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01.
PLOS Computational Biology 2026-06-15

Environmental “knees” and “wiggles” as strong stabilizers of species’ range limits set by interspecific competition

by Farshad Shirani, Benjamin G. Freeman Whether interspecific competition is a major contributing factor to setting species’ range limits has been debated for a long time. Theoretical studies have proposed that the interactions between interspecific competition and disruptive gene flow along an environmental gradient can halt range expansion of ecologically similar species where they meet. However, the stability of such range limits has not been well addressed. We use a deterministic mathematical model of adaptive range evolution over a continuous habitat to show that the range limits set by interspecific competition are unlikely to be evolutionarily stable if the environmental optima for fitness-related traits vary (almost) linearly in space. That is, in a linear environment without a dispersal barrier or a third (or more) species, the range borders formed between two competing species constantly move towards the weaker species. We demonstrate that environmental nonlinearities such as “knees” and “wiggles”—wherein an isolated sharp change or a step-like change occurs in the steepness of a trait optimum—can strongly stabilize competitively formed range limits. The stabilization mechanism relies on the contrast that such nonlinearities create in the level of disruptive gene flow to the peripheral population of each species, and succeeds when an additional process, such as Allee effects, prevents the establishment of an infinitesimal population in the presence of an abundant competitor. We show that the stability of the range limits at these nonlinearities is robust against moderate environmental disturbances. Whether strong disturbances such as rapid high-amplitude climate changes can destabilize such range limits depends on how the competitive dominance of the species changes across the nonlinearity. Therefore, our findings underscore the importance of assessing species’ competitive ability when predicting responses to climate change, and identify geographic regions where established range limits are likely to persist as well as regions where shifting limits may eventually stabilize.

02.
bioRxiv (Bioinfo) 2026-06-11

DeePEn - A Depth sensitive benchmark for Protein Engineering

Recent progress in modeling techniques and high-throughput screening has significantly enhanced the accessibility of protein engineering. Nevertheless, further progress gets hindered by the lack of robust benchmarks that capture the practical challenges for real-world protein engineering. Here, we introduced DeePEn, a Depth-sensitive benchmark for Protein Engineering that quantifies a models generalization capabilities when predicting protein fitness at increasing mutational distance from the wildtype or training data. We defined distance as the number of simultaneous point mutations, i.e., single amino acid variants (SAVs), moving from wild-type to mutant (edit distance in computer science jargon). Specifically selecting four deep mutational scanning (DMS) datasets with sufficient multi-mutation data points from ProteinGym, we assessed recent predictive models, including general and biophysics-informed protein Language Models (pLMs), and a non-transformer neural network. Our results highlight how the performance of all models deteriorates with increasing mutational distance and that no single metric sufficiently captures the diverse requirements of protein engineering. To overcome these shortcomings, DeePEn provides a readily available resource for multi-metric benchmarking that focuses on the prediction of distant variants.

03.
arXiv (CS.CL) 2026-06-12

Two Wrongs, No Right: Auditing Social-Desirability Bias in LLM Annotators for Computational Social Science

作者:

LLM annotators are increasingly used in computational social science (CSS), but it is unclear whether their alignment-shaped errors preserve the empirical conclusions a researcher would report. We audit three open-source 7B instruction-tuned models (Zephyr, Mistral-Instruct, Qwen2.5-Instruct) across six TweetEval tasks under four prompt conditions (72 cells) and find that social-desirability failures do not run in a single direction. Zephyr exhibits leniency bias, systematically under-applying harmful labels (offensive language: false benign rate 0.729, false alarm rate 0.031). Mistral and Qwen exhibit overcorrection, over-applying the same labels (Mistral hate-speech FAR = 0.604). All three models exhibit neutrality bias on abortion stance, underestimating opposition prevalence by 24 to 40 percentage points and inflating the neutral label. None of the four prompting interventions we test (neutral, safety framing, depersonalized, chain-of-thought) corrects these failures across models; safety framing can worsen stance distortion. Strikingly, Zephyr's hate-speech prevalence estimate matches the gold rate exactly while its class-conditional errors are large in both directions, an accidental cancellation that misleads aggregate validation. We translate these patterns into a three-part taxonomy with diagnostic FBR/FAR signatures and a lightweight gold-sample validation protocol. The headline for trustworthy CSS: a model that looks calibrated on aggregate metrics can still flip the substantive empirical conclusion a researcher would report.

