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01.
arXiv (CS.AI) 2026-06-11

Position: Stop Anthropomorphizing Intermediate Tokens as Reasoning/Thinking Traces!

arXiv:2504.09762v4 Announce Type: replace Abstract: Intermediate token generation (ITG), where a model produces output before the solution, has become a standard method to improve the performance of language models on reasoning tasks. These intermediate tokens have been called \say{reasoning traces} or even \say{thinking traces} – implicitly anthropomorphizing the traces, and implying that these traces resemble steps a human might take when solving a challenging problem, and as such can provide an interpretable window into the operation of the model's thinking process to the end user. In this position paper, we present evidence that this anthropomorphization isn't a harmless metaphor, and instead is quite dangerous – it confuses the nature of these models and how to use them effectively, and leads to questionable research. We call on the community to avoid such anthropomorphization of intermediate tokens.

02.
arXiv (CS.AI) 2026-06-24

Context-Aware Prediction of Student Quiz Performance with Multimodal Textbook Features

Authors:

arXiv:2606.24770v1 Announce Type: cross Abstract: Educational platforms often predict student performance from prior interactions, but the assessment content itself also varies in linguistic and visual complexity. This paper studies whether lightweight content features extracted from CourseKata chapter-review questions improve prediction of end-of-chapter quiz scores beyond a student's average prior exercise performance. The study combines 2023 CourseKata student response data with chapter-level text features from review-question wording and image features from textbook visuals. Across 4,742 student-chapter observations from 562 class-student IDs, adding content features improves student-grouped five-fold quiz prediction performance by 9.1% relative to a prior-performance baseline. In leave-chapter-out validation, text features reduce prediction error relative to the baseline, while image-containing models have higher error. This paper suggests that a context-aware model adds useful signal about the text and visual features of questions to better predict student quiz performance compared with using past student performance alone.

03.
arXiv (CS.CV) 2026-06-24

Agentic Collaborative Cognition for Zero-Shot 3D Understanding

Recent advancements have explored agentic zero-shot 3D understanding by reformulating it as video keyframe understanding with Multimodal Large Language Models (MLLMs). However, existing methods face an intrinsic bottleneck due to the finite observation perspectives inherent in videos and the implicit perception of 3D scenes. In this paper, we propose a collaborative multi-agent framework that assigns a Planning Agent to handle high-level viewpoint planning and supplement novel perspectives, and a Perception Agent to explicitly summarize the 3D scene into a structured holistic cognitive map. Specifically, Planning Agent first analyzes this cognitive map to determine query-relevant viewpoints and supplements missing critical perspectives to ensure comprehensive observation. Subsequently, Perception Agent documents object-level attributes from these views by assigning consistent instance identifiers across viewpoints, thereby integrating fragmented observations into the holistic cognitive map. In parallel, it provides feedback to filter out mismatched candidate objects and guide subsequent viewpoint planning. Through this closed-loop iterative process, two agents collaboratively figure out candidates until Perception Agent determines that sufficient information has been captured to complete the task. Extensive experiments demonstrate that our method achieves state-of-the-art performance on 6 benchmarks, with improvements of 11.1\% Acc@0.5 on ScanRefer, 14.6 BLEU-1 on 3D-assisted dialog, and 2.1 EM on SQA3D.

04.
arXiv (CS.LG) 2026-06-19

Shifting-based Optimizable Linear Relaxations for General Activation Functions

arXiv:2606.20292v1 Announce Type: new Abstract: The use of neural networks (NNs) is rapidly increasing, including in safety- and security-critical domains. To provide formal guarantees about NN behavior, many verification methods rely on optimizable linear relaxations of activation functions. However, existing techniques depend on hand-crafted relaxations for each activation function. Extension to state-of-the-art activation functions therefore requires substantial manual effort. In contrast, our approach SLiR (Shifting-based Linear Relaxations) is broadly applicable, requiring only a Lipschitz constant or a set of critical points. SLiR parameterizes relaxations by their slope and computes the corresponding offset via a shifting procedure that ensures sound upper and lower bounds over the input domain, enabling efficient optimization while maintaining correctness. Our experiments show that SLiR produces tight relaxations across a wide range of practical activation functions and enables verification of up to 7.8x more properties compared to state-of-the-art methods.

