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01.
arXiv (CS.CV) 2026-06-12

LatentLens: Revealing Highly Interpretable Visual Tokens in LLMs

Transforming a large language model (LLM) into a vision-language model (VLM) can be achieved by mapping the visual tokens from a vision encoder into the embedding space of an LLM. Intriguingly, this mapping can be as simple as a shallow MLP transformation. To understand why LLMs can so readily process visual tokens, we need interpretability methods that reveal what is encoded in the visual token representations at every layer of LLM processing. In this work, we introduce LatentLens, a novel approach for mapping latent representations to descriptions in natural language. LatentLens encodes a large text corpus and stores contextualized token representations for each token in that corpus. Visual token representations are then compared to these contextualized representations and the top-nearest neighbor representations serve as descriptions of the visual token. We evaluate this method on 15 different VLMs, showing that commonly used methods, such as LogitLens, substantially underestimate the interpretability of visual tokens. With LatentLens instead, the majority of visual tokens are interpretable across all studied models and all layers. Qualitatively, we show that the descriptions produced by LatentLens are semantically meaningful and provide more fine-grained interpretations for humans compared to individual tokens. More broadly, our findings contribute new evidence on the alignment between vision and language representations and open up new directions for analyzing the latent representations of LLMs.

02.
medRxiv (Medicine) 2026-06-18

Urinary Creatine Riboside Complements PSA to Improve Disease Detection in the Diagnostic Gray Zone of Prostate Cancer

Circulating prostate-specific antigen (PSA) discriminates poorly in the diagnostic gray zone (3.0-9.99 ng/mL), where ~75% of biopsies yield no clinically significant prostate cancer (PCa). We evaluated whether urinary creatine riboside (CR), a tumor-derived metabolite excreted through the prostatic urethra, complements PSA for gray-zone detection and independently predicts prostate-cancer-specific mortality (PCSM). In the NCI-Maryland PCa Case-Control Study (951 cases, 962 controls; 47.6% African American men; median follow-up 11.5 years), urinary CR was quantified by UPLC-MS/MS. Within the PSA gray zone (n = 668), urinary CR was complementary to PSA, with markedly higher single-marker discrimination than PSA (AUC 0.93, 95% CI 0.88-0.98 vs 0.77, 0.66-0.89) and additive when combined ({Delta}AUC +0.17, p < 0.001; 91.4% sensitivity at 80% specificity). After adjustment for 11 clinical and sociodemographic covariates, urinary CR independently predicted PCSM complementary to PSA (Fine-Gray SHR 1.72, 1.35-2.19 for CR; 1.35, 1.08-1.68 for PSA; Harrell's C 0.85 for CR + PSA vs 0.77 for PSA alone), with strongest signal in African American men (SHR 2.43, 1.57-3.75 for CR). We conclude that urinary CR is a candidate non-invasive biomarker complementary to PSA - improving gray-zone triage and predicting PCSM; prospective validation in biopsy-referred cohorts is warranted.

03.
arXiv (CS.AI) 2026-06-16

DualGauge: Automated Joint Security-Functionality Benchmarking of Specification-Only Code Generation by LLMs and Coding Agents

arXiv:2511.20709v2 Announce Type: replace-cross Abstract: Large language models (LLMs) and LLM-based coding agents are now used to generate code from natural-language specifications, yet ensuring such code is both functionally correct and secure remains a challenge. We present DualGauge, the first fully automated framework for jointly evaluating correctness and security of specification-only code generation, supported by DualGauge-Bench, a language-agnostic benchmark of 307 coding tasks each paired with functional and security tests derived from the same specification. Evaluating 10 representative LLMs across Python, C++, and JavaScript, we find that functional correctness substantially overestimates reliable code generation: even the strongest model remains below 15% joint security-functionality success in every language. Common model-side factors–scale, extended thinking, quantization, instruction tuning, and code specialization–do not reliably improve joint performance, suggesting secure-and-correct code generation does not simply emerge from stronger coding capability. Evaluation of 3 leading agentic coding systems (Codex, OpenHands, and Claude Code) shows that iterative scaffolding provides no advantage over direct (LLM-based) generation on specification-only tasks. A qualitative audit reveals failures concentrate at the output contract boundary and in guards that exist but are insufficient–patterns that only joint benchmarking reliably exposes.

