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01.
arXiv (CS.LG) 2026-06-19

Spectral DPPs via NEPv: A Scalable Continuous Relaxation of Determinantal MAP for Diversity-Aware Data Selection

arXiv:2606.19411v1 Announce Type: new Abstract: Selecting a small, diverse, high-quality subset from a massive pool of candidates is a recurring primitive in modern machine learning – data curation and coreset selection for training and fine-tuning large models, active-learning batch acquisition, prompt and exemplar selection for in-context learning, retrieval diversification, and experimental design. Determinantal Point Processes (\operatorname{DPP} s) give a principled, well-calibrated notion of diversity for this task, but their MAP objective – pick a size-$k$ subset $S$ maximizing $\logdet(L_S)$ – is NP-hard, and the standard greedy and sampling algorithms scale superlinearly in the ground-set size $n$. This cost is prohibitive precisely in the data-centric regime where diversity matters most, where $n$ ranges over millions to billions of candidate examples, features, or embeddings. We recast \operatorname{DPP}-MAP as a continuous optimization problem over the Stiefel manifold, and show that its first-order optimality conditions form a Nonlinear Eigenvalue Problem with eigenvector dependency (\operatorname{NEP}v) of a previously unstudied form. This \operatorname{NEP}v\ admits a self-consistent field (\operatorname{SCF}) iteration with a spectral-gap-based local contraction guarantee, giving a principled iterative solver where the diversity objective drives an eigenvector-dependent operator. The resulting algorithm, \OurMethod, requires only matrix-vector products with the kernel and runs in time $O\!\big((ndk+nk^2)\,t\big)$ for a small number of iterations $t$, scaling near-linearly in $n$ and integrating directly with low-rank and feature-map kernels common in ML. This paper focuses on the relaxation, solver, and scaling analysis; full real-data benchmarking is left to a planned empirical study.

02.
arXiv (CS.AI) 2026-06-16

Understanding Diversity Collapse in RLVR via the Lens of Overtraining

arXiv:2606.15455v1 Announce Type: cross Abstract: Reinforcement learning with verifiable rewards (RLVR) has become a key approach for enhancing the reasoning abilities of large language models. However, RLVR often suffers from diversity collapse: Pass@$1$ improves while high-$k$ Pass@$k$ degrades, which is viewed as a narrowing of the model's reasoning boundary. We formalize this diversity collapse through the lens of overtraining: once a problem's contribution to the reference metric has effectively saturated, further updates no longer expand what the model can solve but still concentrate probability mass on the trajectories favored by on-policy sampling. Under a standard setup with few rollouts per problem, even a single observed success places a problem in a nearly saturated regime for high-$k$ Pass@$k$, so most updates in standard RLVR are overtraining from the boundary perspective. This perspective also suggests a reading of whether RLVR can expand the model's reasoning abilities beyond the base model: since RLVR is structurally biased against high-$k$ Pass@$k$, its aggregate decline does not by itself mean that no new reasoning gains occurred. Interventionally, restricting updates to problems with zero observed success lifts Pass@$256$ above the base model on difficult benchmarks; observationally, a non-trivial fraction of initially unsolvable problems become solvable during standard RLVR training. Building on these findings, we propose Bayesian Boundary Gating (BBG), which redirects optimization away from overtraining by estimating each problem's marginal contribution to the reasoning boundary. Across multiple reasoning benchmarks, BBG improves average Pass@$k$ across a wide range of $k$.

