achieved remarkable success in predicting brain amyloid positivity and identifying individuals with high risk of being brain amyloid positive. However, individuals in medium risk group still require gold standard tests such as Amyloid PET for further evaluation. Inspired by the recent success of transformer architectures, we propose a geometric deep learning model based on transformer that is both scalable and robust to variations in input volumetric mesh size. Our work introduced a novel tokenization scheme for tetrahedral meshes, incorporating anatomical landmarks generated by a pre-trained Gaussian process model. Our model achieved superior classification performance in AD classification task. In addition, we showed that the model was also generalizable to the brain amyloid positivity prediction with individuals in the medium risk class, where BM alone cannot achieve a clear classification. Our work may enrich geometric deep learning research and improve AD diagnosis accuracy without using expensive and invasive PET scans.

arXiv:2603.02123v2 Announce Type: replace Abstract: The development of affective multimodal language models (MLMs) has long been constrained by a gap between low-level perception and high-level interaction, leading to fragmented affective capabilities and limited generalization. To bridge this gap, we propose a cognitively inspired three-level hierarchy that organizes affective tasks according to their cognitive depth-perception, understanding, and interaction-and provides a unified conceptual foundation for advancing affective modeling. Guided by this hierarchy, we introduce Nano-EmoX, a small-scale multitask MLM, and P2E (Perception-to-Empathy), a curriculum-based training framework. Nano-EmoX integrates a suite of omni-modal encoders, including an enhanced facial encoder and a fusion encoder, to capture key multimodal affective cues and improve cross-task transferability. The outputs are projected into a unified language space via heterogeneous adapters, empowering a lightweight language model to tackle diverse affective tasks. Concurrently, P2E progressively cultivates emotional intelligence by aligning rapid perception with chain-of-thought-driven empathy. To the best of our knowledge, Nano-EmoX is the first compact MLM (2.2B) to unify six core affective tasks across all three hierarchy levels, achieving state-of-the-art or highly competitive performance across multiple benchmarks, demonstrating excellent efficiency and generalization.

arXiv:2506.17871v3 Announce Type: replace-cross Abstract: Despite their impressive capabilities, aligned large language models (LLMs) often generate outputs that lack diversity. What drives this consistency in the generation? We investigate this phenomenon through the lens of probability concentration in the model's output distribution. To quantify this concentration, we introduce the *Branching Factor* (BF) -- a token-invariant measure of the effective number of plausible next steps during generation. Our empirical analysis reveals two key findings: (1) BF often decreases as generation progresses, suggesting that LLMs become more predictable as they generate. (2) alignment tuning substantially sharpens the model's output distribution from the outset, reducing BF by a factor of 2-5 overall, and up to an order of magnitude (e.g., from 12 to 1.2) at the beginning positions. This stark reduction helps explain why aligned models often appear less sensitive to decoding strategies. Building on this insight, we find this consistency has surprising implications for complex reasoning. Aligned Chain-of-Thought (CoT) models (e.g., DeepSeek-distilled models), for instance, leverage this effect; by generating longer reasoning chains, they push generation into later, more deterministic (lower BF) stages, resulting in more stable outputs. We hypothesize that alignment tuning does not fundamentally change a model's behavior, but instead steers it toward stylistic tokens (e.g., "Sure") that unlock low-entropy trajectories already present in the base model. This view is supported by nudging experiments, which show prompting base models with such tokens can similarly reduce BF. Together, our findings establish BF as a powerful diagnostic for understanding and controlling LLM outputs - clarifying how alignment reduces variability, how CoT promotes stable generations, and how base models can be steered away from diversity.

arXiv:2602.18758v1 Announce Type: cross Abstract: Private convolutional neural network (CNN) inference based on secure two-party computation (2PC) suffers from high communication and latency overhead, especially from convolution layers. In this paper, we propose UFO, a quantized 2PC inference framework that jointly optimizes the 2PC protocols and quantization algorithm. UFO features a novel 2PC protocol that systematically combines the efficient Winograd convolution algorithm with quantization to improve inference efficiency. However, we observe that naively combining quantization and Winograd convolution faces the following challenges: 1) From the inference perspective, Winograd transformations introduce extensive additions and require frequent bit width conversions to avoid inference overflow, leading to non-negligible communication overhead; 2) From the training perspective, Winograd transformations introduce weight outliers that make quantization-aware training (QAT) difficult, resulting in inferior model accuracy. To address these challenges, we co-optimize both protocol and algorithm. 1) At the protocol level, we propose a series of graph-level optimizations for 2PC inference to minimize the communication. 2) At the algorithm level, we develop a mixed-precision QAT algorithm based on layer sensitivity to optimize model accuracy given communication constraints. To accommodate the outliers, we further introduce a 2PC-friendly bit re-weighting algorithm to increase the representation range without explicitly increasing bit widths. With extensive experiments, UFO demonstrates 11.7x, 3.6x, and 6.3x communication reduction with 1.29%, 1.16%, and 1.29% higher accuracy compared to state-of-the-art frameworks SiRNN, COINN, and CoPriv, respectively.

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.

arXiv:2601.02085v2 Announce Type: replace-cross Abstract: Strawberry harvesting robots faced persistent challenges such as low integration of visual perception, fruit-gripper misalignment, empty grasping/misgrasp, and strawberry slippage from the gripper due to insufficient gripping force, all of which compromised harvesting stability and efficiency in orchard environments. To overcome these issues, this paper proposed a visual fault diagnosis and self-recovery framework that integrated multi-task perception with corrective control strategies. At the core of this framework was SRR-Net, an end-to-end multi-task perception model that simultaneously performed strawberry detection, segmentation, and ripeness estimation, thereby unifying visual perception with fault diagnosis.Based on this integrated perception, a relative error compensation method based on the simultaneous target-gripper detection was designed to address positional misalignment, correcting deviations when error exceeded the tolerance threshold.To mitigate empty grasping/misgrasp and fruit-slippage faults, an early abort strategy was implemented. A micro-optical camera embedded in the end-effector provided real-time visual feedback, enabling grasp classification during the deflating stage and strawberry slip prediction during snap-off through MobileNet V3-Small classifier and a time-series LSTM classifier. Experiments demonstrated that SRR-Net maintained high perception accuracy. For detection, it achieved a precision of 0.895 and recall of 0.813 on strawberries, and 0.972/0.958 on hands. In segmentation, it yielded a precision of 0.887 and recall of 0.747 for strawberries, and 0.974/0.947 for hands. For ripeness estimation, SRR-Net attained a mean absolute error of 0.035, while simultaneously supporting multi-task perception and sustaining a competitive inference speed of 163.35 FPS.