04.
arXiv (quant-ph) 2026-06-11

Scaling-optimal purification of noisy qubit unitary channels

arXiv:2606.12394v1 Announce Type: new Abstract: We consider the problem of purifying noisy qubit unitary channels. Given the ability to apply an unknown qubit unitary channel followed by depolarizing noise, we aim to construct a superchannel that purifies the noisy unitary back to the original unknown unitary. We first provide numerical evidence that sequential strategies can strictly outperform parallel strategies when the number of channel uses is finite, highlighting the fundamental distinction from state purification. We then provide a concrete $\mathrm{U}(2)$-covariant parallel protocol based on a novel entanglement-assisted quantum error-correcting code that suppresses the first-order noise strength as $O(1/n)$ with $n$ channel uses and show this scaling is asymptotically optimal in the low-noise regime, even when sequential strategies are allowed.

05.
arXiv (CS.AI) 2026-06-15

Thinking Outside the [Chat]Box: Bridging Computer Science and Industrial Design for Cognitive-Inclusive Generative AI

arXiv:2606.14306v1 Announce Type: cross Abstract: Current Generative AI (GenAI) interfaces remain largely constrained to chatbox interaction, which can impose high cognitive demands on users and create substantial barriers for people with intellectual disabilities (ID), including prompt formulation difficulties, response overload, and limited mechanisms to assess information reliability. To explore alternative interaction models for cognitive accessibility, we conducted a cross-disciplinary co-design challenge in which two student cohorts (Computer Science and Industrial Design) developed interface concepts from the same set of functional requirements (e.g., prompt scaffolding, structured output, GUI-based refinement, transparency, and personalization). Comparing the resulting proposals reveals both convergence on foundational requirements (notably initial calibration, proactive prompting, and direct manipulation of response fragments) and complementary contributions that outline a multi-layered support system. Computer Science teams primarily produced structural scaffolding, emphasizing predictability, navigability, and trust through mechanisms such as reliability indicators, explicit sources, and context management for long conversations. Industrial Design teams emphasized experiential scaffolding, focusing on pacing, attention guidance, multimodality, and proactive agency, including step-by-step response flows, focus modes, and assistant-like integrations. We synthesize these findings into a dual-layer scaffolding framework that expands the design space for cognitively accessible GenAI interaction beyond chat-centric models and motivates future work on expert refinement, technical feasibility, and empirical validation with users with ID.

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

Structured Testbench Generation for LLM-Driven HDL Design and Verification-Oriented Data Curation

arXiv:2606.12983v1 Announce Type: new Abstract: Automated testbench generation has become a critical bottleneck in large language model (LLM)-driven Register Transfer Level (RTL) workflows, where large numbers of candidate designs must be verified rapidly and reliably. Existing prompt-based approaches treat testbench generation as unconstrained code synthesis, yielding stochastic outputs with high token cost, low reproducibility, and insufficient coverage. To address this gap, we present STG, a Structured Testbench Generation framework that exploits the inherent structure of hardware designs to generate deterministic testbenches. As a direct verification tool, STG runs 720x faster than an iterative LLM-based testbench generation flow and higher rate of successful compilation, achieves higher coverage, and reduces false-pass verdicts on incorrect DUTs. STG also helps identify errors in RTL generation benchmarks by exposing faulty benchmark testbenches. As a data curation engine, it is 11x faster than LLM-based filtering on a single CPU core with 127x less energy, and the resulting distilled models provide state-of-the-art performance in our multi-benchmark evaluation. As a test-time scaling oracle, it reduces node count by 14-47\%. Our models are available at https://huggingface.co/collections/AS-SiliconMind/siliconmind-v12.