05.
arXiv (quant-ph) 2026-06-17

Hybrid Acousto-Optical Double Dressing of a Two-Level System

arXiv:2509.25847v2 Announce Type: replace Abstract: We experimentally investigate resonance fluorescence from a two-level system in a novel configuration where a strong laser drives an optical Rabi oscillation while an acoustic field parametrically modulates the frequency of the two-level system. We observe emission spectra that deviate markedly from the standard Mollow triplet, including dynamical cancellation of the central peak. A doubly dressed state model incorporating hybridization among the emitter, optical field, and acoustic field captures these features. Guided by this model, we experimentally validate the condition for optimal cooling of acoustic phonons in an emitter-optomechanical system. These results reveal new regimes of strongly driven quantum nonlinear interactions.

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

PLATE: Plasticity-Tunable Efficient Adapters for Geometry-Aware Continual Learning

arXiv:2602.03846v2 Announce Type: replace-cross Abstract: We develop a continual learning method for pretrained models that requires no access to old-task data, addressing a practical barrier in foundation model adaptation where pretraining distributions are often unavailable. Our key observation is that pretrained networks exhibit substantial geometric redundancy, and that this redundancy can be exploited in two complementary ways. First, redundant neurons provide a proxy for dominant pretraining-era feature directions, enabling the construction of approximately protected update subspaces directly from pretrained weights. Second, redundancy offers a natural bias for where to place plasticity: by restricting updates to a subset of redundant neurons and constraining the remaining degrees of freedom, we obtain update families with reduced functional drift on the old-data distribution and improved worst-case retention guarantees. These insights lead to \textsc{PLATE} (Plasticity-Tunable Efficient Adapters), a continual learning method requiring no past-task data that provides explicit control over the plasticity-retention trade-off. PLATE parameterizes each layer with a structured low-rank update $\Delta W = B A Q^\top$, where $B$ and $Q$ are computed once from pretrained weights and kept frozen, and only $A$ is trained on the new task. The code is available at https://github.com/SalesforceAIResearch/PLATE.

07.
arXiv (math.PR) 2026-06-12

Interference Queueing Networks: A Replica Mean-Field Approach in the Symmetric Setting

arXiv:2606.13264v1 Announce Type: new Abstract: We propose a model for evaluating the performance of wireless communication networks beyond the ubiquitous full-buffer assumption, under which every transmitter is always active. The network is represented by N interacting queues arranged on a torus, with homogeneous arrival rate and service rates depending on the activity of neighboring interferers. More precisely, each queue is associated with a transmitter-receiver pair, and its service rate is given by the Shannon capacity, which depends on the corresponding Signal-to-Interference-plus-Noise Ratio (SINR). Since interfering transmitters only emit when their queue is non-empty, the SINR and hence the service rate improves when neighboring queues are empty. We derive the stability region of the system, together with approximations of its stationary distribution and its exponential rate of convergence to stationarity. These approximations are obtained via a replica mean-field limit, for which we establish propagation of chaos and long-time behavior results.

