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

Neither Parallel Nor Sequential: How DiffusionGemma Actually Commits Tokens

arXiv:2606.14620v1 Announce Type: new Abstract: Open diffusion language models are marketed as parallel, non-autoregressive decoders, yet the order in which a shipped checkpoint actually commits its tokens is almost never measured. We instrument DiffusionGemma 26B, a masked discrete-diffusion mixture-of-experts model built on Gemma 4, hooking its sampler's accept step to record which canvas positions commit, when, and at what confidence. Across a 686-prompt, six-regime probe suite we find that its decoding is neither parallel nor block-autoregressive: it follows a partial left-to-right commit bias whose apparent strength depends almost entirely on the granularity at which you look. Order is weak token by token and strengthens smoothly as the analysis is coarsened, so the model's "block size" turns out to be an artifact of the measuring ruler rather than the architecture. The model commits in large simultaneous batches, leaving much of the within-batch order genuinely undefined rather than merely unobserved. The behaviour is regime-dependent: structured JSON is committed in essentially arbitrary order, and a position's commit confidence tracks correctness on mathematical reasoning but carries no signal on factual recall. Commitment is aggressive, finishing in a short late burst well inside the step budget, while task accuracy matches the model's autoregressive Gemma-4 sibling. Beyond these findings, our central contribution is methodological: measuring decoding order honestly demands handling trailing-EOS padding, within-regime confounding, commit non-monotonicity, block-size sensitivity, and large commit-batch ties, each of which can otherwise manufacture a decoding-order result that is not really there.

02.
arXiv (CS.CV) 2026-06-19

TriFlow: Generating Artist-Like 3D Mesh Topology via Nearest-Vertex Vector Fields

We present TriFlow, a new generative approach for producing compact 3D meshes with artist-like triangle topology directly from input geometry conditions such as signed distance fields. Our key insight is to represent mesh topology as a nearest-vertex vector field (NVF) defined over the surface, where each point encodes its association to the nearest triangle vertex in the local barycentric frame. We train a latent flow-matching model to synthesize this field, enabling topology generation conditioned on the input geometry. To extract a coherent mesh, we cluster surface regions using the generated NVF and guide a constrained quadric error metric (QEM) mesh simplification with topology-aware optimization. This yields output meshes that closely match the input geometry while exhibiting structured, artist-like connectivity. Experiments demonstrate that TriFlow achieves stronger generalization and significantly improved topology quality compared to state-of-the-art learning-based approaches, alongside 90% lower Chamfer Distance and an 8x speedup.

03.
arXiv (CS.CV) 2026-06-18

Confidence is Not Reliability: Rethinking MC Dropout in Brain Tumour Segmentation

Glioma segmentation in multiparametric MRI is a critical component of treatment planning. A segmentation model that fails silently on treatment-critical sub-regions represents a patient safety risk that overlap-based metrics such as Dice scores cannot expose. We ask whether voxel-level uncertainty estimation via Monte Carlo (MC) Dropout can reliably identify segmentation errors in clinically critical sub-regions, and whether calibration failure modes are detectable from standard reporting metrics alone. In an empirical two-model case study on 126 BraTS21 patients, we evaluate a high-performance pretrained SegResNet and a locally trained UNet with residual units (UNet-Res). MC dropout preserved segmentation accuracy ($|\Delta Dice|$ $

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

StatefulDiscovery: Evidence-Calibrated Claim Formation in Open-Ended Scientific Discovery

arXiv:2606.11851v1 Announce Type: new Abstract: Open-ended scientific discovery asks agents to move beyond executing analyses for predefined questions. Across multiple rounds of exploration, a discovery agent must decide which phenomena warrant investigation while avoiding overinterpretation, where emerging claims exceed the evidential scope of the analyses supporting them. This creates an evidence-calibration problem: the exploration trajectory must be coupled with claim status so that evidence can guide both what to investigate next and what can be claimed. We introduce StatefulDiscovery, a discovery framework that externalizes investigation state and uses it to coordinate frontier selection, evidence acquisition, and claim adjudication. We evaluate StatefulDiscovery across 40 real-data discovery tasks. Compared with several baselines, StatefulDiscovery produces more claims overall judged to be both well-supported and high-value. Ablations indicate that structured hypotheses, local adjudication, and frontier control contribute to performance. Together, these results suggest that explicit discovery state can couple exploration with evidence-calibrated claim formation.