04.
arXiv (CS.CV) 2026-06-12

VISA: VLM-Guided Instance Semantic Auditing for 3D Occupancy World Models

Semantic 3D occupancy provides a voxelized world state for autonomous driving and robot decision making, but object and rare-class errors can affect free-space interpretation, collision checking, and temporal state propagation. We show that a common VLM strategy, aligning 3D voxel or object features with crop-caption embeddings, improves text-space similarity without reliably improving closed-set occupancy mIoU. Motivated by this mismatch, we propose VISA, a training-time semantic auditing approach for existing occupancy world models. VISA queries an offline VLM on a representative crop of each physical object instance, obtains a structured audit with class hypotheses, plausible confusions, reliability, attributes, and evidence, and propagates it along the object track. The audit is grounded to matched 3D object voxels and distilled into semantic logits through reliability-weighted taxonomy, attribute-factor, and scene-level audit graph losses, while inference remains unchanged and requires no VLM. On nuScenes, averaged across three runs, VISA improves OccWorld from 19.06 to 20.05 mIoU and GaussianWorld from 21.36 to 21.91 mIoU; on GaussianWorld, object mIoU improves from 18.18 to 19.16 and rare-class mIoU from 15.60 to 16.79. These results suggest that VLMs are better suited to closed-set occupancy as reliability-aware semantic auditors than as generic caption-embedding targets.

05.
arXiv (CS.CV) 2026-06-18

Epipolar Geometry Improves Video Generation Models

Video generation models have advanced significantly through the latent diffusion transformers trained with rectified flow techniques. Yet these models still struggle with geometric inconsistencies, unstable motion, and visual artifacts that break the illusion of realistic 3D scenes. 3D-consistent video generation could significantly impact numerous downstream applications in generation and reconstruction tasks. We explore how epipolar geometry constraints improve modern video diffusion models. Despite using massive training data, these models fail to capture fundamental geometric principles. We align diffusion models using pairwise epipolar geometry constraints via preference-based optimization, directly addressing unstable trajectories and geometric artifacts through mathematically principled geometric enforcement. Our approach efficiently enforces geometric principles without requiring end-to-end differentiability. Evaluation demonstrates that classical geometric constraints provide more stable optimization signals than modern learned metrics. Training on static scenes with dynamic cameras ensures metric quality while the model generalizes to various dynamic scenes. By bridging data-driven learning with classical computer vision, we reduce epipolar error by 31% and improve human-rated consistency from 54% to 72% without compromising visual quality.

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

How Far Can Chord-Symbol Time-Series Adaptation Carry Genre Identity? Capabilities and Boundaries in Multi-Genre Chord-Symbol Modeling

作者:

