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01.
arXiv (CS.AI) 2026-06-15

Can Editing 1 Neuron Fix Repetition Loops in LLMs?

arXiv:2606.13705v1 Announce Type: cross Abstract: Yes. Can it cure doom loops? Probably not. The Gemma 4 instruction-tuned models share a reproducible failure: on long factual enumeration prompts, such as listing every episode of a TV series, the 88 IAU constellations, or the 151 original Pokemon, they collapse into repetition, either a tight verbatim loop or a list whose entries decay onto a single answer. These loops occur at rates as high as 95% and survive prompt rewording, inference-engine changes, and most sampling adjustments. In this paper we explore whether this behavior is localized enough to remove by weight edits. To localize the cause, we use per-layer ablation and per-neuron attribution, then confirm the strongest candidates with full-generation sweeps. The loops trace to a small set of MLP neurons (or, in the 26B-A4B Mixture-of-Experts model, a few routed experts) which we suppress with static weight edits. These "surgeries" can be as small as a single sign-inverted neuron (in the E2B model). The size of the effective edits grows with model scale, but in all cases, the loop patterns can be addressed at normal generation budgets while preserving general-purpose benchmark scores. However, the edits do not solve everything: we also study longer thinking budgets, where the two larger models most visibly enter doom looping, i.e. a non-convergent regime in which the model self-corrects in circles over a fact it cannot recall, exhausting the budget without committing to a final answer. We show this residual failure is reduced but not eliminated by the same edits, and argue it is fundamentally a knowledge-precision problem rather than a removable circuit; weight surgery can delete a loop, but it cannot supply a missing fact. Our results are both a feasibility demonstration, that is, evidence that a concrete generation pathology can be localized to a few parameters and edited out, and a delineation of where that approach stops.

02.
arXiv (CS.CV) 2026-06-11

DarkVGGT: Seeing Through Darkness Using Thermal Geometry without Daylight Tax

Recent feed-forward 3D reconstruction methods have demonstrated strong performance and flexibility in efficient end-to-end scene geometry estimation from image streams. However, their reliance on visible-light appearance makes them vulnerable in dark and low-visibility environments, where RGB cues are severely degraded and geometric evidence becomes ambiguous. To address this challenge, we propose DarkVGGT, an RGB-T feed-forward geometry framework that uses physics-aware thermal modeling for robust 3D estimation in low-light scenes. DarkVGGT introduces two complementary modules. First, physics-inspired thermal factorization extracts emissive-dominant, geometry-consistent thermal cues while isolating sparse reflective residuals that may introduce geometric ambiguity. Second, geometry-shared thermal routing isolates modality-invariant geometric structures from thermal-specific patterns, selectively injecting reliability-aware structural guidance into the RGB stream. Together, these components enable accurate thermal-informed geometry estimation under degraded RGB conditions while largely preserving performance in well-lit environments. Experiments on low-visibility RGB-T benchmarks demonstrate consistent improvements in both depth and camera pose estimation over existing feed-forward geometry baselines.

03.
arXiv (CS.LG) 2026-06-15

Dynamic Free-Rider Detection in Federated Learning via Simulated Attack Patterns

arXiv:2604.04611v2 Announce Type: replace Abstract: Federated learning (FL) enables multiple clients to collaboratively train a global model by aggregating local updates without sharing private data. However, FL often faces the challenge of free-riders, clients who submit fake model parameters without performing actual training to obtain the global model without contributing. Chen et al. proposed a free-rider detection method based on the weight evolving frequency (WEF) of model parameters. This detection approach is a leading candidate for practical free-rider detection methods, as it requires neither a proxy dataset nor pre-training. Nevertheless, it struggles to detect ``dynamic'' free-riders who behave honestly in early rounds and later switch to free-riding, particularly under global-model-mimicking attacks such as the delta weight attack and our newly proposed adaptive WEF-camouflage attack. In this paper, we propose a novel detection method S2-WEF that simulates the WEF patterns of potential global-model-based attacks on the server side using previously broadcasted global models, and identifies clients whose submitted WEF patterns resemble the simulated ones. To handle a variety of free-rider attack strategies, S2-WEF further combines this simulation-based similarity score with a deviation score computed from mutual comparisons among submitted WEFs, and separates benign and free-rider clients by two-dimensional clustering and per-score classification. This method enables dynamic detection of clients that transition into free-riders during training without proxy datasets or pre-training. We conduct extensive experiments across three datasets and five attack types, demonstrating that S2-WEF achieves higher robustness than existing approaches.

