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

Refusal Beyond a Single Direction: A Preliminary Comparison of Diff-in-Means and INLP

arXiv:2606.13720v1 Announce Type: new Abstract: Arditi et al. (2024) has shown that refusal in safety fine-tuned chat models is mediated by a single linear direction in the residual stream, recoverable by a difference-in-means (DiM) of harmful and harmless activations. We compare DiM-based interventions (activation addition and directional ablation) with two interventions derived from Iterative Nullspace Projection (INLP) – nullspace projection and counterfactual flipping – on five open-weight chat models, asking whether INLP can match DiM at steering refusal and whether its richer parameterisation yields more tweakable interventions. INLP counterfactual flipping is competitive with DiM directional ablation on refusal suppression, while nullspace projection is consistently weaker. Restricting INLP to the leading directions of the extracted subspace preserves most of the suppression effect at near-baseline perplexity, giving a tunable capability. Geometrically, the two INLP interventions land in qualitatively different regions of activation space: nullspace projection collapses transformed activations between the harmful and harmless clusters, while counterfactual flipping moves them into the opposite cluster, suggesting that the model encodes the absence of a concept differently from its opposite – an intriguing distinction that warrants further investigation in future work.

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

APEX: A Network-Native Time-Series Foundation Model for Forecasting and Anomaly Detection for Wireless Edge Operations

arXiv:2606.11553v1 Announce Type: new Abstract: Generic time-series foundation models transfer poorly to wireless network telemetry whose signals are bursty, zero-inflated, and coupled across protocol layers. We present APEX, a network-native, decoder-only transformer for forecasting enterprise AP telemetry, and evaluate it on DHCP degradation as a representative network task. APEX is pre-trained on 10-channel multivariate telemetry from ~4,500 production wireless networks (~100K AP time series, 34 metrics per AP), and is available as APEX-Large (269M, cloud) and APEX-Edge (10.5M, edge). On a 192-step (4-day) DHCP degradation benchmark, APEX-Large reduces MAE by 18% over the strongest foundation-model baseline (Toto) and 38% over SARIMA, with anomaly-detection F1 = 0.93, while APEX-Edge enables sub-second, privacy-preserving inference on AP-class edge hardware. These results suggest network-native pre-training is a practical foundation for proactive wireless operations.

03.
arXiv (CS.LG) 2026-06-19

Physics-Informed Discovery of Yield Functions in Plasticity via Convex Neural Representations

arXiv:2606.19375v1 Announce Type: new Abstract: Identifying anisotropic yield functions remains challenging since yielding is not directly observed in full-field mechanical measurements, directional calibration can require many loading directions, and selecting an appropriate analytical form is nontrivial. This study proposes a physics-informed framework for discovering yield functions from full-field displacement data and reaction force data, without stress observations, plastic strain measurements, direct yield surface data, or a prescribed parametric yield function. The framework identifies the yield function as a mechanically constrained constitutive component inside elastoplastic stress integration, rather than through direct stress-space supervision. The yield function is represented by a convex neural network that enforces convexity and positive homogeneity of degree one while imposing the assumed tension-compression symmetry, and this neural yield function is trained with a differentiable stress update and a physics-informed force equilibrium loss across multiple loading cases. The proposed framework is validated using finite element (FE) benchmark studies with von Mises, Hill 1948, and Yld2000-2d yield functions, assessing yield contour agreement, displacement-noise sensitivity, identifiability through plastically active stress states, epistemic uncertainty, and polynomial-surrogate deployment. This study provides a mechanics-constrained pathway for discovering anisotropic yield functions from displacement and force data while keeping the identified component within the structure of elastoplastic stress integration.