03.
bioRxiv (Bioinfo) 2026-06-22

PhaseWY: A pipeline for haplotype phasing, sex chromosome identification and extraction of sex-limited sequences

Sex chromosomes are central to many ecological and evolutionary processes. Evidence has accumulated that sex chromosome systems vary extensively in age, turnover and transitions, motivating renewed efforts to study the diversity of sex chromosome systems across the tree of life. However, successful genomic detection of sex chromosomes depends on several factors, including the size and divergence time, background genetic diversity, and the number of sequenced females and males. In addition, technical challenges associated with sequencing and analysing the sex-limited Y/W chromosome remain. Here, we present PhaseWY, an automated Snakemake pipeline that uses whole-genome sequencing data from multiple female and male individuals to identify sex-chromosomal regions and extract the corresponding Y/W sequences. PhaseWY (i) detects sex differences in alignment depth, (ii) applies read-based and statistical haplotype phasing, (iii) identifies sex-linked regions using haplotype clustering, and (iv) subsets autosomal, X/Z- and Y/W-linked variants for downstream analyses. We applied PhaseWY to simulated data to benchmark factors influencing sex-linkage detection and successful extraction of Y/W-linked variants. To demonstrate its practical utility, we further applied PhaseWY to the neo-sex chromosome system in Alauda larks (Alaudidae) and performed a range of downstream analyses demonstrating the scope of applications of the PhaseWY output. We conclude that PhaseWY provides an easy-to-use and reproducible tool for population-genomic analyses in non-model organisms, with particular importance for advancing our understanding of sex-chromosome evolution.

04.
arXiv (CS.LG) 2026-06-25

Two Stages of Folding: Convergent Mechanisms in AI Protein Folding Trunks

arXiv:2602.06020v3 Announce Type: replace Abstract: How do protein structure prediction models fold proteins? We investigate this question through causal interventions on the folding trunks of ESMFold, OpenFold, and Boltz-1. Across all three models, we find a shared two-stage computational structure. In the first stage, early blocks initialize pairwise biochemical signals: features like charge propagate from sequence into pairwise representations through architecture-specific pathways. In the second stage, late blocks develop pairwise spatial features: distance and contact information accumulate in the pairwise representation. We verify these mechanisms causally by showing that steering charge and distance features induces predictable structural changes. Furthermore, these representations are functionally interchangeable: pairwise states can be linearly aligned and substituted across models. Together, these results suggest that folding trunks with different architectures, inputs, and training procedures converge on a shared representational organization for mapping sequence chemistry into spatial geometry.

05.
arXiv (CS.LG) 2026-06-19

Constrained hybrid modelling to predict microbial dynamics and organic matter turnover in soil systems

arXiv:2606.20329v1 Announce Type: new Abstract: Soil microorganisms control organic matter cycling and largely determine how soil systems can cope with and mitigate climate change and environmental threats. Representing microbial dynamics in process-based soil models is therefore critical to predict carbon cycling in soils, albeit highly challenging to inform from data. One promising approach to improve their parametrisation is the integration of genomic data, yet modelling the complex and unknown relationship between genomes and the processes the microbes are driving is an unsolved problem. In this work, we present the first hybrid modeling framework for deriving biokinetic parameter values of a process-based soil organic matter turnover model from metagenome-inferred functional traits based on DNA sequencing data. Our model predicts biokinetic parameters of the process-based model from genomic trait data with a neural network and integrates constraints from ecological theory and literature to ensure realistic behavior, even of non-observed state variables. We evaluate our method on synthetic genomic trait datasets of varying complexity and on real data, showing that our approach improves performance over multiple baselines and learns the dynamics of unmeasurable components of the process-based model effectively, even for small training datasets.

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

DFMU: Data-Frugal Machine Unlearning

arXiv:2606.25410v1 Announce Type: new Abstract: Machine unlearning is an emerging domain that ensures the safe removal of elements (includes concepts, attributes, entity and class) from the trained model along with least drop in model performance. The domain of machine unlearning brings its own indigenous challenges since the removal of pre-trained elements from model will always degrade the model performance on remaining elements. The existing methods basically rely on retraining for removal of elements from the pre-trained model, which is compute extensive. In this work, we propose a machine unlearning method which helps to reduce the computational requirement for faster retain-dataset accuracy convergence which also does not require extensive retraining of the pre-trained model. The proposed method, Data-Frugal Machine Unlearning (DFMU) requires only a single forward and backward pass for computing the importance score of various computational blocks of a model. The importance score computation is based on knowledge preserving pruning which helps to converge faster and requires far less data as compared to the existing methods. Experimentally, it achieves 40% more retain-accuracy with just 13% of data samples in comparison with SOTA method on various public datasets and also averages 88% faster processing time for forgetting a given class.