arXiv:2606.07334v2 Announce Type: replace-cross Abstract: This report treats chord-symbol sequences as an interpretable, controllable time series for genre-local harmonic modeling. The frozen Music Transformer base - released as a pop-jazz fine-tune endpoint but verified in this revision weight-identical to the pop-only Phase-0 baseline, so all gains are measured over a pure-pop prior (see Changes in v2) - is extended to eleven target genres: blues, bossa nova, Bach chorales, country, electronic, folk, funk, gospel, hip-hop, R&B/soul, and rock. The main evaluation compares LoRA, IA3, BitFit, prefix tuning, and full fine-tuning over 11 genres and 3 seeds, a complete 165-cell grid. All five methods improve over the frozen base on held-out chord prediction (macro gains +2.89 to +3.61 percentage points); LoRA and IA3 score highest, but pairwise Wilcoxon tests with Holm and Benjamini-Hochberg correction do not support a decisive winner. A matched-data-size control sharpens this: at a common corpus size IA3 stays on top while LoRA drops to last, so the small method gaps are partly data-driven rather than representational. A control-token baseline is also strong, and wrong-genre adapters often beat the frozen base, suggesting the adaptation effect is largely lightweight conditioning over a reusable harmonic base rather than genre-specific adapter memory. Further diagnostics (rank sweeps, wrong-genre rotation, a base-checkpoint ablation that v2 reinterprets as a same-weights control, chord-only genre classification, output-distribution statistics, real-song evaluation, duplicate analysis) support a bounded conclusion: chord-symbol adaptation reliably improves genre-local harmonic prediction, but chord symbols alone do not carry complete genre identity. Perceived genre authenticity and musical quality are left to controlled listener evaluation.

08.
arXiv (CS.CV) 2026-06-15

Memento: Reconstruct to Remember for Consistent Long Video Generation

Long-form video generation requires recurring subjects to remain consistent across various shots, viewpoints, motions, and scene transitions. Existing temporal decomposition methods improve scalability by generating videos shot by shot. However, they mainly focus on optimizing plausible next-shot continuations without verifying whether the historical memory preserves identity-critical subject evidence. Consequently, as generation proceeds, recurring subjects may be diluted, overwritten, or forgotten. In this paper, we propose Memento, a subject-reconstruction-guided framework that treats subject preservation as an explicit identity grounding problem, based on the premise that a memory bank faithfully preserving a subject should support reconstructing that subject from memory alone. Specifically, Memento jointly trains autoregressive next-shot generation with memory-based subject reconstruction, recovering target appearances using historical memory and global story captions. To disentangle long-range subject evidence from short-range cues, Memento introduces a dual-query memory mechanism, where one query retrieves identity-relevant memory and the other selects short-context keyframes for coherent continuation. Additionally, a subject-aware cinematic data pipeline provides precise reconstruction supervision via consistent, pronoun-free subject descriptions. Experiments demonstrate that Memento achieves state-of-the-art performance in long-term subject consistency, cross-shot coherence, and visual quality.

09.
arXiv (CS.AI) 2026-06-16

Adaptive $k$NN graph model

arXiv:2601.16509v2 Announce Type: replace-cross Abstract: The $k$-nearest neighbors ($k$NN) algorithm is a cornerstone of non-parametric classification in artificial intelligence, yet its deployment in large-scale applications is persistently constrained by the computational trade-off between inference speed and accuracy. Existing approximate nearest neighbor solutions accelerate retrieval but often degrade classification precision and lack adaptability in selecting the optimal neighborhood size ($k$). Here, we present an adaptive graph model that decouples inference latency from computational complexity. By integrating a Hierarchical Navigable Small World (HNSW) graph with a pre-computed voting mechanism, our framework completely transfers the computational burden of neighbor selection and weighting to the training phase. Within this topological structure, higher graph layers enable rapid navigation, while lower layers encode precise, node-specific decision boundaries with adaptive neighbor counts. Benchmarking against eight state-of-the-art baselines across six diverse datasets, we demonstrate that this architecture significantly accelerates inference speeds, achieving real-time performance, without compromising classification accuracy. These findings offer a scalable, robust solution to the inherent inference bottleneck of $k$NN, laying an adaptive structural foundation for graph-based nonparametric learning.

10.
arXiv (math.PR) 2026-06-18

Rigidity of infinite exchangeable sequences with Gaussian marginals

arXiv:2606.18654v1 Announce Type: new Abstract: We study infinite exchangeable sequences with Gaussian one-dimensional marginals. We formulate the conjecture that joint Gaussianity of a single pair of coordinates forces the entire sequence to be a Gaussian process. Although this conjecture remains open, we prove that joint Gaussianity of the first four coordinates is sufficient. We also establish the corresponding two-point criterion under the additional assumption that the directing measure is almost surely infinitely divisible.