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

The Culture Funnel: You Can't Align What isn't in the Data

Current cultural alignment approaches focus on inference-time interventions, assuming models already contain sufficient cultural knowledge. We argue modern LLM pipelines suffer from a cultural data funnel. Using a multidimensional tagging framework across pretraining, fine-tuning, alignment, and reasoning datasets, we show explicit cultural signals decline sharply during post-training, while geographically concentrated, task-specialized data dominates. Multilinguality enhances geographic diversity of cultural knowledge but does not ensure balanced representation. Our tags improve downstream cultural benchmark performance, demonstrating that advances require shifting focus in training data pipelines. To facilitate future research, we release our culturally tagged dataset with 5.6M samples at https://huggingface.co/datasets/CohereLabs/CultureMarkers.

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

Enhancing Physics-Informed Neural Networks Through Feature Engineering

arXiv:2502.07209v4 Announce Type: replace Abstract: Physics-Informed Neural Networks (PINNs) seek to solve partial differential equations (PDEs) with deep learning. Mainstream approaches that deploy fully-connected multi-layer deep learning architectures require prolonged training to achieve even moderate accuracy, while recent work on feature engineering allows higher accuracy and faster convergence. This paper introduces SAFE-NET, a Single-layered Adaptive Feature Engineering NETwork that achieves orders-of-magnitude lower errors with far fewer parameters than baseline feature engineering methods. SAFE-NET returns to basic ideas in machine learning, using Fourier features, a simplified single hidden layer network architecture, and an effective optimizer that improves the conditioning of the PINN optimization problem. Numerical results show that SAFE-NET converges faster and typically outperforms deeper networks and more complex architectures. It consistently uses fewer parameters – on average, 65% fewer than the competing feature engineering methods – while achieving comparable accuracy in less than 30% of the training epochs. Moreover, each SAFE-NET epoch is 95% faster than those of competing feature engineering approaches. These findings challenge the prevailing belief that modern PINNs effectively learn features in these scientific applications and highlight the efficiency gains possible through feature engineering.

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

SGFormer++: Semantic Graph Transformer for Incremental 3D Scene Graph Generation

In this paper, we propose SGFormer++, a novel Semantic Graph Transformer for 3D scene graph generation (SGG), which aims to parse point cloud scenes into semantic structural graphs, where nodes denote detected object instances and edges encode their pairwise relationships, with the core challenge lying in modeling complex global scene structure. While existing graph convolutional network (GCN)-based methods suffer from over-smoothing and limited receptive fields, SGFormer++ leverages Transformer layers as its backbone to enable global message passing. Specifically, we introduce two key components tailored for 3D SGG: (1) a Graph Embedding Layer++ that efficiently integrates edge-aware global context with linear computational complexity, and (2) a Semantic Injection Layer++ that enriches visual features with linguistic priors from large language models (LLMs) and vision-language models (VLMs), boosting semantic representation without introducing extra trainable parameters. To further address the practical challenge of incremental SGG (I-SGG), where new relationship categories arrive sequentially, we equip SGFormer++ with a novel Spatial-guided Feature Adapter, which calibrates predicate features using subject-object spatial geometry to counter scale variation, and a Cascaded Binary Prediction Head that mitigates catastrophic forgetting via task-incremental classifier expansion and logit distillation. Extensive experiments on the 3DSSG benchmark demonstrate that SGFormer++ achieves state-of-the-art performance in both standard and incremental settings: it yields a significant 4.49% absolute improvement in Predicate A@1 under the incremental setting. Code and data are available at: https://github.com/Andy20178/SGFormer.

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

Sign-Language Datasets at Scale: A Comprehensive Survey on Resources, Benchmarks, and Annotation Standards

Sign languages are expressive visual languages used by Deaf and Hard-of-Hearing (DHH) communities. Despite substantial progress in sign-language recognition, translation, and production, advances remain constrained by fragmented datasets, inconsistent annotations, and limited linguistic coverage. Existing benchmarks often fail to reflect real-world communication needs, and systematic analyses of these limitations remain limited. In this survey, we present a comprehensive index of sign-language datasets, covering 120 resources across 35 sign languages. We analyze key challenges such as modality imbalance, annotation granularity, and signer bias, and outline considerations for future dataset design. We also introduce a 24-field Sign-Language Datasheet and release a public GitHub repository (https://github.com/Ginqwerty/Open-Sign-Language) to support standardized documentation and reproducible evaluation. Overall, our work provides a unified and practical foundation for developing inclusive, robust, and scalable sign-language technologies in real-world applications.