04.
arXiv (CS.CV) 2026-06-11

NSVQ: Mitigating Codebook Collapse by Stabilizing Encoder Drift in Vector Quantization

Vector quantization is central to modern generative modeling pipelines, but large-codebook VQ models often suffer from codebook collapse. We identify encoder drift as a key driver of this failure: as the encoder moves the latent distribution, sparsely updated code vectors can lag behind, lose assignments, and increase quantization error, creating a feedback loop through the straight-through estimator. We propose NSVQ, a non-stationary-aware VQ training strategy that combines a dense non-stationary embedding loss, codebook replacement, and stage-wise encoder freezing. NSVQ first helps the codebook track encoder drift during early training, then freezes the encoder to consolidate the codebook under a fixed latent geometry, and finally reintroduces adversarial refinement. Experiments on ImageNet-1k show that NSVQ improves reconstruction quality while maintaining full codebook utilization. On ImageNet-1k at 128$\times$128 with 65,536 codes, NSVQ reduces rFID from 2.39 to 2.10 compared with SimVQ, while both methods maintain 100\% utilization. Additional latent diffusion experiments show that NSVQ also improves downstream ImageNet generation FID.

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

InfoNCE Induces Gaussian Distribution

arXiv:2602.24012v2 Announce Type: replace Abstract: Contrastive learning has become a cornerstone of modern representation learning, allowing training with massive unlabeled data for both task-specific and general (foundation) models. A prototypical loss in contrastive training is InfoNCE and its variants. In this work, we show that the InfoNCE objective induces Gaussian structure in representations that emerge from contrastive training. We establish this result in two complementary regimes. First, we show that under certain alignment and concentration assumptions, projections of the high-dimensional representation asymptotically approach a multivariate Gaussian distribution. Next, under less strict assumptions, we show that adding a small asymptotically vanishing regularization term that promotes low feature norm and high feature entropy leads to similar asymptotic results. We support our analysis with experiments on synthetic and CIFAR-10 datasets across multiple encoder architectures and sizes, demonstrating consistent Gaussian behavior. This perspective provides a principled explanation for commonly observed Gaussianity in contrastive representations. The resulting Gaussian model enables principled analytical treatment of learned representations and is expected to support a wide range of applications in contrastive learning.

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

From Drift to Coherence: Stabilizing Beliefs in LLMs

arXiv:2606.17832v1 Announce Type: new Abstract: Large language models (LLMs) are often hypothesized to perform implicit Bayesian inference, yet a key coherence condition, the martingale property of predictive beliefs, has been shown to fail in controlled synthetic in-context learning settings. We revisit this question in a more typical usage regime: generic multiple-choice question answering. Exploiting the discrete answer space, we compute exact predictive distributions and study belief dynamics induced by autoregressive answer resampling. We introduce prompted predictive resampling (PPR), where an LLM generates a sequence of answers to the same question. Empirically, PPR reveals early-stage belief drift, indicating martingale violations. However, after sufficient resampling steps, the belief process self-stabilizes and converges to a coherent predictive distribution. Based on this observation, we further propose (i) a seed-answer prompting strategy to accelerate stabilization, and (ii) a self-consistency loss that amortizes early-stage drift into the model via fine-tuning. Experiments on multiple-choice QA benchmarks show that our methods substantially reduce belief drift and improve predictive coherence without sacrificing accuracy.

07.
arXiv (CS.LG) 2026-06-16

BRICKS-WM: Building Reusability via Interface Composition Kinetics for Structured World Models

arXiv:2606.16489v1 Announce Type: new Abstract: Model-based Reinforcement Learning (MBRL) has achieved remarkable success in continuous control by leveraging latent world models. However, prevailing approaches typically rely on monolithic latent dynamics, entangling environment dynamics into a coupled process. This coupling severely limits reusability: altering the agent necessitates retraining the entire world from scratch, even if the environment remains constant. To address this, we introduce BRICKS-WM (Building Reusability via Interface Composition Kinetics for Structured World Models), a framework for the modular assembly of structured world models. Driven by the insight that the physical world is composed of independent entities, we posit that global dynamics can be modeled as a composition of distinct dynamical modules interacting via latent interfaces. As a minimal instantiation, we factorize the latent state space into an actuated Agent module and an external Background module, bridged by a learned latent interface. Unlike prior object-centric methods that prioritize visual segmentation, BRICKS-WM enforces a functional separation in transition dynamics, ensuring that background dynamics remains agnostic to the agent's dynamics. Empirically, BRICKS-WM achieves control performance comparable to strong monolithic baselines when trained from scratch, and enables the reuse of frozen background dynamics across agents.