11.
arXiv (CS.CV) 2026-06-15

Catching magnetic resonance imaging outliers in artificial intelligence-supported radiotherapy workflows: unsupervised detection and localization of image anomalies using deep learning

Artificial intelligence is increasingly integrated into radiotherapy workflows, yet such pipelines remain vulnerable to out-of-distribution image data that may introduce unexpected behavior in clinical tasks. Deep learning-based anomaly detection for pelvic magnetic resonance imaging (MRI) remains largely unexplored, and transparent evaluation of its feasibility for full automation is limited. We developed and evaluated a fully automated, unsupervised anomaly-detection framework for pelvic and brain MRI. A two-stage framework was trained on reference images from public datasets: LUND-PROBE for pelvic MRI, and IXI, fastMRI, and fastMRI+ for brain MRI. In the first stage, MRI slices were compressed into discrete tokens; in the second, the distribution of normal tokens was modeled. Anomaly evidence was estimated by combining perceptual image differences with token-surprisal scores based on negative log-likelihood. Automated detection was evaluated on pelvic MRI with synthetic global and real clinical anomalies, and on brain MRI with clinically annotated fastMRI+ abnormalities. Sensitivity, specificity, area under the receiver operating characteristic curve (AUC), and false-positive behavior in held-out normal cases were assessed. The framework achieved robust detection across hidden evaluation cohorts, with AUCs of 0.97 (95% CI, 0.95-0.98) and 0.81 (95% CI, 0.74-0.87) for pelvic and brain MRI, respectively. Heatmap analysis showed strong spatial agreement between detected anomalies and ground-truth locations, supporting localization accuracy and interpretability. These results support the potential of unsupervised anomaly detection as an automated MRI quality-control layer for radiotherapy workflows, with transparent visualization of image regions likely to compromise downstream AI-based tasks.

13.
arXiv (CS.LG) 2026-06-11

Critic Architecture Matters: Dual vs. Unified Critics for Humanoid Loco-Manipulation

arXiv:2606.11891v1 Announce Type: cross Abstract: Multi-objective reinforcement learning for humanoid robots must coordinate locomotion and manipulation within a single policy. A natural design choice is whether to use a single (unified) critic that estimates the combined value of all objectives, or separate (dual) critics with disjoint reward signals. We present a controlled comparison on the Unitree G1 humanoid (23 active DoF) in NVIDIA Isaac Lab, training loco-manipulation policies through a sequential curriculum spanning 13 levels from stationary reaching to walking with variable-orientation targets. In standardized evaluation, dual-critic policies reach targets 3.5$\times$ faster (6.5 vs. 22.6 simulation steps), achieve 2$\times$ higher throughput (14.3 vs. 7.0 validated reaches per 1,000 steps), and attain higher validated reach rates (65.2% vs. 53.8%) compared to the unified-critic policy. Notably, additional anti-gaming reward mechanisms provide no further improvement beyond the architectural change alone (60.9% vs. 65.2%). These results have direct implications for the emerging paradigm of RL fine-tuning of imitation-learned policies: when refining a pre-trained manipulation policy with RL, a unified critic risks suppressing the learned behavior through competing locomotion gradients. These findings demonstrate that critic architecture is a primary - and often overlooked - design choice in multi-objective humanoid RL, with greater impact than reward engineering on reaching efficiency.