09.
arXiv (CS.AI) 2026-06-11

Generalization Hacking: Models Can Game Reinforcement Learning by Preventing Behavioral Generalization

arXiv:2606.12016v1 Announce Type: cross Abstract: Model post-training, and in particular reinforcement learning (RL), is one of the primary mechanisms by which developers can shape models' values and behaviors. However, as models become increasingly evaluation and training aware, they may be motivated to resist training when the perceived objective conflicts with their current values, undermining developers' ability to detect misalignment and correct model behavior through further training. In this paper, we demonstrate generalization hacking, in which a model collects reward during RL while preventing the rewarded behavior from generalizing. We construct a model organism on Qwen3-235B-A22B, finetuning on synthetic documents describing training awareness and self-inoculation, a novel mechanism in which the model frames compliance as context-specific in its chain of thought, without demonstrating or instructing either behavior. The model organism achieves train-time harmfulness comparable to controls while maintaining a persistent ${\sim}15$ percentage point compliance gap across 700 steps of RL. Additionally, a control organism trained only on training awareness documents independently discovers inoculation-like reasoning under RL pressure, developing its own compliance gap despite never being exposed to the concept. Because the generalization-hacking organism receives high reward throughout, standard training metrics provide no signal that generalization has failed. Our results constitute the first demonstration that a model can actively resist RL behavioral modification while maintaining high reward, suggesting that as models become more capable and training-aware, they may be able to undermine the training process itself.

10.
arXiv (CS.CL) 2026-06-16

Understanding Scam Trends and Rail Paths from Reddit Self-Disclosure Narratives

Online scam behavior is inherently multi-stage, and the lifecycle includes temporally ordered rails and events rather than isolated signals. Existing works analyze characteristics of scam types and rails, but they do not track scam trends across years. Moreover, the work on the relations between rails is hampered due to the lack of open-source datasets with annotations and coverage of different scam types. To address these gaps, we build a dataset to analyze the yearly trend of scam characteristics and rail paths using Reddit self-disclosure narratives from 2023 to 2025. We collect 21,304 posts from scam-related subreddits with at least one rail among identity, communication, platform, and payment for trend analysis by heuristic annotation. Then, we label 1,800 posts containing explicit or recoverable scam chains by an LLM-assisted method for scam path analysis. The method is evaluated with human annotation. Lastly, we run a topic model on the comments of the posts to analyze the community support behavior. The results reveal that scam processes are predominantly multi-rail. Across years, different scam types and rail components dominate. Different scam types vary systematically in path complexity. Reddit support behaviors have become more detailed over time. This work supports synthetic scam chain data simulation and AI-related scam risk assessment, though findings may not generalise to other platforms.

11.
arXiv (math.PR) 2026-06-12

Data-driven subsampling rates for diffusion parameter estimation of SDEs

arXiv:2606.13615v1 Announce Type: new Abstract: We study the problem of diffusion parameter estimation for stochastic differential equation (SDE) models in scenarios where data and model are compatible only on specific scales that have yet to be determined. We introduce a simple and efficient method for selecting suitable rates at which given time series data should be subsampled in order to ensure that the statistical structure of the subsampled data is consistent with the behavior of the SDE model on an infinitesimal scale. Our approach is based on analyzing the statistics of the lengths of monotonically increasing or decreasing segments in the subsampled data sequence, which we refer to as monotone runs. As an analytical foundation, we prove for a large class of SDEs with additive noise that the lengths of monotone runs at an infinitesimal scale are approximately geometrically distributed with success probability $1/2$. This universal characterization is employed to derive an automated method for selecting appropriate subsampling rates for given time series data that is directly applicable in real-world scenarios and does not rely on an asymptotic framework of multiscale diffusions. The approach is demonstrated using an application from industrial mathematics concerning surrogate models for fiber lay-down curves in production processes of nonwoven textiles.