04.
PLOS Computational Biology 2026-06-22

CoDaLoMic: An R package for modeling microbiome compositional and longitudinal data

by Irene Creus-Martí, Andrés Moya, Francisco J. Santonja In this paper we present CoDaLoMic, an R package for analyzing longitudinal and compositional microbiome datasets. The CoDaLoMic package implements three models specifically designed for the analysis of microbiome data that are both compositional and longitudinal. Unlike many existing methods that focus solely on pairwise interactions, CoDaLoMic also captures interactions among groups of bacteria, providing a more robust methodological framework for studying microbial relationships at the community level. In addition, the package facilitates the analysis of microbiome variability in relation to host health status and allows for the identification of groups of taxa that exhibit similar temporal dynamics. Working with time series data makes it possible to understand not only the current state of a microbial community but also its dynamics over time, which is essential for identifying patterns of ecological succession, detecting events of dysbiosis or recovery, and inferring potential causal relationships between taxa. On the other hand, focusing on interactions among groups of bacteria, rather than analyzing only pairwise relationships, enables a more integrated and functionally meaningful view of the microbiome. Many key ecological functions are the result of the collective behavior of functionally related groups of taxa. Two datasets have been considered in CoDaLoMic, one real and one simulated. The real dataset contains the information of the genera present in the microbiome of the Blatella germanica cockroach at 105 time points. The simulated dataset is defined taking Lotka-Volterra structure into account. CoDaLoMic is available at CRAN.

05.
arXiv (CS.AI) 2026-06-16

A Learning Method with Gap-Aware Generation for Heterogeneous DAG Scheduling

arXiv:2603.23249v2 Announce Type: replace-cross Abstract: Efficient scheduling of directed acyclic graphs (DAGs) is a core problem in large-scale data-intensive computing systems, where query plans, data-processing workloads, and computation graphs consist of dependent tasks competing for limited heterogeneous resource pools. In practice, achieving high-performance execution requires schedulers to adapt across environments with varying resource pools and task types, while generating schedules under tight runtime budgets. We propose WeCAN, an end-to-end reinforcement learning framework for heterogeneous DAG scheduling that addresses task-pool compatibility coefficients and generation-induced optimality gaps. It adopts a two-stage single-pass design: a single forward pass produces task-pool scores and global parameters, followed by a generation map that constructs schedules without repeated network calls. Its weighted cross-attention encoder models task-pool interactions gated by compatibility coefficients, and is size-agnostic to environment fluctuations. Moreover, widely used list-scheduling maps can incur generation-induced optimality gaps from restricted reachability. We introduce an order-space analysis that characterizes the reachable set of generation maps via feasible schedule orders, explains the mechanism behind generation-induced gaps, and yields sufficient conditions for gap elimination. Guided by these conditions, we design a skip-extended realization with an analytically parameterized decreasing skip rule, which enlarges the reachable order set while preserving single-pass efficiency. Experiments on real-world TPC-H query DAGs, resource-intensive workload datasets, and ML-compiler computation graphs demonstrate improved makespan over strong baselines, with inference time comparable to classical heuristics and faster than multi-round neural schedulers.