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

REVEAL++: Differentiable Phenotypic Grouping for Vision-Language Retinal Modeling of Alzheimer's Disease Risk

arXiv:2606.19522v1 Announce Type: new Abstract: The retina offers a noninvasive window into neurodegenerative disease, capturing subtle structural patterns associated with a risk of future cognitive decline. Vision-language alignment frameworks such as REVEAL have shown that pairing retinal fundus images with structured clinical risk narratives improves early prediction of Alzheimer's disease (AD). A key design choice in these approaches is the use of phenotypic grouping, where individuals with similar risk profiles are treated as multi-positive pairs during contrastive learning. However, existing methods operationalize phenotypic similarity as a discrete construct, relying on hard group assignments that impose rigid supervision and decouple group formation from representation learning. We propose a continuous formulation of phenotypic structure within contrastive learning. Rather than assigning samples to fixed clusters, we model inter-subject similarity as a differentiable weighting function derived from intra-modality embedding similarities in both retinal images and risk profiles. These weights define soft multi-positive relationships through a continuous aggregation operator, enabling graded supervision that reflects the spectrum nature of disease risk. We further introduce a soft-target contrastive objective that jointly learns cross-modal alignment and phenotypic structure in an end-to-end manner. Evaluated on UK Biobank retinal imaging data for incident AD prediction, the proposed framework consistently outperforms discrete group-based contrastive learning and standard vision-language baselines. By treating phenotypic similarity as a learnable, continuous signal rather than a fixed grouping rule, our approach provides a principled and robust foundation for population-scale neurodegenerative risk modeling from multi-modal retinal and clinical data.

09.
arXiv (CS.CV) 2026-06-25

Evidential Perfusion Physics-Informed Neural Networks with Residual Uncertainty Quantification

Physics-informed neural networks (PINNs) have shown promise in addressing the ill-posed deconvolution problem in computed tomography perfusion (CTP) imaging for acute ischemic stroke assessment. However, existing PINN-based approaches remain deterministic and do not quantify uncertainty associated with violations of physics constraints, limiting reliability assessment. We propose Evidential Perfusion Physics-Informed Neural Networks (EPPINN), a framework that integrates evidential deep learning with physics-informed modeling to enable uncertainty-aware perfusion parameter estimation. EPPINN models arterial input, tissue concentration, and perfusion parameters using coordinate-based networks, and places a Normal–Inverse–Gamma distribution over the physics residual to characterize voxel-wise aleatoric and epistemic uncertainty in physics consistency without requiring Bayesian sampling or ensemble inference. The framework further incorporates physiologically constrained parameterization and stabilization strategies to promote robust per-case optimization. We evaluate EPPINN on digital phantom data, the ISLES 2018 benchmark, and a clinical cohort. On the evaluated datasets, EPPINN achieves lower normalized mean absolute error than classical deconvolution and PINN baselines, particularly under sparse temporal sampling and low signal-to-noise conditions, while providing conservative uncertainty estimates with high empirical coverage. On clinical data, EPPINN attains the highest voxel-level and case-level infarct-core detection sensitivity. These results suggest that evidential physics-informed learning can improve both accuracy and reliability of CTP analysis for time-critical stroke assessment. Source code is available at https://github.com/jhlee0619/EPPINN.

10.
arXiv (CS.LG) 2026-06-24

Neural Posterior Estimation of Terrain Parameters from Radar Sounder Data

arXiv:2605.08179v2 Announce Type: replace-cross Abstract: Radar sounders are electromagnetic instruments that can probe deep into the subsurface of Earth and other planetary bodies by processing the echo of transmitted radar waves. Conventional approaches for analyzing such data rely on approximate assumptions and often produce point estimates that ignore parameter correlations as well as galactic and measurement noise. We propose a simulation-based inference approach to terrain parameter inversion from radar sounder data, where synthetic observations from a GPU-based simulator are used to train a neural network-based density estimator for neural posterior estimation (NPE). By explicitly conditioning on reference surface assumptions, the proposed framework allows systematic evaluation of posterior robustness to reference surface variability. We demonstrate that our NPE model is well calibrated on simulated data and transferable to real Mars radar profiles, where we analyze terrain parameters using literature-informed reference values.