07.
arXiv (CS.CV) 2026-06-19

DiffMath: Symbol- and Graph-Aware Latent Diffusion Transformer for Handwritten Mathematical Expression Generation

Handwritten Mathematical Expression Generation (HMEG) is challenging due to the complex two-dimensional layouts and long-range structural dependencies of mathematical expressions. Existing methods typically rely on explicit spatial supervision, such as symbol-level bounding boxes, which incurs high annotation costs and limits scalability. In this work, we propose DiffMath, a symbol- and graph-aware latent diffusion framework that leverages the hierarchical structure inherent in LaTeX as a structural prior, eliminating the need for positional supervision. First, we design a Relational Abstract Syntax Tree (RelAST), a generation-oriented representation that distills MathML trees into compact triplet sequences [S, R, D], where each token directly encodes a symbol identity, spatial relation, or nesting depth. Second, we introduce MathVAE, which learns structure-preserving latent representations through symbol-aware and relation-aware perceptual regularization, ensuring that the latent space captures both character semantics and spatial topology. Third, MathDiT performs conditional denoising in this structured latent space, further guided by a global symbol-count prior via Adaptive Layer Normalization (AdaLN) to improve structural coherence. Experiments show that DiffMath produces structurally consistent handwritten expressions, achieves superior performance over existing methods, and improves the accuracy of downstream OCR models through synthetic data augmentation.

08.
arXiv (CS.CV) 2026-06-18

SVHighlights: Towards Extremely Long Sport Video Highlight Detection

While highlight detection for long-form videos is of great practical importance, most existing methods remain limited to short-form content, largely due to the absence of a suitable benchmark. To bridge this gap, we introduce SVHighlights, to the best of our knowledge, the first benchmark for highlight detection in extremely long sports videos, each exceeding one hour in duration, across multiple sports categories. SVHighlights is constructed from pairs of full-length sports videos and their corresponding official highlight videos using a dataset generation pipeline, enabling scalable label generation without conventional per-clip saliency annotation. The benchmark comprises 320 videos with an average duration of 2.00 hours and a total of 640.18 hours, substantially exceeding previous datasets. Existing methods also face fundamental challenges on long videos: models trained on short clips fail to generalize to hour-long content, and their clip-level scoring lacks the broader context needed to identify highlights. To address this and provide a strong baseline, we present TF-SELECTOR, a training-free segment-based approach that divides each video into context-aware segments by merging adjacent shots sharing the same semantic content, and predicts segment-level saliency scores using a large language model with multimodal inputs including visual captions, transcripts, and audio volume. Experiments demonstrate that TF-SELECTOR achieves superior performance across most metrics compared to Video Temporal Grounding (VTG)-tuned baselines, with improvements of +2.50 in HIT@1, +4.04 in HIT@K, and +2.95 in IoU. These results establish SVHighlights as a challenging testbed for long-form highlight detection and demonstrate that a simple segment-based strategy can effectively scale to hour-long videos.

10.
arXiv (CS.AI) 2026-06-19

Bistable by Construction: Wall-Clock-Calibrated State Monitors Have No Moment-Detection Regime at Agent Cadence

arXiv:2606.19386v1 Announce Type: cross Abstract: Runtime monitors for autonomous agents commonly threshold an accumulated internal state - a behavioural baseline, a drift statistic, or, in our prior work, a modelled affective state. We previously reported a State Saturation Trap: threshold-on-state triggers over a continuous affect engine become near-constant alarms on SWE-bench debugging agents (Modgil 2026). A post-release audit found the engine received dt=0 between actions, so its exponential decay never operated: the published trap is a pure-accumulator result. We correct the record (erratum, v2) and treat the flaw as an experiment. The key variable it exposes is whether a monitor's dynamics are calibrated in sample time (per observation, as in CUSUM) or wall-clock time (half-lives in seconds, as in affect models and EMA baselines). On fixed-rate streams these coincide; on agent streams, where inter-action time varies by orders of magnitude, they do not. A pre-registered sweep over uniform intervals (dt in {0..600}s) on 20 trajectories shows the wall-clock level trigger has two regimes: at dt=60s silent. Every critical dt lies in (1,30]s. Real agent runs measure latency at median 1.53s (p90 2.33s); real coding cadence sits inside the trap regime, vindicating the empirical finding under a corrected mechanism. The structure is a property of the calibration class, not the engine: a minimal wall-clock accumulator over the raw error stream reproduces the same cliff, while a sample-time CUSUM over the identical stream is exactly dt-invariant (20/20). A rising-edge trigger with hysteresis fires 0-3 times per trajectory in every condition. We conclude that wall-clock-calibrated leaky-integrator monitors admit no regime in which they act as moment detectors on agent streams; transition detection escapes the trap at every cadence, but does not recover human intervention timing.