06.
arXiv (CS.AI) 2026-06-15

STaR-DRO: Stateful Tsallis Reweighting for Group-Robust Structured Prediction

arXiv:2604.09737v2 Announce Type: replace-cross Abstract: Structured prediction with large language models requires outputs that are label-accurate, ontology-constrained, structurally valid, and evidence-grounded under label imbalance and heterogeneous group difficulty. We present a unified framework for ontology-constrained generation. First, we introduce a modular prompt-engineering architecture combining XML-style structure, expert disambiguation rules, chain-of-thought reasoning, metadata-aware decision logic, schema contracts, and a self-validation gate. It targets recurrent in-context failures, including format drift, label ambiguity, evidence hallucination, and metadata-conditioned confusion. Second, we propose STaR-DRO, combining Tsallis mirror ascent, sparse entmax-style primal mapback, EMA-smoothed group-loss tracking, rescaled ascent signals, and bounded excess-only multipliers. Unlike conventional DRO, which relies on dense Shannon-entropy exponentiated-gradient updates, can introduce high-variance stochastic reweighting, assigns positive adversarial mass to groups that are not persistently hard, and incurs costs through simplex competition, STaR-DRO upweights only persistently hard groups without suppressing easier ones. We evaluate the framework on EPPC Miner, a clinically grounded high-stakes structured-prediction task requiring hierarchical label prediction and evidence-span extraction from patient-provider secure messages. Across 1B-70B Llama models, prompt engineering improves zero-shot extraction, yielding an average label F1 gain of +14.46 and a Span F1 gain of +17.40. Building on supervised fine-tuning, STaR-DRO further improves accuracy and robustness, increasing average label F1 by +1.08 and +2.20 while reducing mean groupwise validation cross-entropy by 21.3% and 14.8% relative to SFT and standard DRO, respectively. These results advance reliable automated communication mining for patient-centered clinical care analysis.

07.
arXiv (CS.CL) 2026-06-11

Detecting Sensitive Personal Information in Japanese Pre-Training Corpora for Large Language Models

Sensitive personal information can appear in large-scale pre-training corpora for large language models (LLMs). Detecting and filtering such information is therefore essential to ensure compliance with privacy regulations and prevent unintended information leakage. However, in contrast to English and other languages, research into sensitive personal information has been limited in the Japanese language. In this study, we focus on sensitive personal data defined as special care-required personal information (SCPI) under Japan's Act on the Protection of Personal Information (APPI). We construct an SCPI dataset using LLM-based annotation and train machine learning models to rapidly detect SCPI in text. As a result, our SCPI classifier can effectively identify information related to SCPI. This study is the first to explore SCPI detection in Japanese text corpora, highlighting the challenges of accurate detection.

08.
arXiv (CS.CV) 2026-06-19

Single-Stage Hierarchical Rectification for Weakly Supervised Histopathology Segmentation

Existing weakly supervised semantic segmentation (WSSS) methods in computational pathology rely on a multi-stage paradigm: class activation map (CAM) generation, offline pseudo-mask refinement, and fully supervised retraining. While established, this decoupled approach presents fundamental limitations. The multi-stage process not only incurs high computational training costs but also suffers from error propagation: local texture biases in shallow CNN layers generate false-positive artifacts that subsequent refinement steps often fail to correct. To address these persistent challenges through a simple yet highly effective approach, we propose the Single-Stage Hierarchical Rectification (SSHR) framework. Rather than passively refining CAMs post-hoc, our method proactively purifies intermediate feature representations during the forward pass. We introduce a Hierarchical Feature Rectification Module (HFRM) that utilizes deep global semantic context to filter out local anomalies in shallow layers. This mechanism generates high-fidelity activation maps directly within a single training loop. Experiments on the LUAD-HistoSeg and BCSS datasets demonstrate that SSHR outperforms state-of-the-art multi-stage methods. Furthermore, SSHR reduces training duration by 2 to 5 times. This efficiency minimizes computational overhead and accelerates clinical translation for large-scale histopathology workflows. The code is available at: https://github.com/trongduc-nguyen/SSHR

09.
arXiv (math.PR) 2026-06-19

Optimal Sparsification of Gaussian Processes

arXiv:2606.19763v1 Announce Type: new Abstract: We prove an optimal dimension-free sparsification theorem for suprema of centered Gaussian processes. Given a bounded set $T\subseteq\mathbb{R}^n$, we show that the supremum of the canonical Gaussian process on $T$ can be $L^2$-approximated by the supremum of a shifted subprocess indexed by only $\exp(O(1/\varepsilon^2))$ points, with error at most $\varepsilon$ times the Gaussian width of $T$. In particular, the size of the approximating process is independent of both the ambient dimension and the cardinality of the original index set. This improves a recent sparsification theorem of De, Nadimpalli, O'Donnell, and Servedio (2026) by an exponential factor, and we show that the dependence on $\varepsilon$ is tight up to constants in the exponent. As consequences, we obtain an exponentially improved junta theorem for norms over Gaussian space and sharpen results on learning, property testing, and polyhedral approximation of convex sets under the Gaussian measure. The proof is based on an interpolation argument that combines Sudakov's minoration with the Brascamp–Lieb inequality.