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

Physics-IQ Verified

Video generative models ( VGMs) have become a new frontier that can be used not just for video generation but for a multitude of downstream tasks, including world modeling. To advance these tasks, a good video model must understand the physical reality of the world. Evaluating this understanding is an emerging field and has led to the Physics-IQ benchmark, which quantifies this explicitly by comparing model-generated videos to real-world videos of physical experiments. In this work, we present a systematic audit of the Physics-IQ benchmark, expose shortcomings and propose three solutions that sharpen how we can measure physical understanding of VGMs. Specifically, we improve prompt and ground-truth quality to reduce the influence of confounding factors and further introduce a sample-level scoring system that weights each sample and metric equally. Our resulting benchmark, Physics-IQ Verified, refines 57.6\% of all samples and improves over 34.8\% of prompts. In a comparison study using six image-to-video generative models, we observe moderate but meaningful ranking changes (Kendall's $\tau = 0.46$). We hope Physics-IQ Verified advances the community by providing a more reliable signal toward physically accurate VGMs. The code for the benchmark can be accessed at https://github.com/google-deepmind/physics-iq-benchmark

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

Generative Modeling on Metric Graphs via Neural Optimal Transport

arXiv:2606.16273v1 Announce Type: cross Abstract: We introduce, to our knowledge, the first deep generative modeling framework for probability distributions continuously supported on compact metric graphs. Given source and target measures on a metric graph, our method embeds the graph into a smooth ambient space, solves an entropic Kantorovich problem via a neural semidual parameterization, and projects generated samples back onto the original graph. We study two embedded geometries: an extrinsic Euclidean realization and the intrinsic tropical Abel–Jacobi embedding into the Jacobian torus. In both cases, the resulting generator is graph-supported by construction. We prove that, in the joint limit of increasing neural expressivity, the learned generator converges weakly to a valid transport coupling between the original graph measures. Empirically, across a range of geometrically distinct graphs, our method matches or improves upon heuristic transport baselines based on discrete graph OT, while scaling more favorably. Finally, we demonstrate scalability on real-world urban mobility data by training our model on one million Uber pickup locations in Manhattan, New York City.

13.
arXiv (CS.AI) 2026-06-12

From Verdict to Process: Agentic Reinforcement Learning for Multi-Stage Fact Verification

arXiv:2606.13262v1 Announce Type: new Abstract: Recent approaches combining Large Language Models (LLMs) with retrieval-augmented reasoning have shown promise for automated fact verification. To process complex claims, these verification pipelines typically execute multi-stage workflows that coordinate tightly coupled modules, including claim decomposition, evidence gathering, and verdict prediction. However, existing methods optimize individual stages in isolation or rely on fixed heuristics, which limits adaptive coordination among stages and can lead to suboptimal outcomes. In this work, we propose ProFact, an agentic reinforcement learning framework for end-to-end optimization of multi-stage fact verification trajectories. ProFact trains a unified policy to coordinate claim decomposition, evidence seeking, answer generation, and verdict prediction. To address the sparse and delayed supervision provided by final veracity labels, ProFact introduces process-aware rewards that provide stage-level learning signals throughout the verification process. Empirical evaluation shows that ProFact consistently outperforms strong baselines in both verification performance and inference efficiency. These results highlight the effectiveness of process-aware trajectory optimization for multi-stage fact verification.

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

Dehaze-GaussianImage: Zero-Shot Dehazing via Efficient 2D Gaussian Splatting Representation

Existing single image dehazing methods are often constrained by computational redundancy in pixel-level optimization and the lack of physical interpretability in implicit neural networks. These limitations hinder the balance between representation efficiency and reconstruction fidelity. To address these issues, we propose Dehaze-GaussianImage, the first zero-shot framework that introduces 2D Gaussian Splatting (2DGS) into the image dehazing domain to break the traditional pixel-grid processing paradigm. Distinct from static convolutional neural networks (CNNs) or Transformers, our approach models hazy images as continuous and dynamically evolvable anisotropic Gaussian fields. Specifically, we propose a novel reconstruction-decoupling zero-shot learning strategy that embeds the atmospheric scattering model into the Gaussian parameter space. This strategy drives Gaussian primitives to adaptively split, clone, and prune during optimization, achieving geometric-level decoupling of the transmission medium and clear textures. Furthermore, explicit structure-preserving constraints are introduced to suppress artifacts commonly caused by traditional physical priors. Experimental results demonstrate that the proposed method achieves state-of-the-art (SOTA) performance in a fully unsupervised manner with minimal parameters, highlighting the potential of explicit Gaussian representation for low-level vision tasks.