08.
medRxiv (Medicine) 2026-06-16

Deployment-readiness audit of calibration, clinical utility, and fairness in perioperative infection prediction

Objective: Clinical risk scores intended to guide patient-level decisions can show strong average performance. However, predicted probabilities can be systematically too high or too low in specific subgroups even when overall performance is strong. We audited deployment readiness of a strong end-of-surgery postoperative infection model across clinically relevant subgroups and tested mitigation strategies in miscalibrated subgroups. Materials and Methods: We analyzed out-of-fold predictions for 10,719 surgical procedures at a Swiss tertiary hospital, with 504 postoperative bacterial infection events. Prespecified axes were recorded sex, age stratum, and an EHR-derived physiological-reserve proxy. Within subgroups and pairwise intersections, we evaluated discrimination, calibration, threshold-specific errors, and decision-curve net benefit at the prespecified operating threshold. We compared group-specific isotonic recalibration with Wasserstein-barycenter postprocessing and demonstrated portability in SUPPORT2. Results: Overall AUROC was 0.876. While sex-marginal discrimination was similar in women and men (0.878 vs 0.875), age and reserve stratification revealed deployment-readiness failures. Calibration-in-the-large ranged from -0.86 in frail patients to -2.47 in non-frail patients. At the 0.10 operating threshold, decision-curve net benefit was positive in frail patients but negative in pre-frail and non-frail patients. Isotonic recalibration corrected average physiological-reserve-stratified calibration without worsening Brier scores, whereas Wasserstein postprocessing worsened calibration in most procedure clusters. Discussion: Discrimination-only or sex-marginal evaluation would have missed subgroup failures with clinical-utility implications. Conclusion: Subgroup fairness audits for clinical deployment should jointly evaluate discrimination, calibration, and utility. We implemented the audit as the open-source isitfair framework for identifying deployment-relevant subgroup failures, comparing mitigation strategies, and generating structured reports.

09.
bioRxiv (Bioinfo) 2026-06-15

RepGene: Toward a Unified Gene Representation Space Robust to Missing Biological Views

Genes can be described through multiple heterogeneous biological views, including genomic sequence, transcript sequence, protein sequence, textual knowledge, and single-cell expression context, yet existing gene embeddings remain largely modality-specific and difficult to compare or reuse when many views are unavailable. We study a narrower but practically important question: whether pretrained embeddings from these distinct sources can be organized into a shared gene representation interface that remains usable under severe missing-modality conditions. To investigate this question, we introduce RepGene, a lightweight single-branch framework that combines modality adapters, a shared encoder, presence-aware fusion, and self-supervised cross-view objectives to map five biological views into one latent space. Our goal is not to claim a new multimodal learning principle or to establish superiority over all simpler fusion strategies, but to provide an initial technical instantiation for testing whether such a shared interface is feasible in a fixed-feature setting. Under a two-stage protocol in which RepGene is trained self-supervised on frozen upstream embeddings and evaluated by downstream linear probing, we find preliminary evidence that the learned representation is broadly competitive in the full-modality setting and remains informative when only partial modality subsets are observed at inference time. The strongest signal in our study is robustness under missing views: average performance changes are often limited when one modality is removed, and even single-view inference remains non-trivial in the evaluated benchmark regime.These results do not resolve unified biological representation learning, and they should be interpreted in light of incomplete simple-fusion baselines, limited architectural ablation, benchmark dependence, and possible upstream feature exposure. We therefore position RepGene as a feasibility study and a starting point for stronger comparisons, broader benchmarks, and leakage-aware validation.