10.
arXiv (CS.LG) 2026-06-18

EfficientRollout: System-Aware Self-Speculative Decoding for RL Rollouts

arXiv:2606.18967v1 Announce Type: new Abstract: Reinforcement learning (RL) has become a representative post-training paradigm for LLMs, enabling strong reasoning and agentic capabilities. However, rollout generation remains a dominant latency bottleneck because autoregressive sampling decodes responses sequentially and a small number of long-tailed generations often determine completion time. Speculative decoding (SD) offers a natural way to address this bottleneck, as it is a well-established technique for serving fixed LLMs that reduces latency by rapidly drafting tokens and accepting them through parallel verification while preserving the target-model distribution. However, its practical speedups do not directly carry over to RL rollouts: (i) the evolving target policy makes any fixed drafter increasingly mismatched with the policy's output distribution; and (ii) active batch sizes shrink throughout rollout decoding, shifting decoding from compute-bound to memory-bound regimes where parallel verification can exploit underutilized compute. Therefore, accelerating RL rollouts requires both a drafter that remains effective under long, high-temperature generations from an evolving policy and system-aware use of SD that avoids compute-bound regimes. We present EfficientRollout, a system-aware self-SD framework designed to address this gap for RL rollouts. EfficientRollout induces a quantized drafter from the target model (i.e. self-speculative decoding), keeping it coupled to the evolving policy without separate drafter pretraining or online adaptation. It further coordinates a system-aware SD toggle policy with acceptance-aware draft-length adaptation, enabling speculation only in beneficial regimes while matching the drafting budget to evolving drafter quality. EfficientRollout reduces rollout and end-to-end latency by up to 19.6% and 12.7%, respectively, over an accelerated AR rollout baseline, while preserving final model quality.

11.
arXiv (CS.CV) 2026-06-11

Auditing Demographic Bias in Facial Landmark Detection for Fair Human-Robot Interaction

Fairness in human-robot interaction critically depends on the reliability of the perceptual models that enable robots to interpret human behavior. While demographic biases have been widely studied in high-level facial analysis tasks, their presence in facial landmark detection remains unexplored. In this paper, we conduct a systematic audit of demographic bias in this task, analyzing the age, gender, and race biases. To this end, we introduce a controlled statistical methodology to disentangle demographic effects from confounding visual factors. Our analysis demonstrates that visual confounders, particularly head pose and face resolution, heavily outweigh the impact of demographic attributes. Notably, after accounting for these confounders, performance disparities across gender and race vanish. However, we identify a statistically significant age-related bias, with higher localization errors for older individuals. This shows that fairness issues can emerge even in low-level vision components and can propagate through the HRI pipeline. We argue that auditing and correcting such biases is a necessary step toward trustworthy and equitable robot perception systems.

12.
arXiv (CS.LG) 2026-06-16

Exact Federated Continual Unlearning for Ridge Heads on Frozen Foundation Models

arXiv:2603.12977v3 Announce Type: replace Abstract: Foundation models are commonly deployed as frozen feature extractors with a small trainable head to adapt to private, user-generated data in federated settings. The ``right to be forgotten'' requires removing the influence of specific samples or users from the trained model on demand. Existing federated unlearning methods target general deep models and rely on approximate reconstruction or selective retraining, making exactness costly or elusive. We study this problem in a practically relevant but under-explored regime: a frozen foundation model with a ridge-regression head. The exact optimum depends on the data only through two additive sufficient statistics, which we turn into a communication protocol supporting an arbitrary stream of add and delete requests via fixed-size messages. The server maintains a head that is, in exact arithmetic, pointwise identical to centralized retraining after every request. We provide deterministic retrain-equivalence guarantees, order and partition invariance, two server-side variants, and a Bayesian certificate of zero KL divergence. Experiments on four benchmarks confirm the guarantees: both variants match centralized ridge retraining to within $10^{-9}$ relative Frobenius error and complete each request at orders-of-magnitude lower cost than federated retraining baselines.