07.
arXiv (CS.CL) 2026-06-11

DuDi: Dual-Signal Distillation with Cross-Lingual Verbalizer

Small language models (SLMs) are efficient and scalable, but their multilingual capabilities degrade severely at sub-billion scales, especially for Southeast Asian (SEA) languages. We introduce DuDi, a dual-signal multilingual distillation framework that combines an online sequence-level signal with off-policy and on-policy token-level signals. DuDi further uses a cross-lingual verbalizer to refine teacher feedback and improve teacher-student transferability in multilingual settings. Experiments on SEA-HELM across multiple model families, scales, and teacher-student settings show that DuDi consistently outperforms competitive distillation baselines. Ablations and analyses confirm that sequence-level optimization, token-level supervision, and cross-lingual verbalization provide complementary and transferable learning signals for multilingual SLMs.

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

LLMZero: Discovering Adaptive Training Strategies for RL Post-Training via LLM Agents

RL post-training strategies are dataset-dependent and reveal a recurring empirical pattern: capacity parameters accumulate monotonically across stages, while regularization parameters predominantly oscillate in response to shifting training dynamics. This distinction matters because fixed schedules commit all parameters to fixed trajectories and therefore cannot express the non-stationary exploration-exploitation tradeoffs that regularization must track; the principle provides actionable design rules for multi-stage training. We discover this through LLMZero, a system where LLM agents search over training trajectories via tree search, diagnosing pathologies at each checkpoint and proposing coordinated multi-parameter transitions. Across 4 diverse GRPO tasks, LLMZero discovers strategies that improve over the base model by 9% to 140% relative and over grid search by 6% to 15% relative, consistently outperforming random search and the skill-based agent. The structural principle transfers across tasks, providing an explanation for why discovered strategies take qualitatively different forms yet share similar parameter dynamics.

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

The Tatoxa System for Text Detoxification in Low-Resource Languages: The Case of Tatar

Text detoxification, the automated detection and mitigation of abusive and harmful content, is essential for ensuring the safety of online communities and protecting users. However, low resource languages such as Tatar have received little research attention. In this paper we present Tatoxa, a novel state-of-the-art system for text detoxification in the Tatar language. Comparative experiments show that the proposed approach outperforms existing open source and proprietary commercial LLMs on key quality metrics. We also introduce a new dataset for text detoxification in Tatar, designed for fine tuning and evaluation in low resource settings. Finally, cross lingual transfer experiments indicate that transfer from other languages, including the culturally close Russian, performs significantly worse than training on native Tatar data even when a large Russian corpus is available.

10.
arXiv (quant-ph) 2026-06-11

Mach's principle in atomic transitions

arXiv:2606.11608v1 Announce Type: new Abstract: We investigate the atomic transition probabilities in atom-mirror set-ups that are in circular motion. In one scenario, the atom is in circular motion inside a static cylindrical mirror. In the other scenario, the cylindrical mirror rotates around its central axis while the atom remains static. We report structural similarity in the atomic transition probabilities between these two cases – these probabilities are equivalent upon interchanging the field frequencies between the two scenarios. We interpret such an observation as a semi-classical phenomenon analogous to the classical Mach's principle.