11.
Nature (Science) 2026-06-10

‘Hidden hero’ peptides guard crops against sudden cold

Authors: Unknown Author

A protein signal remains silent under normal conditions but is activated under cold stress to protect developing pollen. This ‘on-demand’ resilience mechanism could enable the development of ‘climate smart’ crops that maintain high yields in good years and food security under climate stress. A peptide signal ensures that, in cold conditions, developing pollen receives nutrients at the right time.

12.
arXiv (CS.CV) 2026-06-18

Toward Training-Free Zero-Shot Anomaly Detection in 3D Medical Images: A Batch-Based Approach Using 2D Foundation Models

Authors:

Zero-shot anomaly detection (ZSAD) is attractive for medical imaging because clinical systems must handle heterogeneous acquisition protocols, changing patient populations, and pathologies for which annotated training data may be unavailable. Most existing zero-shot anomaly detection methods are designed for 2D images, and their direct extension to 3D medical volumes is limited by the scarcity of large-scale volumetric foundation models or by the difficulty of utilizing volumetric context. We propose CS3F, a training-free batch-based framework for ZSAD in 3D medical images using 2D foundation models. Each volume is decomposed along multiple anatomical axes and encoded slice-wise by a 2D vision transformer. These are then converted into localized volumetric tokens by pooling neighboring slice features. Anomaly scores are obtained from cross-subject mutual similarity: tokens that lack close analogues in other subjects are assigned higher anomaly scores. To reduce the attenuation of focal lesion signals caused by depth pooling, we introduce a coarse-to-fine tokenization strategy that enables fine-resolution volumetric scoring without exhaustive matching. CS3F is evaluated on brain MRI across metastases, glioma, and stroke, as well as validated on lung CT to test generalizability beyond atlas-aligned brain MRI. The results show that frozen 2D foundation models can support anomaly localization in 3D medical images, and that the benefit of fine tokenization depends strongly on lesion contrast and imaging modality.

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

From Seeing to Experiencing: Scaling Navigation Foundation Models with Reinforcement Learning

Navigation foundation models trained on massive web-scale data enable agents to generalize across diverse environments and embodiments. However, these models, which are trained solely on offline data, often lack the capacity to reason about the consequences of their actions or adapt through counterfactual understanding. They thus face significant limitations in real-world urban navigation, where interactive and safe behaviors, such as avoiding obstacles and moving pedestrians, are critical. To tackle these challenges, we introduce the Seeing-to-Experiencing (S2E) learning framework to scale the capability of navigation foundation models with reinforcement learning. S2E combines the strengths of pretraining on offline videos and post-training through reinforcement learning. It maintains the model's generalizability acquired from large-scale real-world videos while enhancing its interactivity through reinforcement learning in simulation environments. Specifically, we introduce two innovations: (1) an Anchor-Guided Distribution Matching strategy for offline pretraining, which stabilizes learning and models diverse motion patterns through anchor-based supervision; and (2) a Residual-Attention Module for reinforcement learning, which obtains reactive behaviors from simulation environments without erasing the model's pretrained knowledge. Moreover, we establish a comprehensive end-to-end evaluation benchmark, NavBench-GS, built on photorealistic 3D Gaussian Splatting reconstructions of real-world scenes that incorporate physical interactions. It can systematically assess the generalizability and safety of navigation foundation models.