13.
medRxiv (Medicine) 2026-06-17

Investigating shared genetic overlap of immune-mediated inflammatory diseases and cardiometabolic diseases

Abstract Background: Immune-mediated inflammatory diseases (IMIDs) are associated with increased risk of cardiometabolic diseases. Investigating genetic overlap among these conditions can provide insights into their clinical management. Methods: Genetic correlation was assessed using linkage disequilibrium score regression (LDSC). Then, a meta-analysis was conducted using Association Analysis Based on SubSETs (ASSET) to pinpoint independent single nucleotide polymorphisms (SNPs) shared across the diseases. Each independent SNP was then used to define a genomic window (+/-500KB) for colocalisation analysis and Local Analysis of [co]Variant Association (LAVA) to offer multiple layers of regional pleiotropic evidence. Over-representation analysis was then run to identify enriched biological pathways, which then were used for drug target analysis. Results: The LDSC analysis showed a significant global genetic correlation for rheumatoid arthritis (RA) and cardiometabolic diseases including hypertension, coronary artery disease (CAD), heart failure (HF), stroke, atrial fibrillation (AF), and type two diabetes mellitus (T2DM) ranging from rg = 0.09 to 0.24. ASSET meta-analysis identified 164 independent SNPs shared across RA and the cardiometabolic diseases with P < 5 x 10- in the overall one-sided meta-analysis P-value, FDR < 0.05 in both individual GWASs, and TRUE phenotype matrix. Colocalisation analysis revealed multiple loci with strong evidence (Posterior probabilities [&ge;] 80) of single causal SNPs between the trait pairs. LAVA analysis was then used as an additional layer of confirmation for the findings generated by ASSET and colocalisation and thus several loci were highlighted. Over-representation analysis showed significant enriched immune-related pathways across RA-hypertension, RA-CAD, RA-AF, and RA-T2DM trait pairs. Drug target analysis highlighted several drugs which could be further tested for their effectiveness in RA and its common comorbidities. Conclusion: The findings revealed a shared genetic architecture and key immune-related biological pathways underlying RA and its associated cardiometabolic comorbidities. The identified genes and drugs provide opportunities for further therapeutic assessment which could improve clinical management strategies.

14.
arXiv (CS.AI) 2026-06-16

ToolMenuBench: Benchmarking Tool-Menu Filtering Strategies for Reliable and Efficient LLM Agents

arXiv:2606.15508v1 Announce Type: new Abstract: Tool-augmented large language model agents increasingly operate over large tool libraries, but existing evaluations often focus on whether a model can call a tool correctly rather than how the visible tool menu shapes reliability, efficiency, and safety-relevant risk exposure. We introduce ToolMenuBench, a benchmark for evaluating tool-menu construction in multi-step LLM agents. ToolMenuBench varies tool-menu size, distractor type, state-dependent task structure, and risk exposure, and reports both filter-level and downstream agent metrics, including visible-tool count, risky-tool exposure, task success, wrong-tool calls, premature actions, and token usage. In a controlled evaluation across seven model backends, three tool-menu sizes, six filtering methods, and seven evaluation settings, CMTF improves task success from 32.1% under all-tools exposure to 85.7%, while reducing average token usage by roughly 98%. Causal minimal tool filtering achieves the strongest overall tradeoff, reducing visible tools, wrong-tool calls, premature actions, and risky-tool exposure relative to unfiltered exposure, lexical filtering, state-aware filtering, and broader causal-path baselines. ToolMenuBench provides a reusable evaluation framework for studying the agent-interface problem: which tools should be visible, when they should be visible, and under what cost or risk constraints.

15.
arXiv (CS.LG) 2026-06-16

Robust Transformer-Based One-Step Stock Index Forecasting via Shifted Data Augmentation

arXiv:2606.15701v1 Announce Type: new Abstract: Transformers have shown remarkable success in sequence modeling, yet their direct application to financial time series remains challenging due to noisy signals, short-memory dynamics, and distributional shifts. This paper proposes a modified Transformer architecture for one-step stock index forecasting, combined with advanced learning-rate scheduling and a novel Shifted Data Augmentation (SDA) technique. We evaluate the proposed framework on two benchmark stock index datasets, VN30 and S&P 500. Experimental results demonstrate that cosine annealing with warmup consistently improves forecasting accuracy over the generalized inverse-power scheduler. Furthermore, SDA substantially reduces forecasting errors and run-to-run variability while improving robustness to hyperparameter selection. The combination of cosine annealing scheduling and SDA achieved the best performance on both datasets, indicating that data augmentation can play a more important role than increasing model complexity in Transformer-based financial forecasting. These findings provide a practical and computationally efficient approach for robust stock index forecasting in noisy financial environments.