14.
bioRxiv (Bioinfo) 2026-06-14

Somatic variant detection in normal tissues from single-cell sequencing data

A crucial advantage of single-cell sequencing (SCS) is its ability to identify somatic variants in individual cells, enabling phylogenetic analysis of cellular populations within bulk tissues. While identifying somatic variants in tumor tissues via SCS has become a common practice, doing so in normal tissues remains challenging due to the rarity of somatic variants in normal cells. To evaluate the feasibility of somatic variant calling from widely available single-nucleus RNA-seq (snRNA-seq) and single-nucleus ATAC-seq (snATAC-seq) data, we profiled a Cell-line mix of six HapMap samples prepared by the SMaHT consortium using 10x Genomics 5' snRNA-seq (12k cells with 36k mean reads per cell) and snATAC-seq (11k cells with 14k median high-quality fragments per cell) for variant calling. PacBio long-read whole genome sequencing (WGS) data (109x) generated from individual cell lines were used as ground truth. Two computational tools, Monopogen and SComatic, were used for somatic variant calling from the SCS data. Monopogen achieved single nucleotide variant (SNV) detection accuracies of 93.30% in the snRNA-seq and 99.64% in the snATAC-seq data, both of which outperformed SComatic (74.35% and 94.29%, respectively). Monopogen also consistently detected somatic SNVs at cellular fractions as low as 0.5% (2.54% in snRNA and 0.81% in snATAC) in individual samples. Notably, snATAC-seq exhibited higher genomic coverage breadth and larger number of variants detected than snRNA-seq. While the SCS data have lower overall genome coverage than that of the bulk WGS, the single-cell level variant resolution allows Monopogen to assign variants to their cells of origin with over 80% accuracy in both RNA and ATAC modalities, thereby facilitating studies of clonal evolution and cell-type-specific mutagenesis. Other benchmarking methods were also evaluated (DeepVariant, Cellsnp-lite and Mutect2) for comparison. In conclusion, our study demonstrated the feasibility of performing reliable single-cell somatic mutation calling in a cell-line mixture and discussed the strengths and limitations of current computational methods when applied to normal tissues.

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

Controlled Dynamics Attractor Transformer

arXiv:2606.15207v1 Announce Type: cross Abstract: Transformer architectures have dramatically advanced representation learning and inference in deep models through self-attention mechanisms. In parallel,associative memory (AM) frameworks map representations onto energy landscapes, offering interpretable retrieval mechanisms. However, their continuous-time inference dynamics lack the biological plausibility of classical Continuous Attractor Neural Networks (CANNs). To bridge this gap, we propose Controlled Dynamics Attractor Transformer (CDAT), which couples a mixture von Mises-Fisher (Mo-vMF) attention energy with a Hopfield refinement energy, while augmenting energy descent with a CANN-inspired excitation-inhibition modulation. CDAT instantiates a topology-constrained dynamical system whose couplings encode relational structure among tokens, thereby linking attractor-style dynamics to modern energy-based attention. We further provide a constructive dissipation analysis to formally establish their controlled inference dynamics. Benefiting from these robust and structured dynamics, CDAT achieves state-of-the-art performance across multiple benchmarks in graph anomaly detection and graph classification.

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

Edge Flow: A Tractable and Predictive Continuous-Time Model for Gradient Descent at the Edge of Stability

arXiv:2606.18080v1 Announce Type: new Abstract: Gradient descent in deep learning may operate at the edge of stability (EoS), a regime in which the largest eigenvalue of the loss Hessian hovers near the stability threshold $2/\eta$, where $\eta$ is the learning rate. Classical analysis tools such as gradient flow and the descent lemma do not apply here, motivating the search for a continuous-time model valid at EoS. We propose Edge Flow, a system of three coupled ordinary differential equations that provides a tractable, faithful, and predictive model of gradient descent dynamics at EoS. Edge Flow decomposes the dynamics into a center, an oscillation direction, and an oscillation magnitude. The center follows a modified gradient flow on a symmetrized loss; the direction tracks a top eigenvector of the Hessian via Rayleigh quotient dynamics; and the magnitude grows or decays exponentially depending on whether the sharpness exceeds or falls below the threshold $2/\eta$. Crucially, sharpness stabilization emerges from the coupled dynamics via a self-stabilization feedback loop. Discretizing Edge Flow only requires two gradient evaluations and one Hessian–vector product at each iteration. We demonstrate empirically that Edge Flow tracks the dynamics of gradient descent at least as faithfully as previously proposed continuous-time EoS models, while in addition resolving the oscillation of the sharpness at the onset of EoS, and that it provides a principled framework for understanding and mitigating instabilities in this regime.