11.
bioRxiv (Bioinfo) 2026-06-24

trAIt: Species-by-Trait Data Retrieval using Large Language Models

Biological research often requires information about species' traits. Manual literature collation can be time-consuming and miss parts of the literature. To address this gap, we developed trAIt, a publicly available software for the retrieval of characteristics of species from scientific literature catalogued in the Europe PubMed Central (PubMed) database. trAIt provides a graphical user interface in which users specify species and characteristics of interest. Leveraging a large language model (LLM), trAIt retrieves relevant papers, combines their content through a consensus-based summarization model, and outputs a species-by-characteristic table. For a case study involving frog species, trAIt recovered 47.1% of trait-species combinations in 2.75 hours, while an expert curator independently recovered 62.4% over months. The consensus-based summarization substantially aids accuracy compared to single-source extraction. Across three case studies of vertebrate taxa, an expert confirmed the accuracy of 70.9% of trait-species entries recovered by trAIt. We observed considerable variation across taxa in trAIt's accuracy, which is possibly due to heterogeneity in open-access literature availability and inconsistencies in species and trait terminology. In sum, our analysis suggests that LLM-based tools can accelerate biological data synthesis but should be used to support domain experts' research, rather than replace their judgment.

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

Multi-Token Residual Prediction

arXiv:2605.18817v2 Announce Type: replace Abstract: Diffusion Language Models (DLMs) generate text by iteratively denoising masked token sequences, offering a tradeoff between parallelism and quality compared to autoregressive models. In current practice, the number of tokens decoded per step is controlled by a confidence threshold, and quality degrades monotonically as more tokens are denoised per step. We introduce Multi-token Residual Prediction (MRP), a lightweight module that enables dependency-aware multi-token denoising within a single backbone forward pass. MRP exploits a key property of the denoising process: the logit distributions at adjacent denoising steps are remarkably similar. Rather than running the backbone a second time to obtain the next-step logits, MRP predicts the residual between steps from the backbone's hidden states, effectively denoising more tokens per backbone forward at a fraction of the cost. We apply MRP across the two operating regimes of DLM decoding. In the high-quality-low-throughput static denoising regime, MRP serves as a drafter for speculative decoding: its proposals are verified against the backbone, yielding lossless acceleration of up to 1.4x in SGLang. In the low-quality-high-throughput dynamic denoising regime, MRP instead drives a remasking scheme that revokes over-eager reveals, recovering most of the accuracy lost to aggressive low-threshold decoding and improving accuracy by up to 22.6 points on code generation task HumanEval and 17.7 points on reasoning task GSM8K.

13.
arXiv (quant-ph) 2026-06-15

Quantitative and Optimal Device-Independent Lower Bounds on Detection Efficiency

arXiv:2511.19302v2 Announce Type: replace Abstract: This paper examines a quantitative and optimal lower bound on the detector efficiency in a (2,2,2) Bell experiment within a fully device-independent framework, whereby the detectors used in the experiment are uncharacterized. We provide a tight lower bound on the minimum efficiency required to observe a desired Bell-CHSH violation using the Navascués-Pironio-Acín (NPA) hierarchy, confirming tightness up to four decimal places with numerical optimization over explicit quantum realizations. We then introduce the effect of dark counts and demonstrate how to quantify the minimum required efficiency to observe a desired CHSH violation with an increasing dark count error. Finally, to obtain an analytical closed-form expression of the minimum efficiency, we consider the set of no-signaling behaviors that satisfy the Tsirelson bound, which are easier to characterize than the quantum set. Using such behaviors, we find a simple closed-form expression for a lower bound on the minimum efficiency which is monotonically increasing with the CHSH violation, though the analytically obtained lower bounds are meaningfully below the numerically tight lower bound.

14.
arXiv (math.PR) 2026-06-24

Toeplitz Determinants and Admissible Correlation Intervals

作者:

arXiv:2606.24603v1 Announce Type: new Abstract: For a homogeneous one-dimensional random field, positive semidefiniteness of finite Toeplitz correlation matrices imposes non-trivial constraints on admissible correlation coefficients. The widths of the corresponding admissible intervals are closely related to determinants of principal Toeplitz submatrices. Using the classical Desnanot–Jacobi determinant identity, I derive a simple determinantal representation for the widths of admissible correlation intervals. As an immediate consequence, I recover the product expressions for admissible interval widths previously stated by Schneider & Hartlap (2009). The argument places these relations into the general framework of classical Toeplitz determinant theory.