15.
arXiv (CS.CV) 2026-06-25

SSMNBench: Diagnosing Image-based Cross-View Human-Object Understanding via Single-View Sufficiency and Multi-View Necessity

Multimodal Large Language Models (MLLMs) have shown remarkable progress in single-image perception, yet their ability to reason about complex cross-view human-centric scenes remains largely unverified. Current multi-view benchmarks evaluate models using a fixed "bag of frames" and thus conflate a model's robustness to visual distraction with its genuine ability to fuse fragmented cross-view evidence. To address this issue, we introduce SSMNBench, a diagnostic benchmark comprising 3,300 curated QA pairs for cross-view human and human-object understanding. SSMNBench uniquely categorizes tasks into Single-View Sufficiency (SVS) and Multi-View Necessity (MVN). By systematically perturbing view availability across 17 state-of-the-art MLLMs, critical limitations are revealed: models suffer from severe "distraction degradation" when presented with redundant views (SVS), and fail to integrate fragmented geometric evidence across cameras (MVN). Our evaluations demonstrate that modern MLLMs rely on multiple single-image semantic averaging and view preference rather than genuine cross-view synthesis. By exposing these fundamental vulnerabilities, SSMNBench provides a rigorous diagnostic framework to drive the advancement of future cross-view-aware multimodal architectures. The code is available at: $ \href{https://github.com/gtc-gh/SSMNBench}{SSMNBench} $

16.
arXiv (CS.CV) 2026-06-19

U$^2$Mamba: A Two-level Nested U-structure Mamba for Salient Object Detection

Mamba-based models have emerged as a promising alternative for salient object detection (SOD), offering significant advantages in modeling long sequences. However, existing models often fail to explore contextual information and the depth of the entire architecture. This paper introduces U$^2$Mamba, a powerful and innovative U-structured network for salient object detection. We propose multiscale Mamba U-blocks (MMUBs) that enhance the model depth to improve local feature extraction capabilities. Our newly developed nested U-structure, incorporating MMUBs, enables the network to integrate various receptive fields from shallow and deep layers, thereby collecting richer contextual information and longer-range data without being constrained by resolution. Instead of using the traditional deep supervision scheme and top-level supervised training, we propose a hierarchical training supervision method where the loss is computed at each level during the training process. Extensive experiments demonstrate that U$^2$Mamba achieves highly competitive performance against state-of-the-art methods. The source code is available at \url{https://github.com/JL021/U2Mamba}.

17.
arXiv (CS.CL) 2026-06-18

Dual Dimensionality for Local and Global Attention

Decoder-only Transformers compute attention over the KV cache of preceding tokens. Keys (and Values) are typically represented with the same dimensionality, regardless of its distance from the prediction target. In natural language, however, the next word is most strongly influenced by the immediately preceding tokens. We hypothesize that local and distant tokens impose asymmetric demands on representational capacity: local tokens are more critical for predicting immediate outputs and thus require richer representations, whereas distant tokens primarily serve as long-range memory, for which lower-dimensional representations may suffice. We formalize this idea as Distance-Adaptive Representation (DAR), implemented in a controlled setting that preserves full-dimensional representations within a local context window while assigning reduced-dimensional representations (e.g. 1/4 of the original dimensionality) to tokens beyond that window. Across multiple pretraining scales (70M to 410M parameters), as well as continued supervised fine-tuning on a 1B-scale model, this approach closely matches the performance of full-dimensional baselines. In contrast, uniformly reducing dimensionality across all token positions leads to worse performance. These results challenge the common assumption that key and value dimensionality should be uniform across token positions. Our findings suggest a new direction for designing attention architectures that adaptively allocate representational capacity across sequences, enabling further reductions in KV cache during inference.