10.
arXiv (quant-ph) 2026-06-12

Non-invertible symmetries out of equilibrium: Eigenstate order and Floquet physics

arXiv:2508.14213v2 Announce Type: replace-cross Abstract: Through the study of the Rep($D_8$) non-invertible symmetry, we show how non-invertible symmetries manifest in dynamics. Results are presented for dynamics generated by Hamiltonians as well as Floquet unitaries. For both examples, the role of the non-invertible symmetry is studied through the appearance of non-invertible symmetry protected edge modes. In addition, the role of the non-invertible symmetry for the Hamiltonian is studied through eigenstate order. In particular, by considering the effect of symmetry preserving disorder, the non-invertible symmetry is shown to give rise to degeneracies in the spectra of the Hamiltonian that can only be completely lifted at orders of perturbation that scale with system size. The eigenstates of disordered Hamiltonians, whose ground state correspond to non-trivial symmetry protected topological (SPT) states, are shown to have either trivial or non-trivial SPT order that are detected as non-zero expectation value of string order-parameters. In contrast, non-trivial SPT order is absent in the eigenstates of trivial SPT Hamiltonians with disorder. The interface between two different SPT phases host edge modes whose dynamics is studied numerically and analytically. The edge mode is shown to oscillate at frequencies related to different effective chain lengths that are weighted by the temperature, becoming an exact zero mode in the limit of zero temperature. A Floquet model with the non-invertible symmetry is constructed whose edge mode is shown to exhibit period-doubled dynamics at low effective-temperatures. The zero and period-doubled edge modes differ from those in conventional SPTs by being symmetric under the invertible symmetry, while being charged under the non-invertible symmetry.

11.
arXiv (CS.AI) 2026-06-18

Graph Grounded Cross Attention Transformer Neural Network for Structurally Constrained Full Event Sequence Generation in Predictive Process Monitoring

arXiv:2606.18726v1 Announce Type: cross Abstract: Structurally constrained event sequence generation remains challenging because generated paths must preserve transition feasibility, temporal order, termination, and attribute consistency. In predictive process monitoring (PPM), this challenge appears as full event sequence generation, whereas existing work mainly addresses component tasks such as next activity, remaining time, outcome, and attribute prediction. This paper proposes the Graph Grounded Cross Attention Transformer Neural Network (GGATN) for this unified PPM task. GGATN uses a global process graph as structured activity memory, contextualizes sequence positions through Transformer self attention, and injects process topology through graph grounded cross attention. Unlike autoregressive decoding, GGATN generates activities, timestamps, length, and event level and sequence level attributes in a single pass, followed by Viterbi style graph constrained decoding for feasible paths and explicit termination. Experiments on six benchmark event logs show more reliable generation quality than local instruction prompted LLM baselines. GGATN achieves strong performance on sequence similarity, Damerau Levenshtein similarity, bigram based control flow similarity, and duration distribution, while maintaining zero hallucinated activities and zero sequence level attribute inconsistency. Ablation analyses confirm the global graph encoder as a stable structural prior. Interpretability analyses show how graph structure, sequence context, feedback refinement, and constrained decoding shape generation.

12.
arXiv (quant-ph) 2026-06-17

A Quantum Approach to Stochastic Optimization in Insurance Underwriting

arXiv:2605.01169v2 Announce Type: replace Abstract: The presence of stochastic elements in combinatorial optimization problems makes them particularly challenging, as such problems quickly become intractable for classical computers even at relatively small sizes. In this work, we propose a novel quantum-classical hybrid scheme for solving a class of stochastic optimization problems known as chance-constrained knapsack problems, in which item weights follow probability distributions and constraints may be violated within a specified risk tolerance. Our method employs knapsack-specific QAOA-based circuits to generate samples which, when combined with a new self-consistent classical recovery scheme introduced in this work, produce high-quality solutions. Experiments carried out on IBM Heron processors, using circuits with depths up to 177 and comprising 3443 gates acting on as many as 150 qubits, yield solutions that indicate performance comparable to classical optimization schemes. The proposed quantum-classical scheme paves the way to tackling such problems, with the potential to outperform approaches that rely solely on classical computation.