14.
arXiv (CS.LG) 2026-06-19

Neural Architectures as Functional Priors in Physics-Informed Control Problems

arXiv:2606.19368v1 Announce Type: cross Abstract: In this work we investigate the role of neural architectures as implicit functional priors in control problems governed by ordinary differential equations. Rather than focusing on highly complex problems, our objective is to investigate architecture-dependent effects in controlled dynamical systems within the simplest physically interpretable settings possible. In particular, we study a controlled linear RLC electrical circuit and a nonlinear Duffing-type dynamical system. Both systems are analyzed first through classical optimal-control formulations and later through PINN-based approaches. We compare different combinations of multilayer perceptrons (MLPs) and Fourier-based KAN-like architectures, and analyze their influence on the resulting controls. The numerical experiments suggest that different architectural choices systematically generate qualitatively distinct controls, even under identical governing equations, loss functionals, initial and target states, training parameters and physical constraints. Significant differences appear in the spectral structure, smoothness, energy distribution, and phase-space behavior of the learned solutions. A central observation of this work is the emergence of a functional specialization phenomenon when the neural architectures are allowed sufficient freedom to shape the structure of the learned controls. More specifically, in the systems considered here, Fourier-based architectures tend to produce trajectories with richer oscillatory content, whereas smoother low-frequency-biased architectures tend to generate more regular and energetically efficient controls. This suggests that different functional components of the control problem may be handled more efficiently by different neural architectures, leading to an implicit specialization between state representation and control generation.

15.
arXiv (CS.LG) 2026-06-17

Broadcast Product: Redefining Shape-aligned Element-wise Multiplication and Beyond

arXiv:2409.17502v2 Announce Type: replace Abstract: Broadcast operations are widely used in scientific computing libraries, yet their mathematical formulation is often implicit and inconsistently represented in machine learning literature. This problem frequently leads to invalid equations when element-wise products are written despite mismatched tensor shapes. In this paper, we formalize such operations by introducing the broadcast product $\boxdot$, which explicitly extends the Hadamard product through shape-aligned element duplication. We provide a rigorous definition of the broadcast product, analyze its algebraic properties, and show how it can be expressed using standard linear algebra. Building on this framework, we formulate least-squares problems and sketch a proof-of-concept broadcast decomposition. As a preliminary illustration, we show that the formalism enables a new family of decompositions with distinct structural properties from conventional tensor decompositions. This work establishes a mathematical foundation for broadcast-aware tensor operations, connecting practical implementations with rigorous tensor analysis.

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

Boundary-Centric Clip-Budgeted Active Learning for Temporal Action Segmentation

Temporal action segmentation (TAS) in untrimmed videos requires dense temporal supervision. However, most of the annotation cost is spent identifying action transitions where segmentation errors concentrate and small temporal shifts can disproportionately degrade segment-level metrics. We introduce B-ACT, a clip-budgeted active learning framework that explicitly allocates supervision to these error-prone boundary regions. B-ACT operates in a hierarchical two-stage loop: (i) it ranks and queries unlabeled videos using predictive uncertainty, and (ii) within each selected video, it detects candidate transitions from the current model predictions and selects the top-$K$ boundaries via a novel boundary score. The boundary score fuses neighborhood uncertainty, class ambiguity, and temporal prediction dynamics to reveal the underlying importance of each frame. Importantly, our annotation protocol requests labels only at the boundary frames while still training on boundary-centered clips to exploit temporal context through the model's receptive field. Extensive experiments on GTEA, 50Salads, and Breakfast demonstrate that boundary-centric supervision delivers strong label efficiency and consistently surpasses representative TAS active learning baselines and prior state of the art under sparse budgets. Gains are largest on datasets where performance is highly sensitive to boundary placement, as measured by edit and overlap-based F1 metrics.