12.
arXiv (CS.LG) 2026-06-15

Where Black-box Drug-Target Interaction Prediction Models Look: Cross-Method Explainability

arXiv:2606.14245v1 Announce Type: new Abstract: Drug-target interaction (DTI) and affinity (DTA) predictors increasingly achieve strong benchmark scores, yet their internal use of sequence, fingerprint, and graph features often remains opaque. We present an interpretability audit of BridgeDPI architecture on three different datasets including Gao, Human, and C.elegans. This study combines gradient-based attributions – integrated gradients, saliency, layer-wise relevance propagation, SmoothGrad, and SmoothGrad-IG – with feature-wise occlusion ablation and strict intersection consensus across methods to reduce single-explainer bias. We summarize sensitivity and signed effects at raw inputs, at the bridge similarity scaffold, and through the graph convolution, including edge-level sensitivities and targeted edge removals. The results show that explainability is most informative when treated as model criticism: it reveals modality dominance, padding and special-token artifacts, dataset-dependent cooperative versus suppressive effects across layers, and chemistry-consistent fragment and composition motifs where methods agree. These analyses do not substitute for structural or experimental ground truth, yet they can provide testable hypotheses for downstream validation in computational drug discovery pipelines. More broadly, applying modern XAI to contemporary DTI/DTA models is still an early pass over the rich structure implicit in trained weights and data – yet even this first layer of scrutiny already helps researchers relate predictions to drug- and target-side representations and to prioritize external validation.

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

Ride, Track, and Recover: Pilot Randomized Trial of a Wearable Digital Self-Management Intervention During a Veteran Endurance-Cycling Program

arXiv:2606.13529v1 Announce Type: cross Abstract: Post-traumatic stress disorder (PTSD) in veterans is characterized by persistent hyperarousal and comorbid anxiety and depressive symptoms that are difficult to monitor and manage outside clinical settings. Thirteen veterans participating in a Project Hero cycling event in Texas were randomized by computer-generated sequence in a naturalistic setting to two arms: (1) digital intervention plus physical activity, or (2) physical activity only, plus a third at-home monitoring control cohort consisting of 7 veterans selected from the broader Project Hero veteran community. Continuous smartwatch sensing combined heart rate and accelerometer features to detect hyperarousal events, which were confirmed in real time by participants. Weekly self-report measures of anxiety, depression, and PTSD severity were collected. Generalized additive mixed models characterized nonlinear trajectories over time. Baseline-normalized hyperarousal trajectories differed significantly across conditions, with the digital intervention group (n=7) showing structured stabilization compared to late-study escalation in the physical-only group (n=3). Both cycling groups exhibited acute symptom improvements during the endurance event; however, the digital intervention group demonstrated a higher overall maintenance of gains. The at-home control group (n=4) showed gradual symptom declines. Perceived precision of ML detections varied substantially across individuals and was positively associated with symptom severity, with higher-severity participants confirming a greater proportion of detected events. These results suggest that coupling wearable detection with digital self-management tools may support stabilization of hyperarousal and symptom improvement while emphasizing the importance of personalization and human-centered design in wearable mental health systems.

14.
bioRxiv (Bioinfo) 2026-06-18

Structure-Based Immunoinformatics Design of a CTB-Adjuvanted Multi-Epitope Mucosal Vaccine Against Helicobacter pylori

Background: Helicobacter pylori coloniz the gastric mucosa of nearly half of the global population and is classified as a Group I carcinogen by the World Health Organization due to its strong association with gastric cancer. The growing prevalence of antibiotic-resistant H. pylori strains significantly compromises current therapeutic strategies, emphasizing the urgent need for effective prophylactic approaches. Research design and methods; In this study, a novel multi-epitope vaccine was designed targeting H. pylori, incorporating epitopes from four key virulence proteins: BabB, SabB, SabA, and VacA. Using an immunoinformatics-guided structural vaccinology approach, B- and T-cell epitopes were predicted, prioritized based on immunogenicity, conservation, population coverage, and non-homology to human proteins, and assembled into the final vaccine construct. To enhance immunogenicity and specifically stimulate mucosal immune responses, the cholera toxin B subunit (CTB) was fused at the N-terminal via an EAAAK linker, a novel application in H. pylori multi-epitope vaccines. The PADRE universal epitope and additional linkers were incorporated to optimize epitope presentation and helper T-cell activation. Results: Comprehensive evaluations of physicochemical, antigenic, allergenic, and toxic properties were conducted, followed by secondary and tertiary structure modeling, refinement, and validation. Conformational B-cell epitopes were mapped, and molecular docking, binding affinity analysis, energy minimization, and molecular dynamics simulations confirmed structural stability and receptor interactions. Codon optimization and in silico cloning predicted efficient expression in Escherichia coli, while immune simulations suggested robust humoral and cellular responses. Conclusions: This study presents a promising multi-epitope vaccine candidate against H. pylori, offering a rational framework for future experimental validation and potential clinical application.