13.
arXiv (CS.CV) 2026-06-16

GroupToM-Bench: Benchmarking Group Theory of Mind and Nonlinear Social Emergence in MLLMs

True general intelligence requires not only a model of the physical world but also a social world model: the capacity to infer how individual mental states interact and crystallize into group-level outcomes. Despite notable progress in individual-level Theory of Mind (ToM) reasoning, existing multimodal large language models fail at this broader task. Collective behavior emerges non-linearly from social tensions, conformity dynamics, and structural constraints, meaning it cannot be recovered by merely summing individual intentions. We present GroupToM-Bench, the first multimodal benchmark for group-level ToM, built around a causal chain spanning micro-level BDI states (belief, desire, intention), meso-level group tension and structural constraints, and macro-level outcome prediction and mechanistic attribution. To probe this full arc, we develop a seven-level cognitive audit framework. Experiments reveal a gap between current models and human baselines, highlighting a failure to process social structures and non-linear collective dynamics.

14.
arXiv (CS.LG) 2026-06-11

Mitigating Disparate Impact of Differentially Private Learning through Bounded Adaptive Clipping

arXiv:2506.01396v2 Announce Type: replace Abstract: Differential privacy (DP) has become an essential framework for privacy-preserving machine learning. Existing DP learning methods, however, often have disparate impacts on model predictions, e.g., for minority groups. Gradient clipping, which is often used in DP learning, can suppress larger gradients from challenging samples. We show that this problem is amplified by adaptive clipping, which will often shrink the clipping bound to tiny values to match a well-fitting majority, while significantly reducing the accuracy for others. We propose bounded adaptive clipping, which introduces a tunable lower bound to prevent excessive gradient suppression. Our method improves worst-class accuracy by over 10 percentage points on Skewed and Fashion MNIST compared to unbounded adaptive clipping, 7 points compared to Automatic clipping, and 5 points compared to constant clipping. The code is available at https://github.com/TrustworthyMLHelsinki/adaptive-clipping-fairness.

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

DecompSR: A dataset for decomposed analyses of compositional multihop spatial reasoning

arXiv:2511.02627v3 Announce Type: replace Abstract: We introduce DecompSR, decomposed spatial reasoning, a large benchmark dataset (over 5m datapoints) and generation framework designed to analyse compositional spatial reasoning ability. The generation of DecompSR allows users to independently vary several aspects of compositionality, namely: productivity (reasoning depth), substitutivity (entity and linguistic variability), overgeneralisation (input order, distractors) and systematicity (novel linguistic elements). DecompSR is built procedurally in a manner which makes it is correct by construction, which is independently verified using a symbolic solver to guarantee the correctness of the dataset. DecompSR is comprehensively benchmarked across a host of Large Language Models (LLMs) where we show that LLMs struggle with productive and systematic generalisation in spatial reasoning tasks whereas they are more robust to linguistic variation. DecompSR provides a provably correct and rigorous benchmarking dataset with a novel ability to independently vary the degrees of several key aspects of compositionality, allowing for robust and fine-grained probing of the compositional reasoning abilities of LLMs.

16.
arXiv (CS.CL) 2026-06-11

When Probing Accuracy Saturates, Fragility Resolves: A Complementary Metric for LLM Pre-Training Analysis

Standard linear probing declares a property "encoded" when a classifier on hidden states achieves high accuracy. The protocol works well on a snapshot but breaks across pre-training: probe accuracy saturates within the first few thousand steps, leaving most of training invisible to the instrument. We introduce fragility, a complementary per-layer metric defined as the activation-noise level at which probe accuracy collapses. Fragility is sensitive to both the margin of separability and the redundancy of representation, both of which keep evolving long after accuracy plateaus. Applied to open-checkpoint language models, fragility recovers structure that accuracy alone cannot see. Moralized representations emerge along a lexical $\to$ compositional gradient: lexical moral detection first, compositional moral encoding later. Because probe accuracy on its own tracks how lexically separable a dataset is, we establish the compositional encoding directly, by showing it transfers across construction types that share no contrast tokens. A layer-depth robustness gradient develops monotonically across training while accuracy stays flat. And matched fine-tuning corpora that produce identical probing accuracy leave distinct fragility fingerprints, showing that data curation reshapes probe robustness without changing probe accuracy. In every comparison we test, where probing accuracy returns a flat answer, fragility returns a structured one.