18.
arXiv (CS.LG) 2026-06-19

Toward all-optical unsupervised Hebbian learning in deep photonic neuromorphic networks

arXiv:2601.22300v3 Announce Type: replace-cross Abstract: We propose a deep photonic neuromorphic network (PNN) architecture based on phase-change material (PCM) synapses and local optical feedback for online, unsupervised Hebbian learning. The proposed architecture combines optical vector-matrix multiplication, non-volatile PCM synaptic weighting, and local coincidence-driven synaptic adaptation within a multilayer photonic crossbar framework compatible with photonic integrated circuits. Unlike conventional PNNs that rely on externally computed gradients, repeated optical-electrical-optical conversions, or global backpropagation, the proposed framework employs local Hebbian learning governed directly by correlated pre- and post-synaptic optical activity. To investigate the feasibility of the proposed learning mechanism, we implemented the PNN design using fiber-optic components, programmable variable optical attenuators, and real-time software control that incorporates PCM thermal dynamics. Supervised and unsupervised learning behaviors were experimentally evaluated under both offline and online learning conditions using representative image-recognition tasks. The experimental results demonstrate adaptive synaptic evolution, successful optical inference, and autonomous pattern encoding through local Hebbian learning under realistic fiber-optic hardware conditions. These results establish a pathway toward future integrated photonic neuromorphic systems capable of scalable and energy-efficient online Hebbian learning.

19.
arXiv (CS.LG) 2026-06-16

Enhancing Visual Feature Attribution via Weighted Integrated Gradients

arXiv:2505.03201v4 Announce Type: replace-cross Abstract: Integrated Gradients (IG) is a widely used attribution method in explainable AI, particularly in computer vision applications where reliable feature attribution is essential. A key limitation of IG is its sensitivity to the choice of baseline (reference) images. Multi-baseline extensions such as Expected Gradients (EG) assume uniform weighting over baselines, implicitly treating all baseline images as equally informative. In high-dimensional vision models, this assumption often leads to noisy or unstable explanations. This paper proposes Weighted Integrated Gradients (WG), a principled approach that evaluates and weights baselines to enhance attribution reliability. WG introduces an unsupervised criterion for baseline suitability, enabling adaptive selection and weighting of baselines on a per-input basis. The method preserves the core axiomatic properties of IG in a generalized weighted-baseline form. Under an expected, proxy-based fitness–relevance monotonicity assumption, WG provides a probabilistic justification for assigning larger weights to more informative baselines. Experiments on commonly used image datasets and models show that WG improves over EG under our protocol, with up to 36% gains across evaluated convolutional and Transformer architectures. These gains come with additional fitness-evaluation cost, so WG should be viewed as an attribution-fidelity trade-off rather than a faster alternative to EG. By moving beyond the assumption that all baselines contribute equally, Weighted Integrated Gradients offers a clearer and more reliable approach to explaining computer-vision models, improving both understanding and practical usability in explainable AI.