15.
arXiv (CS.AI) 2026-06-24

A global log for medical AI

arXiv:2510.04033v2 Announce Type: replace Abstract: Modern computer systems rely on syslog, a universal protocol that records critical events across heterogeneous infrastructure. Medicine's rapidly growing AI stack has no equivalent. As medicine deploys AI tools at scale, there is no standard way to record how, when, by whom, and for whom these models are used. Without such records, it is difficult to measure real-world performance and outcomes, detect adverse events, or identify bias and dataset drift. Here we introduce MedLog, a protocol for event-level logging of medical AI. Each time an AI model interacts with a human, another algorithm, or an automated workflow, MedLog creates a record. Each record contains nine core fields: header, model, user, target, inputs, artifacts, outputs, outcomes, and feedback. We apply MedLog across four deployments in the US, Switzerland, and Vietnam: ICU deterioration prediction, tetanus progression monitoring from wearable signals, automated sepsis quality reporting, and patient attendance prediction. MedLog records capture model behavior, workflow interactions, and downstream outcomes, including AI performance degradation during severe weather events in patient attendance prediction and increased laboratory testing after ICU deterioration alerts. MedLog limits the data footprint through risk-based sampling, lifecycle-aware retention policies, and write-behind caching, enabling deployment in low-resource settings. It also supports detailed traces for complex, agentic, or multi-stage workflows, creating a foundation for continuous monitoring, auditing, and improvement of medical AI.

16.
medRxiv (Medicine) 2026-06-22

Clinical-grade Cuffless Blood Pressure Monitoring via Deep-tissue Diffuse Speckle Pulsatile Flowmetry

Blood pressure (BP) is a vital sign which is measured to diagnose and manage hypertension. However, current methods to measure BP use inflatable cuffs which cause discomfort and limit the frequency at which measurements can be made, or intra-arterial catheters which are invasive and pose infection risks. Here, we propose and evaluate the use of Diffuse Speckle Pulsatile Flowmetry (DSPF) as a cuffless BP measurement method to address these limitations. DSPF is a laser speckle-based technique which simultaneously records blood flow rate and blood volume (i.e. photoplethysmography or PPG) signals from relatively deep vascular tissue. Using information from these signals, we studied DSPFs effectiveness in measuring systolic BP (SBP) and diastolic BP (DBP) through an outpatient study in which 133 patients were recruited, and in measuring beat-to-beat BP waveforms through an inpatient study in which two patients were recruited. In the outpatient study, the DSPF method was able to achieve mean absolute errors (MAEs) of 4.17 mmHg and 2.42 mmHg for SBP and DBP respectively compared to conventional cuff-based methods. It was also able to fulfil the requirements of the AAMI/ESH/ISO 81060-2:2018 standard for BP measurement devices and attain an "A" grade according to the British Hypertension Society grading scheme. For the inpatient study, it produced BP waveforms which had MAEs of 2.35 mmHg and 3.06 mmHg compared to arterial-line measurements for the two patients, respectively. Compared to PPG which has been studied more extensively as a cuffless BP measurement method, we found through ablation studies that DSPF was able to reach significantly lower MAEs and hence better accuracies. DSPF augments the performance of PPG-only methods by leveraging additional information from the blood flow rate signal, and we therefore find it to be a superior cuffless BP measurement method which can potentially be used in outpatient, inpatient, and remote settings.

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

StreamKL: Fast and Memory-Efficient KL Divergence for Boosting Attention Distillation