17.
arXiv (quant-ph) 2026-06-16

Exactly Solvable Quantum Model with Spin-Dependent Coulomb Interaction

arXiv:2501.05103v5 Announce Type: replace Abstract: In this work, we report an exactly solvable quantum model featuring a spin-dependent Coulomb interaction, described by the spin vector potential \(\vec{\mathcal{A}} = k (\vec{r} \times \vec{S}) / r^2\) together with a Coulomb-type scalar potential \(\varphi = \kappa / r\) . The model is governed by the Schrödinger-type Hamiltonian \(\mathcal{H}_S = \vec{\Pi}^2 / (2M) + q \varphi\) in nonrelativistic quantum mechanics and by the Dirac-type Hamiltonian \(\mathcal{H}_D = c \vec{\alpha} \cdot \vec{\Pi} + \beta M c^2 + q \varphi\) in relativistic quantum mechanics, where \(\vec{\Pi} = \vec{p} - (q/c)\vec{\mathcal{A}}\) is the canonical momentum. We demonstrate two main results: (i) Just as the Coulomb-type scalar potential \(\mathcal{S}_Maxwell = \{\vec{\mathcal{A}} = 0,\ \varphi = \kappa / r\}\) is a local exact solution of Maxwell's equations on $r\neq0$, the gauge potential \(\mathcal{S}_YM = \{\vec{\mathcal{A}} = k (\vec{r} \times \vec{S}) / r^2,\ \varphi = \kappa / r\}\) constitutes a local exact solution of the Yang–Mills equations on the punctured region $r\neq0$. (ii) Both Hamiltonians \(\mathcal{H}_S\) and \(\mathcal{H}_D\) can be solved exactly in the presence of this spin-dependent Coulomb interaction. The resulting energy spectra are derived, and they naturally reduce to those of the ordinary hydrogen atom when the spin-dependent terms are neglected. Finally, we clarify the quantization conditions and the fixed-background interpretation of the model.

18.
PLOS Computational Biology 2026-06-01

BeetleAtlas 2: An enhanced <i>Tribolium castaneum</i> web resource for tissue and developmental transcriptomics allowing refinement of gene predictions

by David P. Leader, Muhammad T. Naseem, Janina L. Rinke, Kenneth Veland Halberg BeetleAtlas is an online resource for tissue- and stage-specific transcriptomics in the red flour beetle, Tribolium castaneum. On updating from the original Tcas5.2 genome assembly to the more recent improved icTriCast1.1 genome assembly it became evident that there were major discrepancies between the gene models of the two genome annotations in use: the OGS3 and the NCBI gene sets. As neither was clearly superior we implemented a new design in BeetleAtlas 2 (beetleatlas.org) comprising two parallel ‘modes’ — one incorporating results using the NCBI gene models and a second incorporating those using the OGS3 gene models. This allows direct comparison where equivalent gene models exist: 50–57% of cases. To aid resolution of discrepancies between the two gene model sets and verification of results, gene models are linked to a custom visualization of RNA-seq read coverage of the genome in the UCSC Genome Browser. This displays reads from 22 tissues and life stages superimposed on the icTriCast1.1 genome assembly. Reference tracks show the NCBI gene models, the OGS3 gene models after translation of their coordinates from the Tcas5.2 assembly, and 1050 discontinued NCBI gene models from the previous assembly after a similar transfer of coordinates. We document various situations in which distinct patterns of expression of the tissues can be used to confirm and extend correlations between the two gene sets, resolve discrepancies between them, make corrections and identify putative genes or exons absent from the current gene sets. BeetleAtlas 2 allows those involved in Tribolium research to avoid the pitfalls inherent in incorrect gene models when planning experiments on specific genes and interpreting the results. It also demonstrates how BeetleAtlas 2 might play an important role in establishing a revised gene set for Tribolium castaneum in the future.