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

Learning Sparse Latent Predictive Foundation Model for Multimodal Neuroimaging

Brain MRIs are routinely acquired as multiple complementary sequences with unique contrast weighting, including T1-weighed imaging (T1w) anatomic and fluid-sensitive T2-weighted (T2w) contrasts. However, methods for learning unified representations across the multitude of MRI contrast mechanisms at health-system scale are lacking. In this study, we introduce Neuro-JEPA, a sparse multimodal neuroimaging foundation model that combines a latent predictive objective with a Mixture-of-Experts architecture to encode brain MRI across core T1w, T2w, and fluid-suppressed FLAIR imaging (FLAIR). We further provide a systematic methodological study of architectural, masking, objective, and sparsity design choices beneficial for robust neuroimaging multimodal representation learning. Neuro-JEPA was pretrained on 1,551,862 scans from 428,647 studies after modality-specific preprocessing with data curation across three core structural brain MRI sequences. We evaluated the learned representations across clinical and research settings, including 25 tasks from three health systems: NYU Langone, NYU Long Island, and Massachusetts General Hospital, and 22 tasks from 12 public datasets, covering unimodal, multimodal and cross-domain evaluation configurations. Across these benchmarks, existing neuroimaging foundation models showed inconsistent gains over a simple convolutional neural network (CNN) baseline, whereas Neuro-JEPA achieved stronger and more consistent performance across all evaluated settings. These results establish a scalable methodological framework for multimodal neuroimaging representation learning and highlight the need for foundation model evaluation protocols that include simple baselines, clinically heterogeneous cohorts and controlled multimodal comparisons.

21.
arXiv (quant-ph) 2026-06-25

Distillation of supersinglet states

arXiv:2509.20962v2 Announce Type: replace Abstract: We introduce an entanglement distillation (purification) protocol for supersinglet states composed of N qubits. The supersinglet state we target is a total spin zero state with zero spin variance, and has a fully entangled structure involving all qubits. In our distillation protocol, three copies of an initial spin zero state are measured in the local total spin basis such that a higher fidelity supersinglet state is generated upon postselection. The initial state can be prepared using conventional Bell state distillation methods distributed in a way to target the supersinglet symmetries. The protocol uses only local operations and classical communications, and is suitable for long-distance applications such as quantum clock synchronization and cryptography, and avoids a high dimensional Schur transform such that it can be used for tasks such as quantum metrology.

22.
arXiv (CS.LG) 2026-06-17

A Bayesian Boolean Matrix Factorization with Application to Copy Number Analysis in Cancer

arXiv:2606.17491v1 Announce Type: cross Abstract: Binary data factorization is common, but real-valued methods ignore discreteness and yield hard-to-interpret factors. Boolean Matrix Factorization (BooMF) instead decomposes a binary matrix into two lower-rank binary matrices via logical AND and OR, expressing the data as a Boolean disjunction of interpretable patterns. In cancer genomics, BooMF can reveal coordinated feature changes that may drive tumor evolution, unlike rotational or additive decompositions. Most existing BooMF methods are heuristic, greedy, sensitive to initialization, prone to local optima, and do not support principled model selection or uncertainty quantification. We introduce Bayesian Boolean Matrix Factorization (BBMF), a fully conjugate generative model with sparsity-inducing priors. It enforces Boolean constraints, yields interpretable latent factors with coherent uncertainty quantification, and admits Gibbs sampling with closed-form full conditionals. Because cancer evolution often involves widespread, near-simultaneous chromosome-number changes (e.g., whole-genome duplication followed by instability and selection), Boolean factorizations capture these patterns more naturally than additive models. Applied to arm-level copy-number alteration data in multiple myeloma, where entries indicate presence/absence of chromosomal-arm amplifications, BBMF finds a small set of interpretable bicliques linking patient subsets to recurrently co-altered chromosomal arms, providing a compact, biologically meaningful summary of tumor heterogeneity and demonstrating BBMF's utility for uncovering discrete latent structure in complex binary data.

23.
arXiv (CS.AI) 2026-06-25

Dense Supervision Is Not Enough: The Readout Blind Spot in Looped Language Models