18.
arXiv (CS.AI) 2026-06-16

Retro-Expert: Collaborative Reasoning for Interpretable Retrosynthesis

arXiv:2508.10967v3 Announce Type: replace-cross Abstract: Retrosynthesis prediction aims to infer the reactant molecules based on a given product molecule, which is a fundamental task in chemical synthesis. However, existing methods rely on a static pattern-matching paradigm, which limits their ability to perform effective logical decision-making from chemical data, leading to a black-box process. We propose Retro-Expert, an interpretable retrosynthesis framework that performs collaborative reasoning by combining the complementary strengths of Large Language Models and specialized models via pure reinforcement learning. It outputs natural language explanations grounded in chemical logic through three components: (1) specialized models provide chemical knowledge that is distilled into a high-quality chemical decision space, (2) LLM-driven critical reasoning to generate predictions with an interpretable reasoning path, and (3) knowledge-grounded policy optimization refines the interpretable decision policy. Experiments show that Retro-Expert surpasses both LLM-based and specialized models across different metrics, while generating chemically grounded explanations that enhance chemists' trust in practice. The source code for this paper is available at https://github.com/MagixRab-ll/Retro-Expert.

19.
bioRxiv (Bioinfo) 2026-06-22

EventHorizon: A Foundation Model for Clinical Flow Cytometry

Flow cytometry is an essential tool for diagnosis of hematologic malignancies, but existing clinical workflows are highly dependent on expert manual interpretation. Existing machine learning approaches typically require extensive labeled data and are sensitive to variability in panel design, instrumentation, and laboratory workflows, limiting their generalizability. We present EventHorizon, a self-supervised foundation model for clinical flow cytometry that produces unified specimen-level representations from heterogeneous multi-panel data. EventHorizon employs a two-stage hierarchical transformer architecture with marker-aware tokenization, enabling seamless integration of cells measured across different antibody panels into a single shared latent space. We pre-train the model using a DINO-inspired self-distillation strategy with a variety of flow cytometry-specific augmentations on a dataset of more than 100,000 clinical specimens across 17 distinct panels. We evaluate the resulting embeddings on three clinically relevant classification tasks spanning common and rare panels, demonstrating that simple k-nearest neighbor probing of frozen EventHorizon embeddings achieves performance comparable to a fully supervised baseline model and a prior panel-specific self-supervised model. To ensure EventHorizon is not simply shortcut learning on features such as the markers/panels run for a given specimen, we perform a graph-theoretic analysis of EventHorizon's latent space which argues that specimen embeddings are organized primarily by biological diagnosis. Taken together, these results demonstrate that EventHorizon produces biologically meaningful, panel-agnostic specimen representations from clinical flow cytometry data which, with further development and validation, could provide a potential basis for scalable, reproducible diagnostic support across diverse clinical laboratory settings.

20.
arXiv (CS.AI) 2026-06-16

Cognitive Debt: AI as Intellectual Leverage and the Dynamics of Systemic Fragility