19.
arXiv (quant-ph) 2026-06-11

Permutation-Invariant N-body gates via Tavis-Cummings Hamiltonian

arXiv:2506.03453v3 Announce Type: replace Abstract: Global control provides a promising route to implementing multi-qubit gates without individual qubit addressing. This is especially appealing for permutation-invariant (PI) gates, whose symmetry is often broken when they are compiled into individually addressed one- and two-qubit gates. Important examples include SWAP, $\sqrt{iSWAP}$, and the n-qubit controlled-Z gate, which is equivalent, up to two single-qubit Hadamard gates, to the multi-qubit Toffoli gate. Motivated by this global-control perspective, we show that all PI unitaries on an arbitrary number of qubits can be realized using the Tavis-Cummings (TC) interaction, the multi-qubit version of the Jaynes-Cummings interaction, together with global uniform z and x fields. Here, the $n$ qubits are identically coupled to a single bosonic mode (oscillator), which is initialized in and returned to its vacuum state. A corollary is that all PI states, including GHZ and Dicke states, can be prepared using the same global control. For the case n=2 qubits, which is particularly important in quantum computing, we also find explicit pulse sequences for implementing all PI qubit unitaries that conserve angular momentum in the z direction, using only the TC interaction and global z fields. This includes controlled-Z, SWAP, and $\sqrt{iSWAP}$.

20.
bioRxiv (Bioinfo) 2026-06-11

VFUSE: Virulent Feature Understanding with Sparse autoEncoders

Generative models have shown remarkable progress in a variety of domains such as protein design, but such power enables the opaque generation of hazardous proteins. In this work, we introduce VFUSE (Virulent Feature Understanding with Sparse autoEncoders), a mechanistic interpretability approach that trains SAEs on diffusion-transformer activations to audit protein models for hazard-aware features. We apply VFUSE to RoseTTAFold3 and RFDiffusion3, popular open-weight models for protein folding and synthesis. We find that for certain blocks, linear probes detect hazardous designs significantly better when fit in the SAE latent space over the original model's representations: improving interpretability without sacrificing model performance. Furthermore, we identify monosemantic features from the SAE that fire only on hazardous designs at up to AUROC 0.84 (q < 10-13).

21.
Nature (Science) 2026-06-08

GPR15-guided CD8<sup>+</sup> T regulatory cells control intestinal inflammation

作者:

Inflammatory bowel disease (IBD) causes chronic suffering from gastrointestinal inflammation and dysfunction that can progress to colon cancer1,2. The disease prevalence is increasing and there is an urgent need to better understand its pathogenic mechanisms to improve treatment. We show that GPR15, a G protein-coupled receptor (GPCR) expressed in immune cells and previously described as an entry co-factor for human and simian immunodeficiency viruses3, is a marker and homing receptor for a subset of intramucosal GPR15-guided regulatory CD8+ T lymphocytes (CD8+ TIGR). Deleterious GPR15 gene variants in humans cause defective homing of CD8+ TIGR and are associated with severe early-onset IBD. Moreover, CD8+ TIGR cells are reduced in the intestinal mucosa of sporadic IBD patients. In mice, GPR15 deficiency impairs colonic homing of CD8+ TIGR cells, leading to accumulation of inflammatory macrophages and increased susceptibility to colitis. CD8+ TIGR cells potently kill macrophages activated by intestinal damage or disease using Fas ligand (FasL) and TNF-related weak inducer of apoptosis (TWEAK). The identification of CD8+ TIGR cells yields new insights into organ-specific immune regulation and potential therapeutics for IBD.

22.
arXiv (CS.AI) 2026-06-12

DCD: Domain-Oriented Design for Controlled Retrieval-Augmented Generation

arXiv:2604.07590v2 Announce Type: replace-cross Abstract: Retrieval-Augmented Generation (RAG) is widely used to ground large language models in external knowledge sources. However, when applied to heterogeneous corpora and multi-step queries, Naive RAG pipelines often degrade in quality due to flat knowledge representations and the absence of explicit workflows. In this work, we introduce DCD (Domain-Collection-Document), a domain-oriented design to structure knowledge and control query processing in RAG systems without modifying the underlying language model. The proposed approach relies on a hierarchical decomposition of the information space and multi-stage routing based on structured model outputs, enabling progressive restriction of both retrieval and generation scopes. The architecture is complemented by smart chunking, hybrid retrieval, and integrated validation and generation guardrail mechanisms. We describe the DCD architecture and workflow and discuss evaluation results on synthetic evaluation dataset, highlighting their impact on robustness, factual accuracy, and answer relevance in applied RAG scenarios.