arXiv:2606.24898v1 Announce Type: cross Abstract: Looped language models turn hidden states into runtime state: each state is decoded for prediction and fed back into future computation. This creates a basic supervision question: which state variables does cross-entropy actually control? We show that dense per-loop cross-entropy controls the variables exposed by the readout, not every variable active in the recurrent transition. Hidden-state scale gives a concrete failure mode. Scale-invariant readouts such as RMSNorm and LayerNorm hide radial scale from the immediate cross-entropy loss, while pre-norm residual recurrence continues to carry and update that same scale. Thus per-loop loss can make early exits usable without controlling recurrent scale. In 44M and 129M looped transformers without inter-loop normalization, per-loop cross-entropy through RMSNorm readouts still drives final hidden-state norms into the thousands or tens of thousands. Scale-visible readouts and explicit norm penalties keep norms in the tens, and scale-removing recurrence is the complementary architectural fix. The resulting design rule is simple: dense supervision trains exits; recurrent scale control requires either making scale visible to a loss or removing it from the loop. Consistent with this rule, scale-controlled variants achieve lower perplexity at matched inference-depth operating points in our variable-depth benchmarks.

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

MPC-Patch-Bench: Security-Aware LLM Code Patch for Multi-Party Computation

arXiv:2606.11416v1 Announce Type: cross Abstract: Repository-level benchmarks for evaluating Large Language Model (LLM) code repair on Secure Multi-Party Computation (MPC) software do not yet exist, and directly transplanting general-purpose benchmarks such as SWE-bench fails on three structural fronts: (i) MPC repositories are dominated by generic Python infrastructure rather than cryptographic logic; (ii) high-value MPC fixes lack the standardized tests rigid extraction pipelines require; and (iii) standard fail-to-pass evaluation is insufficient for code that must also be cryptographically safe. MPC is increasingly deployed for privacy-preserving machine learning, biomedical collaboration, and secure analytics. Existing MPC-specific code-synthesis efforts cover only operator-level or single-framework tasks; evaluating LLM agents on real repository-level MPC repair instead demands MPC-aware data curation and a verifier matched to the security and numerical-fidelity guarantees MPC programs must obey neither of which existing benchmarks provide. We introduce MPC-Patch-Bench, a repository-level benchmark organised around two frameworks. (1)The Data Curation Framework combines a domain-specific curation agent that filters raw pull requests through three cryptographic layers with a human-AI completion engine that synthesizes missing problem statements and Fail-to-Pass/Pass-to-Pass tests, yielding 205 fully verified instances. (2)The MPC Verifier provides dedicated security and numerical-fidelity checks via dynamic differential testing against plaintext oracles and MPC-specific static analysis rules that flag unsafe reveals, insecure arithmetic, and illegal public/private casts. The strongest evaluated LLM functionally resolves only 22.9% of MPC-Patch-Bench tasks; the MPC Verifier further reduces verified resolution to 17.1%, with up to 40% of functionally-passing patches rejected for cryptographic or numerical-fidelity violations.

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

libhmm: A Modern C++20 Library for Hidden Markov Models with Correct MLE Emission M-Steps

Authors:

arXiv:2605.29208v2 Announce Type: replace-cross Abstract: We describe libhmm, a C++20 library for Hidden Markov Model parameter estimation, sequence decoding, and model selection. libhmm addresses two gaps in existing software: the absence of a well-maintained, zero-dependency C++ HMM library suitable for embedding in production systems, and the widespread use of method-of-moments (MOM) approximations in the emission distribution M-step of the Baum-Welch algorithm. The library implements correct maximum likelihood estimators for sixteen scalar emission distributions, including an ECME algorithm for the location-scale Student-t distribution, Newton-Raphson maximization for Gamma, Beta, Weibull, and Negative Binomial distributions, and the von Mises distribution for circular data. All forward-backward and Viterbi calculations operate in full log-space. SIMD acceleration is provided for AVX-512, AVX2, SSE2, and ARM NEON via compile-time dispatch with scalar fallback. Version 4 adds multivariate observation support via the BasicHmm template, with three multivariate emission families (diagonal Gaussian, full-covariance Gaussian, and independent components) each with correct weighted MLE M-steps. Python bindings are available via the companion package pylibhmm. We compare libhmm against established C and C++ HMM libraries and against published R reference packages on seven real-data benchmarks, and discuss the architectural tradeoffs made in the design.