arXiv:2606.20005v1 Announce Type: cross Abstract: Attention distillation, which trains one attention distribution to match another by minimizing their Kullback-Leibler (KL) divergence, is widely used in knowledge distillation, model compression, continual learning, and sparse-attention LLM training. However, existing approaches materialize both attention distributions before computing the KL reduction, incurring $O(N_QN_K)$ memory and IO costs that become prohibitive at long context lengths. We present StreamKL, the first fused GPU primitive for attention KL divergence that eliminates this quadratic materialization. StreamKL derives a novel online formulation for the coupled two-distribution KL reduction, enabling a single one-pass forward kernel that streams query-key tiles through on-chip SRAM. For the backward pass, StreamKL recomputes attention probabilities tile-by-tile, avoiding storage of quadratic intermediates. We further design and implement efficient GPU kernels with dedicated optimizations. Experiments show StreamKL delivers up to $43\times$ and $14\times$ speedups over baseline methods in the forward and backward passes, respectively. Most importantly, StreamKL reduces the extra HBM footprint of attention distillation from $O(N_QN_K)$ to $O(1)$, enabling long-context distillation on a single GPU.

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

Hölder++: Improving the Quality-Coherence Trade-off in Multimodal VAEs

arXiv:2606.13381v1 Announce Type: new Abstract: Existing approaches for multimodal variational autoencoders (VAEs) face a trade-off between generative quality and coherence-i.e., they struggle to generate realistic and diverse samples that, at the same time, are semantically consistent across modalities. A recent work shows that using a simple approximation to Hölder pooling as an aggregation method improves coherence over the SOTA MMVAE+, despite assuming a single shared representation across all modalities. Yet, it slightly compromises sample diversity. Inspired by this insight, we propose Hölder++, a novel multimodal VAE that improves the generative quality-coherence trade-off through: (i) the first implementation of Hölder pooling without any approximation for multimodal VAEs; (ii) an extended architecture that models distinct shared and private (i.e., modality-specific) representations (Hölder+); and (iii) hierarchical inference that further enhances the disentanglement between the shared and private representations (Hölder++). Our experiments corroborate that Hölder++ consistently improves the generative quality-coherence trade-off, yields more structured latent spaces, and learns shared representations that are informative for downstream tasks.

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

From Privacy to Workflow Integrity: Communication-Graph Metadata in Autonomous Agent Interoperability

arXiv:2606.07150v2 Announce Type: replace-cross Abstract: Agent-interoperability protocols such as A2A and MCP standardize what agents say to one another but assume address-based transport. Whether over HTTP(S) or a content-protecting binding such as MLS-based SLIM, these transports protect message content yet leave the communication graph exposed: which agent contacts which, when, and how often. In agent systems this graph is more consequential than a privacy framing suggests. Endpoints are capability-labeled, workflows are structured and chained, and interactions are coupled to real actions, so an observer recovers more than past relationships: it can infer the pending workflow and, at machine speed, act on that inference before the workflow completes. The threat is therefore one of workflow integrity, not privacy alone. We formalize a threat model for the communication graph and locate what makes its metadata distinctively consequential: not stronger fingerprinting, which we measure to be comparable to other machine traffic, but exposure across independent trust domains, coupled to autonomous action. We define transport- and bootstrap-layer privacy properties, evaluate candidate transports, and give an A2A case study where a metadata-protecting binding surfaces the protocol's implicit identity assumptions. On a generative model anchored to a real capture and over a live A2A binding, a label-blind classifier recovers a task's class from passive metadata well above chance, and from only its opening; a defense-aware adversary does not overturn this, and only the full set of properties drives recovery toward chance. The leverage of acting on the leak is distinct from recoverability: under a fixed budget an adversary realizes most of a clairvoyant attacker's advantage from a workflow's opening, governed by precision over the top-ranked workflows rather than overall accuracy, so a defense suppresses it even while recovery stays above chance.

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

HiST: A Hierarchical Sparse Transformer for Cross-Modal Spatial Transcriptomics Modeling

Spatial transcriptomics (ST) links gene expression with tissue morphology but remains expensive and low-throughput, motivating surrogates that infer expression from routine histology. Whole-slide H&E-to-ST inference pairs a gigapixel image with gene measurements at a sparse, irregular set of locations, making multiscale modeling challenging without incurring dense-grid overhead or quadratic token mixing. We propose HiST, a hierarchical sparse transformer that treats measured locations as a lattice-indexed sparse field and builds a dyadic encoder–decoder directly on the active tissue footprint. HiST combines sparse window attention for local geometric correspondence with resolution-changing operators for rapid multiscale context integration. For a fixed window size, the dominant runtime and memory scale with the number of observed locations rather than the dense slide area. To mitigate slide-specific acquisition variation, HiST adds a bottlenecked global conditioning pathway via a slide calibration token that summarizes slide-level context and conditions local representations. On a multi-organ benchmark spanning diverse tissues and acquisition sources, HiST improves predictive performance over recent baselines while reducing runtime and peak memory.