23.
arXiv (CS.CV) 2026-06-16

Through-Foliage Surface-Temperature Reconstruction for Early Wildfire Detection

We present a method to reconstruct surface temperatures through forest vegetation by combining signal processing and machine learning, enabling fully automated aerial wildfire monitoring with drones for early fire detection. Synthetic aperture (SA) sensing reduces canopy occlusion but introduces thermal blur. To overcome this, we train a visual state space model to recover subtle thermal signals of partially occluded soil and fire hotspots from blurred data. To address limited real-world training data, we generate realistic surface temperature simulations using a latent diffusion model, temperature augmentation, and procedural thermal forest modeling. On simulated datasets, our method reduces RMSE by 2-2.5 versus conventional thermal and uncorrected SA imaging; in field experiments on hotspots, RMSE improved by 12.8-fold and 2.6-fold, respectively. Our approach also generalizes to other thermal signals, including human signatures, capturing morphology and extent – critical where simple thresholding fails – while conventional imaging struggles with partial occlusion.

24.
arXiv (CS.LG) 2026-06-11

FlexiBrain: Resolution-Agnostic Voxel-Level Encoding for Native fMRI

arXiv:2606.11500v1 Announce Type: cross Abstract: The success of large-scale deep learning models in neuroscience is fundamentally constrained by severe data heterogeneity. Native fMRI data aggregated from diverse sources exhibit substantial variation in both spatial and temporal resolutions. Consequently, most existing frameworks rely on lengthy, rigid preprocessing pipelines that enforce uniformity across datasets. This practice introduces two critical limitations: (1) potential degradation of subject-specific anatomical information; (2) significant computational overhead, often requiring hours of processing per subject. Here, we propose FlexiBrain, a resolution-agnostic voxel-level encoding framework for native fMRI based on Mamba-JEPA. FlexiBrain defines patch sizes in real-world physical units and employs a dynamic patch resizing, thereby bypassing destructive spatial standardization while enabling direct ingestion of data in native space. We instantiate the framework using an efficient Mamba-JEPA backbone to model high-dimensional 4D fMRI signals. Across five diverse downstream neuroscience tasks, FlexiBrain consistently outperforms recent state-of-the-art methods, achieving gains of up to 12 percentage points without external data augmentation. Importantly, FlexiBrain functions as a seamless plug-in module, substantially reducing preprocessing costs and accelerating the development of robust voxel-level fMRI foundation models. Code is available at https://github.com/OneMore1/FlexiBrain.

25.
arXiv (CS.LG) 2026-06-17

CoCoEmo: Composable and Controllable Human-Like Emotional TTS via Activation Steering

arXiv:2602.03420v2 Announce Type: replace-cross Abstract: Emotional expression in human speech is nuanced and compositional, often involving multiple, sometimes conflicting, affective cues that may diverge from linguistic content. In contrast, most expressive text-to-speech systems enforce a single utterance-level emotion, collapsing affective diversity and suppressing mixed or text-emotion-misaligned expression. While activation steering via latent direction vectors offers a promising solution, it remains unclear whether emotion representations are linearly steerable in TTS, where steering should be applied within hybrid TTS architectures, and how such complex emotion behaviors should be evaluated. This paper presents the first systematic analysis of activation steering for emotional control in hybrid TTS models, introducing a quantitative, controllable steering framework, and multi-rater evaluation protocols that enable composable mixed-emotion synthesis and reliable text-emotion mismatch synthesis. Our results demonstrate, for the first time, that emotional prosody and expressive variability are primarily synthesized by the TTS language module instead of the flow-matching module, and also provide a lightweight steering approach for generating natural, human-like emotional speech.