16.
arXiv (CS.AI) 2026-06-16

LaWAM: Latent World Action Models for Efficient Dynamics-Aware Robot Policies

arXiv:2606.15768v1 Announce Type: cross Abstract: Vision-Language-Action models (VLAs) leverage large-scale vision-language pretraining for semantic robot control, but often lack explicit foresight into how robot actions change the scene. World-Action Models (WAMs) address this limitation by conditioning policies on predicted futures, yet existing approaches typically rely on computationally expensive video generation with substantial pixel-level redundancy. We present LaWAM, a Latent World Action Model that exposes predictive dynamics to robot policies through compact latent visual subgoals instead of reconstructed future video. At the core of LaWAM is a latent-action-conditioned Latent World Model (LaWM). We obtain LaWM by training a latent action model in the latent space of a pretrained vision foundation model and repurposing its forward decoder to predict future observation features for scene evolution. LaWAM then conditions action generation on these predicted latent visual subgoals to enable dynamics-aware robot control. LaWAM achieves state-of-the-art or competitive success rates (SRs) across LIBERO (98.6% SR), RoboTwin (91.22% SR), and real-world manipulation tasks while retaining low-latency inference. LaWAM runs in 187 ms per action-chunk prediction and achieves up to 24x lower wall-clock latency than pixel-space WAMs.

17.
arXiv (CS.CL) 2026-06-17

Do Large Language Models Always Tell The Same Stories?

Recent advances in large language models (LLMs) have enabled the generation of high-quality prose, yet the question of whether these models are capable of generating diverse outputs remains contested. In this work, we investigate the diversity of LLM-generated stories through the framework of narrative similarity. Using a contrastive framework and a dataset of human-written stories and prompts from r/WritingPrompts, we collect narrative similarity judgments across 10 representative LLMs, utilizing both human evaluations and three different automatic annotation methods. Our findings reveal a consistent trend: LLM-generated narratives are consistently more similar to each other than human-written stories are. We demonstrate that frontier models in particular converge on a ``mean'' generic narrative that approximates individual human stories but lacks the collective diversity of human authors. Finally, we show that common mitigation strategies, including negative prompting and temperature scaling, fail to meaningfully address this homogeneity.

18.
bioRxiv (Bioinfo) 2026-06-16

MetaPilot: genome-aware adaptive search-space refinement for unified DDA and DIA metaproteomics

Metaproteomic peptide identification is constrained by the structure and size of the protein search space. Pooled gene catalogues provide coverage but obscure genome-level evidence, and current workflows for data-dependent (DDA) and data-independent (DIA) acquisition diverge in their database strategies. We present MetaPilot, a genome-aware workflow that uses conserved marker-protein evidence to rank candidate genomes from MGnify catalogues and construct adaptive, sample-specific search spaces. Applied to paired DDA/DIA datasets of defined mixtures and fecal samples, MetaPilot adapted genome selection to community complexity and reproduced published peptide evidence while expanding the detectable peptide space. In DDA-independent reanalysis of Orbitrap human gut DIA data, MetaPilot identified 24.4% more peptides than the published DDA-derived library and 2.06-fold more than the matched DDA-assisted DIA search. On timsTOF DIA-PASEF mouse intestinal data, it outperformed uMetaP by 41.8~119.7%, enabling genome-resolved functional interpretation without DDA-PASEF input.

19.
arXiv (CS.CL) 2026-06-11

TokenRatio: Principled Token-Level Preference Optimization via Ratio Matching

Direct Preference Optimization (DPO) is a widely used RL-free method for aligning language models from pairwise preferences, but it models preferences over full sequences even though generation is driven by per-token decisions. Existing token-level extensions typically decompose a sequence-level Bradley-Terry objective across timesteps, leaving per-prefix (state-wise) optimality implicit. We study how to recover token-level preference optimality using only standard sequence-level pairwise comparisons. We introduce Token-level Bregman Preference Optimization (TBPO), which posits a token-level Bradley-Terry preference model over next-token actions conditioned on the prefix, and derive a Bregman-divergence density-ratio matching objective that generalizes the logistic/DPO loss while preserving the optimal policy induced by the token-level model and maintaining DPO-like simplicity. We introduce two instantiations: TBPO-Q, which explicitly learns a lightweight state baseline, and TBPO-A, which removes the baseline through advantage normalization. Across instruction following, helpfulness/harmlessness, and summarization benchmarks, TBPO improves alignment quality and training stability and increases output diversity relative to strong sequence-level and token-level baselines.