17.
arXiv (CS.AI) 2026-06-16

PISA: A Pragmatic Psych-Inspired Unified Memory System for Enhanced AI Agency

arXiv:2510.15966v2 Announce Type: replace Abstract: Memory systems are fundamental to AI agents, yet existing work often lacks adaptability to diverse tasks and overlooks the constructive and task-oriented role of AI agent memory. Drawing from Piaget's theory of cognitive development, we propose PISA, a pragmatic, psych-inspired unified memory system that addresses these limitations by treating memory as a constructive and adaptive process. To enable continuous learning and adaptability, PISA introduces a trimodal adaptation mechanism (i.e., schema updation, schema evolution, and schema creation) that preserves coherent organization while supporting flexible memory updates. Building on these schema-grounded structures, we further design a hybrid memory access architecture that seamlessly integrates symbolic reasoning with neural retrieval, significantly improving retrieval accuracy and efficiency. Our empirical evaluation, conducted on the existing LOCOMO benchmark and our newly proposed AggQA benchmark for data analysis tasks, confirms that PISA sets a new state-of-the-art by significantly enhancing adaptability and long-term knowledge retention.

18.
medRxiv (Medicine) 2026-06-17

Determinants of non-utilization of insecticide-treated nets among children under five in Rwanda: analyses of the 2024 Rwanda malaria indicator survey

Background Insecticide-treated nets (ITNs) are effective for preventing malaria among children under five years, who bear a disproportionate burden of malaria. This study assessed the prevalence and determinants of ITN non-utilization among children under five in Rwanda using data from the 2024 Rwanda Malaria Indicator Survey (RMIS).Methodology This cross-sectional study utilized nationally representative data from the 2024 RMIS. Analyses were restricted to children under five residing in households that owned at least one ITN. The outcome was non-utilization of ITN, defined as not sleeping under an ITN the night preceding the survey. Survey-weighted descriptive statistics were used to estimate the prevalence of ITN non-utilization. Factors associated with non-utilization were identified using a survey-weighted Poisson regression model. Adjusted prevalence ratios (aPRs), 95% confidence intervals and p-values were reported.Results A total of 1,979 children were included in the study. The weighted prevalence of ITN non-utilization among children under five years was 20.11% (95% CI: 17.81 - 22.63). After adjusting for other factors, children aged 2 - 3 years were associated with an 83% higher prevalence of ITN non-utilization compared with those aged [&le;]1 year (aPR = 1.83, 95% CI: 1.423 - 2.352, p < 0.001). Compared with households that owned only one ITN, children in households with three or more ITNs were associated with a 76% lower prevalence of ITN non-utilization (aPR = 0.24, 95% CI: 0.171 - 0.332, p < 0.001). Children living in households with 5 - 7 members were associated with an 87% higher prevalence of ITN non-utilization compared with those in households with 1 - 4 members (aPR = 1.87, 95% CI: 1.476 - 2.358, p < 0.001).Conclusion The findings suggest that ITN utilization among children is influenced not only by household access to nets but also by household composition and dynamics that shape the allocation and use of available preventive resources.

19.
arXiv (CS.CL) 2026-06-17

Moderating Illicit Online Image Promotion for Unsafe User-Generated Content Games Using Large Vision-Language Models

Online user generated content games (UGCGs) are increasingly popular among children and adolescents for social interaction and more creative online entertainment. However, they pose a heightened risk of exposure to explicit content, raising growing concerns for the online safety of children and adolescents. Despite these concerns, few studies have addressed the issue of illicit image-based promotions of unsafe UGCGs on social media, which can inadvertently attract young users. This challenge arises from the difficulty of obtaining comprehensive training data for UGCG images and the unique nature of these images, which differ from traditional unsafe content. In this work, we take the first step towards studying the threat of illicit promotions of unsafe UGCGs. We collect a real-world dataset comprising 2,924 images that display diverse sexually explicit and violent content used to promote UGCGs by their game creators. Our in-depth studies reveal a new understanding of this problem and the urgent need for automatically flagging illicit UGCG promotions. We additionally create a cutting-edge system, UGCG-Guard, designed to aid social media platforms in effectively identifying images used for illicit UGCG promotions. This system leverages recently introduced large vision-language models (VLMs) and employs a novel conditional prompting strategy for zero-shot domain adaptation, along with chain-of-thought (CoT) reasoning for contextual identification. UGCG-Guard achieves outstanding results, with an accuracy rate of 94% in detecting these images used for the illicit promotion of such games in real-world scenarios.