作者:

arXiv:2606.15078v1 Announce Type: new Abstract: We develop a formal theory of cognitive debt: the stock of unverified reasoning obligations that accumulates when individuals use AI as a substitute rather than a complement for first-principles cognition. The model features two state variables per agent, cognitive capital and cognitive debt, and a multiplicative production technology in which cognitive capital functions as collateral that determines the return to AI adoption. We establish six propositions. Rational agents incur positive cognitive debt because the costs are deferred, partially external, and masked by short-run productivity gains. Tranquil periods lower subjective risk assessments, raise AI substitution intensity, and compound leverage, generating a cognitive Minsky moment in which subjective risk falls while true systemic fragility rises. Expected crisis losses are convex in aggregate leverage. Post-crisis, output-target pressure can produce a false-correction loop in which agents patch AI failures with more AI. The decentralised equilibrium over-adopts substitutive AI relative to the social optimum because of systemic risk, cognitive public goods, and arms-race externalities. In a two-type heterogeneous-agent economy, high-cognitive-capital agents adopt AI more intensively and may eventually erode their unaided cognitive capital below that of initially lower-skilled agents.

21.
arXiv (CS.CL) 2026-06-11

Beyond Third-Person Audits: Situated Interaction Auditing for User-Centered LLM Bias Research

Research on bias in large language models (LLMs) has predominantly focused on third-person audits, which study how models represent or evaluate demographic groups as external subjects. However, this paradigm overlooks a structural blind spot because the user is absent from the audit. In practice, LLMs are used in open-ended, personal interactions, during which the model implicitly represents the user and adjusts its responses accordingly. When identical requests yield different responses depending on who is asking, bias manifests not in how the model describes others but in how it treats its interlocutor. We propose Situated Interaction Auditing (SIA), a user-centered framework for studying how user profile signals – implicit sociodemographic markers, writing style, and stated identity – systematically shape LLM response quality, content, and tone. We demonstrate the framework through a case study that intersects gender and socioeconomic status signals across multiple task domains and outline a research agenda for SIA as a new mission for natural language processing.

22.
arXiv (quant-ph) 2026-06-19

Sparse positive maps on qutrits with exact nondecomposability thresholds and PPT-entanglement transitions

arXiv:2606.19765v1 Announce Type: new Abstract: We study a family of sparse positive maps on qutrits for which positivity, decomposability, and PPT entanglement can all be analysed explicitly. The block structure of the associated Choi matrices reduces positivity to a Hermitian biquadratic form and leads to exact positivity boundaries for three representative parametric families. For the same families we determine the exact transition between decomposable and non-decomposable maps and construct associated PPT states of two classes. The first consists of witness-adapted deformations naturally tied to the non-decomposability analysis. The second consists of analytically tractable families whose full PPT-entangled branch is detected by fixed positive maps, yielding exact thresholds between separability and bound entanglement. For the trace-preserving subclass, we further compare positivity with a recent eigenvalue bound for 2-positive maps, thereby making the gap between positivity and higher-order positivity fully explicit within this family.

23.
arXiv (CS.CV) 2026-06-11

PIGEON: VLM-Driven Object Navigation via Points of Interest Selection

Object navigation in unseen indoor environments requires agents to perform semantic search under partial observability. Vision-language models (VLMs) provide strong semantic-spatial priors for this task, but how to interface them with robot navigation remains challenging: dense VLM inference is expensive, while abstracting environments into symbolic memories often separates high-level reasoning from the raw visual evidence that supports it. We propose we propose PIGEON (Point of Interest Guided Exploration for Object Navigation), a VLM-driven framework that formulates object navigation as raw-observation-grounded sparse decision problem. PIGEON introduces Points of Interest (PoIs) as sparse visual decision units that couple geometrically executable waypoints with raw egocentric observations. Rather than using VLMs as dense controllers or restricting them to frontier ranking, PIGEON enables VLMs to select among task-critical PoIs, including exploration frontiers, suspected target objects, traversable stairs, and floor-level summaries, while low-level planners execute continuous motion between them. This PoI interface further makes high-level navigation decisions verifiable, allowing us to develop an RLVR pipeline that improves local VLMs without manual Chain-of-Thought annotations. Extensive experiments on Habitat ObjectNav benchmarks show that PIGEON achieves state-of-the-art zero-shot performance, scales consistently with foundation model capacity, and transfers to Active Embodied Question Answering with only prompt modifications. Real-world deployments on physical robots further demonstrate its robustness and efficiency.