20.
bioRxiv (Bioinfo) 2026-06-14

Virtual phenotypic screening discovers novel scaffolds inhibiting the PI3K/mTOR pathway

Phenotypic drug discovery has yielded many first-in-class small-molecule drugs by discovering modulators of disease phenotypes in physiologically relevant cellular systems. However, high-content phenotypic assays lack the ultra-high-throughput scalability of target-based screens. Recent advances in virtual screening present an opportunity to address this bottleneck, but have been limited to simple phenotypes like viability, restricted to small repurposing libraries, or lack in-depth biological validation. Here, we present PhenoCompass, a multimodal co-embedding model that aligns compound structures and high-content phenotypic imaging to enable virtual phenotypic screening over billion-compound libraries. Following training on the Joint Undertaking in Morphology dataset with more than 100,000 Cell Painting compound profiles, retrospective validation with historical biochemical high-throughput screening data demonstrates that PhenoCompass ranks compounds according to their biochemical target engagement. Leveraging PhenoCompass, we performed a prospective screen of 3.8 billion Enamine REAL compounds for inhibitors of PI3K/mTOR pathway, a critical signaling cascade whose aberrant activation is a common tumor driver. This search identified 11 novel compounds with pathway-consistent Cell Painting readout and diverse scaffolds, a 54-fold enrichment over the training set. Orthogonal validation experiments using a FOXO3A reporter assay and direct kinase inhibition confirmed seven structurally novel inhibitors with distinct mechanisms of action. These results highlight the convergence of diverse molecular target profiles onto a shared morphological pathway signature and establish PhenoCompass as a robust framework for high-content phenotypic virtual screening.

21.
arXiv (CS.CV) 2026-06-15

Multi-Agent Embodied Autonomous Driving: From V2X Information Exchange to Shared World Models

Autonomous driving is shifting from isolated vehicle intelligence toward multi-agent embodied systems that share perception, infer intent, and coordinate action under uncertainty. This survey examines this transition through the lens of Shared World Models (SWMs): predictive cross-agent representations maintained across vehicles, infrastructure, and other traffic participants. We review more than 380 publications spanning vehicle-to-everything (V2X) communication, collaborative perception, inter-agent cognition, cooperative planning, end-to-end cooperative driving, and simulation and data engines for closed-loop validation. The organizing question is how exchanged observations become aligned state, intent-aware interaction, and coordinated downstream action. Across the surveyed literature, evaluation remains concentrated in simulation, curated benchmarks, and offline protocols. Foundation-model-based coordination also lacks verified real-time safety guarantees in open traffic. These gaps motivate key research priorities for multi-agent embodied autonomous driving (MAEAD): verifiable shared-state maintenance, robust intent and plan alignment, and safe coordinated action under communication, latency, and deployment constraints.

22.
medRxiv (Medicine) 2026-06-22

The Protective Role of Belonging and Socioeconomic Status in Dropout Intent Among Minority Ethnic Students: A Mixed Methods Study

Improving minority ethnic student retention is a global higher education priority. This mixed-methods study investigated how institutional belonging and socioeconomic status interact to shape dropout intentions among minority university students in the UK (N = 182). Quantitative results revealed that perceived course difficulty and lower subjective socioeconomic status were the strongest predictors of dropout intent. While the interaction between socioeconomic status and difficulty was non-significant, qualitative accounts showed distinct structural vulnerabilities. Financial strain restricted social integration, turning socioeconomic disparities into campus isolation. Conversely, representative curricula, diverse peer networks, and stable cultural in-groups (e.g., religious affiliations, living in the parental home) functioned as essential psychological buffers against academic exhaustion and alienation. Universities must shift from transactional models to sustained structural equity to protect vulnerable student groups.