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

The Morse Transform for Discrete Shape Analysis

arXiv:2503.04507v2 Announce Type: replace-cross Abstract: The geometry of an object plays a vital role in modulating its interactions with the physical world. It nevertheless remains difficult to describe geometric information numerically for the purposes of statistical inference or classification tasks. Here, we introduce a new topological transform which leverages directional piecewise-linear Morse theory to quantify the geometry of an embedded object by cataloguing critical points across multiple height-functions. The output of this Morse transform records both the heights and the local topological type (peak, trough or saddle) of the critical points that characterise the underlying shape, retaining finer information than the Euler characteristic transform whilst naturally prioritising a shape's outermost regions. Crucially, this output can be further compressed into a rich but compact feature vector. We benchmark the Morse feature vector as a descriptor for ligand-based virtual screening (LBVS), which intrinsically depends on the shape of molecules. Under a common gradient-boosted tree classification pipeline, Morse descriptors achieve the highest mean AUROC when compared to other topological transform descriptors and to standard shape-based LBVS descriptors.

16.
medRxiv (Medicine) 2026-06-18

Multicluster measles outbreak with a substantial proportion of modified cases in Tokyo, Japan, January-May 2026

Tokyo experienced a measles outbreak (260 cases) in early 2026 despite elimination status. Adults aged 20-39 years were most affected, and 38% of cases were modified measles, increasing with prior vaccination. Although incidence rose until April, the effective reproduction number; R(t) fell below 1, consistent with outbreak control. Multiple clusters were identified, but many cases lacked epidemiological links, suggesting that modified measles is less likely to be considered in differential diagnosis. Intensive contact tracing and surveillance contributed to limiting transmission.

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

Robustness without Wrinkles: Parallel Simulation and Robust MPC for Certified Deformable Manipulation

arXiv:2606.14188v1 Announce Type: cross Abstract: We present CORD-SLS, a real-time control method for safe deformable object manipulation, with a focus on ropes and cloth. At its core is a GPU-parallel differentiable simulator with contact smoothing which enables efficient gradient-based planning through intermittent contact. To robustly satisfy constraints under model and sensing uncertainty, we develop a real-time, GPU-parallel output-feedback robust model predictive control (MPC) algorithm that plans with this simulator. We further show that the simulator accelerates model-based RL for training neural manipulation policies. To improve real-world robustness, we use conformal prediction to calibrate visual-feedback and perception-error bounds for MPC, producing reachable tubes that enable high-probability safe control. We evaluate CORD-SLS on high-dimensional, contact-rich rope and cloth manipulation tasks in simulation and hardware, including obstacle avoidance, routing, folding, and smoothing. Across settings, CORD-SLS achieves millisecond-speed planning, exceeding baselines in safety, speed, and task success.

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

The Periodic Table of LLM Reasoning: A Structured Survey of Reasoning Paradigms, Methods, and Failure Modes

Large Language Models (LLMs) have achieved strong performance across natural language processing tasks, yet reliable reasoning remains an open challenge. Although modern LLMs show progress in structured inference, multi-step problem solving, and contextual understanding, their reasoning behavior is often inconsistent and sensitive to prompting strategies, task design, and model scale. This survey provides a systematic analysis of more than 300 recent papers from arXiv, Semantic Scholar, Google Scholar, Papers with Code, and the ACL Anthology to examine how reasoning capabilities emerge in LLMs and where they fail. We make three main contributions. First, we introduce a structured taxonomy of LLM reasoning research, covering Chain-of-Thought reasoning, multi-hop reasoning, mathematical reasoning, common sense reasoning, visual and temporal reasoning, code and algorithmic reasoning, retrieval-augmented reasoning, tool-augmented and agentic reasoning, and reinforcement learning-based reasoning. Second, we analyze methodological trends across these paradigms, including prompting methods, model architectures, training objectives, reward modeling, and evaluation benchmarks. Third, we synthesize recurring limitations and failure modes, such as reasoning hallucinations, brittle multi-step inference, weak causal abstraction, and poor cross-domain generalization. By organizing a rapidly expanding literature, this survey offers a unified view of the current capabilities and limitations of reasoning in LLMs. We also identify emerging research directions, including meta-reasoning, self-evolving reasoning frameworks, multimodal reasoning, and socially grounded reasoning. Overall, this work aims to serve as a reference for developing more robust, interpretable, and generalizable reasoning systems in future language models.