20.
arXiv (CS.CV) 2026-06-15

Prompt2Effect: Training-Free Image-to-Video Model Specialization via LoRA Generation

Personalizing Image-to-Video (I2V) diffusion models with specific visual effects is increasingly demanded for high-end video generation. Current practice requires training a separate Low-Rank Adaptation (LoRA) module for each effect, incurring substantial data curation and iterative optimization costs that hinder interactive control. We present Prompt2Effect, a weight-driven hypernetwork that amortizes per-effect training by directly synthesizing effect-specific LoRA weights in a single forward pass. Unlike prior hypernetworks that regress adapter weights purely from semantics, Prompt2Effect is explicitly conditioned on the frozen base model weights, grounding weight prediction in the structural geometry of each layer. Furthermore, instead of predicting raw LoRA matrices, we introduce an SVD-canonicalized parameterization that resolves factorization ambiguity and stabilizes large-scale weight synthesis. Together, these design principles enable accurate and scalable LoRA prediction for high-dimensional I2V diffusion models. Extensive experiments demonstrate that Prompt2Effect achieves on-par or superior video quality and effect alignment compared to conventional LoRA fine-tuning, while reducing the computational cost from 56 GPU training hours to 3.3 seconds of hypernetwork inference. When used as initialization for subsequent fine-tuning, our predicted weights further improve final performance and accelerate optimization by approximately 10x.

21.
bioRxiv (Bioinfo) 2026-06-16

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

Performance bottlenecks in widely used genomics and bioinformatics software present a substantial and growing burden as biological datasets continue to increase in size and number. Relieving these bottlenecks relies largely on expert manual optimization and therefore remains difficult to scale. Here we present AutoZyme, an agentic framework for scientific software optimization. Given a target function, AutoZyme builds benchmarks, identifies bottlenecks, and iteratively tests code changes, retaining only those that improve runtime while preserving output. We evaluated AutoZyme on 45 functions, improving runtime without substantial memory increases in over 95% of cases considered. Across 38 functions from Seurat, Scanpy and related packages in genomics and bioinformatics, AutoZyme reduced runtime by a median of 8.52-fold, with the largest reductions exceeding 676-fold. The optimized functions are distributed through AutoZyme-Library as drop-in replacements for existing analysis pipelines. We also release AutoZyme as a reusable framework for optimizing additional user-specified packages and functions.

22.
arXiv (CS.CL) 2026-06-18

Probing Semantic Alignment, Lexical Invariance, and Syntactic Influence in LLM Metaphor Processing

Large language models (LLMs) achieve strong performance on metaphor detection and interpretation tasks, yet it remains unclear what such behavioral success reveals about metaphor processing. We present a diagnostic analysis that examines the limits of behavioral evidence by probing three complementary dimensions: semantic attribute alignment, lexical invariance, and syntactic sensitivity. Using geometric probing, we assess whether model-generated interpretations align with reference semantic attributes; through context-varying substitution, we analyze the stability of lexical associations between metaphorical and literal expressions; and via controlled syntactic perturbations, we examine sensitivity in metaphor detection. Our analysis reveals that LLM-generated interpretations can exhibit semantic drift relative to reference attributes; stable lexical anchors persist across contextual conditions, potentially supporting conventional metaphors while biasing novel metaphors requiring contextual integration; and detection performance is sensitive to syntactic irregularities. These findings suggest that strong behavioral performance may reflect heterogeneous underlying signals, highlighting the need for caution when interpreting metaphor benchmarks as evidence of robust, integrated semantic understanding.