21.
arXiv (CS.CL) 2026-06-17

Fine-tuning LLMs for Passive Depression Severity Estimation from AI Mental Health Dialogue

Depression is the leading cause of disability worldwide, and early detection of symptom change is essential for timely intervention. Validated instruments such as the Patient Health Questionnaire-9 (PHQ-9) support symptom monitoring at scale, but real-world completion rates are low, introducing response bias and systematic missingness. Passive approaches that infer severity from routinely generated data could close this gap. We address this by predicting PHQ-9 total scores directly from transcripts of conversations between users and an AI mental health application, requiring only conversation text and no additional clinical data. We fine-tune a Qwen3.5-27B backbone with a regression head, augment 3,111 ground-truth labels with pseudolabels generated by a reasoning model (Claude Opus) and iteratively trained intermediate models, for a combined dataset of 6,283 users. On a held-out test set of 842 users, our best model achieves MAE = 2.6, RMSE = 4.0, Pearson r = 0.80, and AUC = 0.91 at the PHQ-9 >= 10 clinical threshold. We also find AUC > 0.87 at every severity threshold from PHQ-9 >= 3 to PHQ-9 >= 24, demonstrating that the model captures depression severity across the full clinical spectrum. This work opens the door to passive, continuous symptom monitoring in AI mental health platforms, without requiring users to complete self-report measures.

22.
arXiv (CS.AI) 2026-06-24

ARIA: Adaptive Region-Based Importance Allocation for Conditional Diffusion Distillation

arXiv:2606.23898v1 Announce Type: cross Abstract: Distilling conditional diffusion models aims to transfer the behavior of a large teacher to a smaller student while preserving alignment across conditioning inputs. Unlike recognition tasks, knowledge distillation in conditional diffusion often struggles to transfer knowledge beyond the training distribution, since the predicted noise strongly depends on the conditioning signal. As a result, effective distillation requires exploring a large conditioning space. In practical settings, this creates a major bottleneck. Paired image-condition data may be limited, and generating synthetic images for every available condition is often computationally infeasible, while the pool of conditions, such as text prompts, can be extremely large. Recent work addresses this issue by switching conditions during training, exposing the student to a broader conditioning space without changing the distillation objective. Yet this raises a complementary question: once a large conditioning corpus is available, how should the training effort be allocated? In this work, we introduce ARIA, a framework that adaptively allocates training effort across coarse regions of the conditioning space. By maintaining online estimates of teacher-student discrepancy at the region level, ARIA focuses updates where misalignment persists while preserving the original distillation objective. Empirically, ARIA improves over RC across most architectures and settings, with the clearest gains observed in unseen and underrepresented regimes. We also provide a theoretical analysis showing that the proposed tracking mechanism follows the evolving discrepancy during training under bounded variance and drift assumptions.

23.
bioRxiv (Bioinfo) 2026-06-16

Expanding gene regulatory networks from transcriptome data through graphical modeling with heterogeneous priors