23.
Nature (Science) 2026-06-10

Whole-genome duplication shaped cell-type evolution in the vertebrate brain

Authors:

The complex brains of vertebrates have more cell types than those of their closest relatives. Whole-genome duplications (WGDs) occurred during early vertebrate evolution1, but it is unclear whether the duplicated genes (ohnologues) facilitated cell-type evolution. Here using brain single-cell transcriptomes from five chordates—human2, mouse3, lizard4, lamprey5 and amphioxus—we report that many cell-type families with conserved core transcription factors in vertebrates do not show one-to-one homology with amphioxus. Moreover, ohnologues, particularly those from the first WGD, were more important than small-scale duplication paralogues for vertebrate cell-type evolution. To explore whether ohnologues are mechanistically important for this process, we predicted ancestral cell-type states and compared them to amphioxus and experimentally investigated macroglia. The findings indicate that ohnologues had a role in early vertebrate cell-type diversification. Moreover, by examining paralogue expression across cell types and species, we show that expression changes were mainly driven by dosage selection and subfunctionalization. We also link ohnologues to cellular diversity at different anatomical and cell-type scales. Our findings demonstrate the importance of WGDs for the evolution of early vertebrate brain complexity and highlight that the resultant ohnologues continued to capacitate cell-type evolution long after they were formed. Analyses of brain single-cell transcriptomes from human, mouse, lizard, lamprey and amphioxus reveal that duplicated genes (ohnologues) played a pivotal part in early vertebrate cell-type diversification.

24.
arXiv (CS.CL) 2026-06-17

Incumbent Advantage: Brand Bias and Cognitive Manipulation Dynamics in LLM Recommendation Systems

Large language models (LLMs) are becoming a major way for consumers to find products, but we do not yet understand how brands compete in this new channel. We study brand dynamics in LLM recommendations using skincare products – a category where consumers cannot easily judge quality before buying and must rely on brand reputation – across three commercial LLMs (GPT-4o-mini, Claude Sonnet, Gemini 3 Flash), with a robustness check on search goods. In three experiments, we find: (1) a Conditional Monopoly where well-known brands get recommended 100% of the time (IAI = 10.0) when all products have the same specifications, but this dominance disappears with less than a +0.1-star rating advantage for a competitor; (2) authority-style marketing language, including fabricated clinical-evidence claims, breaks this monopoly at a Bias Surplus Value equal to +0.17 rating points, with each model responding differently; and (3) a social dilemma in multi-brand GEO competition: when all brands adopt the same optimization strategy, individual payoff falls from +0.802 to +0.007 in our payoff proxy, and non-participating brands receive zero recommendations in our tests. Our results suggest that generative engine optimization (GEO) should be studied not only as a security risk, but also as an emerging marketing practice that shapes market competition.

25.
bioRxiv (Bioinfo) 2026-06-11

TifBERT: a self-supervised foundation model for normalization-robust bulk RNA-seq representation learning

Bulk RNA sequencing remains central to translational genomics, yet foundation-model development has largely focused on single-cell data. Existing transformer approaches for bulk RNA-seq often rely on expression discretization, numerical reconstruction, external gene embeddings, or restricted gene sets, limiting robustness across normalization schemes and cohorts. Here, we introduce TifBERT, a self-supervised framework for full-transcriptome bulk RNA-seq representation learning. TifBERT converts each unordered expression profile into a sample-specific gene sequence using term frequency-inverse document frequency (TF-IDF) ordering, prioritizing genes that are both highly expressed within a sample and selectively expressed across the cohort. It is then pretrained using masked gene modeling, predicting gene identities from transcriptomic context rather than reconstructing expression values. Pretrained on harmonized TCGA Pan-Cancer data spanning five RNA-seq normalization schemes, TifBERT learns contextual representations across approximately 10,000 genes without expression binning, landmark-gene restriction, or external biological embeddings. Across 33 TCGA cancer types, TifBERT achieved 90.83% accuracy, 0.996 macro AUC-ROC, and 0.903 MCC. It also captured pathway-level biology, achieving mean sample-wise and pathway-wise Pearson correlations of 0.754 and 0.762 across 1,387 PARADIGM pathway activities. Independent evaluation on GTEx healthy tissues showed preservation of tissue-level transcriptomic structure without retraining. In comparison with existing models, TifBERT achieves competitive subtype discrimination with substantially greater stability and produces markedly richer embedding geometry (effective rank 95.6 versus 6.3), without requiring expression discretization or in-distribution pretraining exposure. Together, TifBERT provides a scalable, normalization-independent foundation model for reusable bulk transcriptomic representation learning