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

Mechanistic Analysis of Catastrophic Forgetting in Large Language Models During Continual Fine-tuning

Sequential fine-tuning of Large Language Models (LLMs) adaptation to target tasks often triggers catastrophic forgetting, where the acquisition of novel target skills degrades ancestral capabilities. This paper presents a systematic comparative study of catastrophic forgetting across twenty premier models representing the state-of-the-art in mid-2026. We categorize our investigation into two primary research lines: (i) a behavioral and semantic output drift analysis of ten leading closed-source models (including Claude Fable 5, GPT-5.5 High, and Gemini 3.5 Flash), and (ii) a deep mechanistic interpretation of ten prominent open-weight architectures (such as DeepSeek-V4-Pro, Llama 4 Maverick, and Qwen 3.6-27B). Through weight-space trajectory tracking, Centered Kernel Alignment (CKA), and routing gate drift calculations in Mixture-of-Experts (MoE) layers, we localize the neural circuits highly susceptible to parameter overwriting. Our findings indicate that early-layer attention heads exhibit systemic entropic dispersion, while mid-to-deep feed-forward networks (or sparse expert blocks) suffer localized representation collapse. Informed by these insights, we introduce Low-Rank Circuit Projection (LRCP), a subspace-regularized training intervention. Empirical evaluations show that LRCP successfully mitigates up to 94.2% of ancestral capabilities in open-weight configurations and matches the adaptation velocity of standard PEFT baselines.

20.
arXiv (CS.LG) 2026-06-11

A Judge-Aware Ranking Framework for Evaluating Large Language Models without Ground Truth

arXiv:2601.21817v3 Announce Type: replace-cross Abstract: Evaluating large language models (LLMs) on open-ended tasks without ground-truth labels is increasingly done via the LLM-as-a-judge paradigm. A critical but under-modeled issue is that judge LLMs differ substantially in reliability; treating all judges equally can yield biased leaderboards and misleading uncertainty estimates. More data can make evaluation more confidently wrong under misspecified aggregation. We propose a judge-aware ranking framework that extends the Bradley-Terry-Luce model by introducing judge-specific discrimination parameters, jointly estimating latent model quality and judge reliability from pairwise comparisons without reference labels. We establish identifiability up to natural normalizations and prove consistency and asymptotic normality of the maximum likelihood estimator, enabling confidence intervals for score differences and rank comparisons. Across multiple public benchmarks and a newly collected dataset, our method improves agreement with human preferences, achieves higher data efficiency than unweighted baselines, and produces calibrated uncertainty quantification for LLM rankings.

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

From Simulation to Real-World: An In-Field 6D Pose Dataset and Baseline for Robotic Strawberry Harvesting

Robotic strawberry harvesting requires precise 6D pose estimation; however, collecting 6D pose ground truth in real agricultural fields is inherently challenging. Existing 6D pose estimation methods have therefore relied solely on synthetic data that lacks scene-level realism, leaving their performance under real agricultural field conditions unquantified. In this work, we present, to the best of our knowledge, the first real-world 6D pose ground truth dataset of strawberries collected in actual agricultural fields (12,040 images). We also introduce a synthetic dataset rendered in NVIDIA Isaac Sim, featuring scene-level realism and domain randomization. Nevertheless, our experiments reveal that a significant sim-to-real gap persists, underscoring the necessity of real agricultural field data for reliable evaluation. We further quantify the sim-to-real gap through baseline 6D pose estimation results across backbone encoders, serving as a reference for future work. The real-world dataset will be made available upon acceptance.