Gene regulatory network inference is widely used to reconstruct large-scale networks and identify functional genes from transcriptome data. Meanwhile, in many biological fields, core regulatory genes have been extensively studied, leading to the establishment of small-scale gene regulatory networks, and novel genes connected to these networks remain to be identified. However, methods for expanding existing gene networks by identifying novel regulatory interactions, rather than reconstructing the entire network, are not well established. Here, we propose a method for gene network expansion that incorporates known regulatory relationships and evaluates each candidate gene individually to infer its regulatory connections to the existing network. Using simulated datasets from the DREAM4 benchmark and the PRECISE-1K experimental dataset, our method outperformed conventional methods by incorporating prior knowledge. In particular, it improved the ability to distinguish true regulatory interactions from indirect associations arising from strong correlations among genes in the existing network. The method also showed strong performance for interactions involving genes with high outdegree or centrality. Furthermore, it maintained stable performance as the size of the existing network increased and was robust to noise in prior information. These results demonstrate that our method provides an effective framework for expanding existing gene regulatory networks by leveraging prior knowledge.

24.
bioRxiv (Bioinfo) 2026-06-18

Structure Bioinformatics of Eight Human ATP Synthase Fo Subunits and Their AlphaFold3-Predicted Water-Soluble QTY Analogs

Human mitochondrial ATP synthase is an essential rotary motor enzyme that produces most of the cellular ATP through oxidative phosphorylation. Its membrane-embedded Fo sector contains highly hydrophobic transmembrane subunits that are challenging to study in aqueous environments without detergents. This study explores whether applying the QTY code can reduce the hydrophobicity of selected ATP synthase Fo subunits while preserving their overall molecular structures. We applied the QTY code to eight human ATP synthase Fo subunits: ATP6, ATP8, ATPK, ATP68, ATPMK, AT5G1, AT5G2, and AT5G3. Hydrophobic amino acids leucine (L), isoleucine (I), valine (V), and phenylalanine (F) in transmembrane regions were systematically replaced with hydrophilic glutamine (Q), threonine (T), and tyrosine (Y). Four native subunits with available CryoEM structures from human ATP synthase (PDB: 8H9S) were superposed with their AlphaFold3-predicted QTY analogs. The native ATP synthase Fo subunits superposed well with their respective QTY analogs. For the CryoEM-native comparisons, RMSD values ranged from 0.565[A] to 2.546[A]. For the AlphaFold3-native comparisons of subunits without CryoEM structures, RMSD values ranged from 0.204[A] to 0.297[A]. Despite substantial QTY substitutions in the transmembrane regions, ranging from 38.89% to 50.79%, the QTY analogs retained similar overall folds, molecular weights, and isoelectric points. Hydrophobic surface analysis showed that the QTY analogs had reduced hydrophobic patches compared with their native counterparts, with average hydrophobicity decreasing from 0.2959 in native proteins to -1.1023 in QTY analogs. These structural bioinformatics studies suggest that the QTY code can be applied to ATP synthase Fo subunits to generate more hydrophilic, potentially water-soluble analogs while preserving overall structural similarity. These results extend the application of the QTY code to the membrane-embedded Fo sector of ATP synthase and provide a foundation for future experimental studies testing whether these QTY analogs can be expressed, purified, and evaluated for assembly or proton-transfer-related functions.

25.
arXiv (CS.AI) 2026-06-24

Beyond the Autoregressive Horizon: A Comprehensive Survey of Diffusion Models, World Modelling, and State Space Models for Code

arXiv:2606.23690v1 Announce Type: cross Abstract: Autoregressive (AR) language models have driven significant progress in automated software engineering, enabling powerful code generation and assistance systems. However, the next-token prediction paradigm introduces structural limitations for code reasoning, including restricted global planning, challenges in maintaining long-range dependencies, and limited grounding in program execution semantics. Noting the heavy skewness of existing literature towards AR models, we discuss emerging paradigms that could potentially overcome the logic and scaling bottlenecks of next-token prediction by unlocking next-generation architectural capabilities for code intelligence. Specifically, we discuss the potential of Diffusion Models, which generate code via holistic denoising that captures long-range syntactic constraints often missed by AR models. We also discuss Code World Models (CWMs), which simulate execution states to support reasoning, and State Space Models (SSMs), which provide linear-time efficiency for massive contexts. By connecting these developments with findings from cognitive neuroscience, we outline directions for developing "System 2" code generation agents.