24.
bioRxiv (Bioinfo) 2026-06-18

Benchmarking gene expression reconstruction from single-cell latent representations

Single-cell transcriptomics is typically modeled in low-dimensional latent representations that improve the signal-to-noise ratio of the data. Such representations underpin data integration, cell state discovery, and perturbation prediction, with applications ranging from large-scale organ atlases to latent trajectory modeling. Recent virtual cell approaches further leverage these representations to predict cellular responses as distributional shifts in latent space. Each of these applications ultimately requires faithful gene expression reconstruction from latent spaces for biological interpretation, enabling gene-level analysis of predicted perturbed or batch-corrected cells. Yet representation choice is typically treated as an implementation detail rather than a primary modeling decision, with no systematic evaluation of how well latent representations support gene expression reconstruction. Here, we introduce ReconEval, a benchmark for evaluating gene expression reconstruction from single-cell latent spaces. We benchmark two classes of latent representations: end-to-end trained models such as PCA, autoencoders, and variational autoencoders, and pretrained single-cell foundation model embeddings coupled to newly trained decoders. Reconstruction is evaluated both directly and after latent-space perturbation prediction. Across perturbational and observational datasets totaling over 100 million cells, our metric suite quantifies statistical fidelity; biological signal preservation, including differential expression, coexpression, cell-cycle structure, cytokine response and pathway activity; and perturbation-specific effects. We find that autoencoders achieve the strongest stand-alone reconstruction at low dimensionality, while variational regularization does not improve generalization in reconstruction. Frozen foundation model embeddings retain recoverable gene-level information, with reconstruction quality depending strongly on decoder architecture and pretraining objective. In latent perturbation modeling, high-dimensional PCA matches foundation model embeddings, while low-dimensional AE embeddings are optimal for flow-based generative models. Overall, reconstruction depends critically on the interplay between representation and downstream model, and simpler representations can outperform complex alternatives given appropriate capacity. Our benchmark establishes reconstruction as a critical evaluation axis for single-cell foundation models. We envision it improving the biological interpretability of latent-space modeling, a prerequisite for future virtual cell models to be validated by domain experts and grounded in biology.

25.
arXiv (CS.CL) 2026-06-16

Do You Really Need a GPU to Guard Your LLM? CPU-Class Classifiers and Multi-Stage Pipelines for Safety Enforcement at Scale

Safety classifiers that screen LLM inputs for jailbreak attempts have become standard deployment components, yet almost all production systems rely on GPU-based models: fine-tuned transformers and LLM-as-a-judge pipelines. These approaches impose significant per-query latency and infrastructure cost. Very little research has asked whether CPU-based classifiers, such as support vector machines and gradient-boosted trees trained on TF-IDF features, can match their accuracy across the conditions that production deployments encounter. We evaluate five CPU classifier families, Mamba-130M as an SSM-based GPU classifier, and transformer-based GPU models (DeBERTa-v3 and Gemma-2B with LoRA) across nine jailbreak sources and three regimes: in-distribution (D1), out-of-distribution (D2), and adversarially obfuscated (D3). On D1, the best CPU classifier matches the best transformer GPU model at roughly one-fifth the deployment cost. On D2, CPU classifiers fail via confident miscalibration, producing high-confidence false negatives that bypass escalation entirely. On D3, CPU classifiers outperform transformer GPU models by more than 26 percentage points in F1. Based on these complementary failure modes, we design GuardChain, a three-stage safety pipeline (Regex -> CPU -> GPU) that routes each prompt to the cheapest stage capable of a confident decision. The CPU stage alone resolves 80\% of in-distribution prompts at near-peak accuracy, and the GPU stage recovers the out-of-distribution failures. For practitioners deploying LLM safety at scale, this work provides evidence that GPU-class infrastructure is unnecessary for the majority of traffic.