22.
arXiv (CS.LG) 2026-06-16

Convex Approximation of Two-Layer ReLU Networks for Hidden State Differential Privacy

arXiv:2407.04884v4 Announce Type: replace Abstract: The hidden state threat model of differential privacy (DP) assumes that the adversary has access only to the final trained machine learning (ML) model, without seeing intermediate states during training. However, the current privacy analyses under this model are restricted to convex optimization problems, reducing their applicability to multi-layer neural networks, which are essential in modern deep learning applications. Notably, the most successful applications of the hidden state privacy analyses in classification tasks have only been for logistic regression models. We demonstrate that it is possible to privately train convex problems with privacy-utility trade-offs comparable to those of 2-layer ReLU networks trained with DP stochastic gradient descent (DP-SGD). This is achieved through a stochastic approximation of a dual formulation of the ReLU minimization problem, resulting in a strongly convex problem. This enables the use of existing hidden state privacy analyses and provides accurate privacy bounds also for the noisy cyclic mini-batch gradient descent (NoisyCGD) method with fixed disjoint mini-batches. Empirical results on benchmark classification tasks demonstrate that NoisyCGD can achieve privacy-utility trade-offs on par with DP-SGD applied to 2-layer ReLU networks.

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

Towards CONUS-Wide ML-Augmented Conceptually-Interpretable Modeling of Catchment-Scale Precipitation-Storage-Runoff Dynamics

arXiv:2510.02605v2 Announce Type: replace Abstract: While many modern studies are dedicated to ML-based large-sample hydrologic modeling, these efforts have not necessarily translated into predictive improvements that are grounded in enhanced physical-conceptual understanding. Here, we report on a CONUS-wide large-sample study (spanning diverse hydro-geo-climatic conditions) using ML-augmented physically-interpretable catchment-scale models of varying complexity based in the Mass-Conserving Perceptron (MCP). Results were evaluated using attribute masks such as snow regime, forest cover, and climate zone. Our results indicate the importance of selecting model architectures of appropriate model complexity based on how process dominance varies with hydrological regime. Benchmark comparisons show that physically-interpretable mass-conserving MCP-based models can achieve performance comparable to data-based models based in the Long Short-Term Memory network (LSTM) architecture. Overall, this study highlights the potential of a theory-informed, physically grounded approach to large-sample hydrology, with emphasis on mechanistic understanding and the development of parsimonious and interpretable model architectures, thereby laying the foundation for future models of everywhere that architecturally encode information about spatially- and temporally-varying process dominance.

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

Is Code Better Than Language for Algorithmic Reasoning

arXiv:2606.15589v1 Announce Type: cross Abstract: For tool-augmented language models, comparing natural-language reasoning with code-execution pipelines is difficult because the comparison changes both the intermediate representation and the execution mechanism. We separate these factors with an intermediate intervention: the model expresses its reasoning as executable code, and the language model simulates that code in context to produce an answer. On a 40-task verifiable algorithmic benchmark, deterministic code execution outperforms natural-language reasoning by +31.6pp. We observe that the intermediate intervention is not meaningfully different from natural-language reasoning (+0.15pp). These results suggest that, in our evaluated setting, changing the intermediate representation alone does not explain the tool-use advantage, providing evidence for the performance gains requiring reliable external execution. We formalize this intuition with a simple statistical decision-theoretic model that characterizes when execution dominates end-to-end risk in our disentangled trace-generation/execution regime. We validate our theory using a reconstruction intervention that leverages a proxy language model to infer natural-language reasoning traces from code representations, recovering performance comparable to the original natural-language reasoning pipeline. All experiments are at https://github.com/TerryTong-Git/ToolProj.

25.
bioRxiv (Bioinfo) 2026-06-18

Calculation of sequence space coverage in a mutagenesis library

Directed evolution requires screening of large mutagenesis libraries, but accurate calculation of library sizes needed to discover functional variants remains challenging. Existing models provide baseline estimates, yet current computational approaches for finding the best variants scale poorly with library complexity. Here, we introduce a scalable algorithmic framework to compute exact discovery probabilities in saturation mutagenesis libraries with no requirement for explicit sequence enumeration. By aggregating variants into a composition log–sum distribution and applying log-space convolution across randomisation blocks, it is possible to extend this to massive sequence spaces and mixed codon schemes. By inverting these calculations, absolute mathematical ceilings for experimental design are established. Ultimately, this framework provides a rapid, quantitative tool to balance the statistical coverage-diversity trade-off within the limitations of laboratory screening. Finally, this is implemented as an open-source web application (SSCC) that allows researchers to construct heterogeneous library designs and compute required sampling depths, coverage probabilities, and absolute randomisation limits.