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

Multimodal Ordinal Modeling of Alzheimer's Disease Severity Using Structural MRI and Clinical Data

arXiv:2606.11794v1 Announce Type: cross Abstract: Neurodegenerative diseases such as Alzheimer's disease (AD) require accurate and scalable tools for assessing disease severity, yet current clinical staging remains time-intensive and prone to variability. We propose an attention-enhanced multimodal machine learning framework with ordinal regression for automated and interpretable AD severity staging. The framework integrates T1-weighted MRI with demographic and genetic variables and compares unimodal and multimodal architectures using ordinal and non-ordinal prediction heads. Models were trained and validated using cohort-stratified splits derived from the ADNI, AIBL, and NIFD datasets. A strictly held-out test set was constructed using subjects excluded from all training, validation, preprocessing, and hyperparameter tuning procedures, with subject-level splitting employed throughout to prevent data leakage. Among unimodal approaches, the T1-weighted MRI model achieved slightly higher adjacent-stage accuracy (0.963) and agreement with clinical staging (QWK 0.444) than the tabular model (QWK 0.433). Integrating imaging, demographic, and genetic information improved overall performance. The multimodal non-ordinal baseline achieved the lowest prediction error (MAE 0.340), whereas the ordinal multimodal model achieved the highest adjacent-stage accuracy (0.970) and strongest agreement with clinical staging (QWK 0.549). These findings indicate that ordinal formulations better capture the ordered structure of the CDR scale and yield predictions more consistent with clinical staging. Explainability analyses using Grad CAM++ and SHAP demonstrated anatomically and clinically plausible model behavior, supporting transparent decision-making. Overall, attention-based multimodal learning with ordinal regression represents a robust, interpretable, and scalable approach for automated AD severity staging and AI-assisted clinical decision support.

24.
arXiv (CS.CL) 2026-06-16

Tying the Loop – Tied Expert Layers in Mixture-of-Experts Language Models

Authors:

Mixture-of-Experts (MoE) architectures efficiently scale Large Language Models (LLMs) by activating only a small fraction of their experts per token, yet the full parameter count - dominated by the expert parameters - must be held in training and inference memory. To address this, we introduce Expert Tying, an architectural modification that shares expert parameters across consecutive transformer layers while preserving independent, layer-wise routing and attention. We evaluate this approach across common, state-of-the-art architectures, including OLMoE, Qwen3, and DeepSeek-style MoEs. Our pretraining experiments demonstrate that tying experts can reduce memory footprint by almost 2x at virtually no degradation in perplexity or downstream quality. By exploiting the parameter redundancy inherent in MoE pathways, our method provides a highly favorable compute-to-memory trade-off, advancing efficient training and scaling of next-generation LLMs.

25.
arXiv (CS.LG) 2026-06-11

Knowledge Manifold: A Riemannian Geometric Framework for Semantic Mapping and Geodesic Analysis of Scientific Literature

arXiv:2606.05907v2 Announce Type: replace-cross Abstract: We present the knowledge manifold: a Riemannian geometric space in which a corpus of documents is arranged according to semantic positional relationships derived from character n-gram TF-IDF representations. The framework proceeds in five tightly coupled stages. First, each document is converted to a character-level n-gram TF-IDF vector (4-7 grams, up to 250,000 features, L2-normalized) and embedded in a two-dimensional knowledge map via constrained stress minimization with repulsion, variance, and centering regularizers. Second, knowledge at an arbitrary query point is estimated through Smoothed Particle Hydrodynamics (SPH) interpolation using a cubic-spline kernel, yielding an interpolated TF-IDF feature vector that can be linguistically characterized. Third, directional knowledge gradients at 0, 45, and 90 degrees are computed from the SPH interpolation map, and pairwise directional similarity is quantified via inner product and cosine similarity. Fourth, a Gaussian Process Regression (GPR) model, with a Constant x RBF + White kernel fitted on a 10-dimensional SVD projection, provides a Bayesian posterior mean, uncertainty estimate, and per-document contribution rate at the query point. Fifth, geodesics in the knowledge space are obtained by minimizing a discrete Riemannian path energy derived from the SPH-induced metric tensor, using L-BFGS-B with seven deterministic initial-path candidates. We apply the formulation to a corpus of 20 papers in fiber-reinforced composite materials and aerospace structural mechanics, showing that the semantic map recovers meaningful research clusters, geodesic paths reveal natural conceptual bridges between distant topics, and SPH/GPR interpolation enables the generation of virtual knowledge: hypothetical paper abstracts describing unstudied but geometrically predicted research directions.