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

Communication Policy Evolution for Proactive LLM Agents

arXiv:2606.14314v1 Announce Type: new Abstract: LLM agents have rapidly evolved into autonomous systems, yet a persistent information gap remains between users and agents: communication is costly, while users' identical preferences further limit information exchange. To investigate how agents should communicate across modalities, this paper formalizes Communication Policy, establishes textual and UI-based policies, and then evaluates communication policies across diverse environments, personas, and model combinations. Building information asymmetry for proactive agents, we set up two complementary settings, User-Agent and Planner-Executor. Experimental results reveal complementary strengths between interaction channels: text-based interaction often facilitates task performance, while structured UI improves agents' response quality and persona compliance. Motivated by that, a hybrid method combines these advantages. We further propose Communication Policy Evolution (CPE), a self-evolution framework for refining communication policies through rollout and prompt-level evolving. Without model modification, CPE achieves the best task success across multiple settings using prompt refinement alone. Our findings identify communication behavior as a critical yet underexplored design dimension for LLM agents.

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

ProMUSE: Progressive Multi-modal Uncertainty-guided Staged Evidential Alzheimer Disease Classification

arXiv:2606.19371v1 Announce Type: cross Abstract: Alzheimer's disease (AD) is a fatal disorder that destroys memory and cognitive skills in the elderly population. Most treatments for AD are effective in the early stage, leading to an increasing demand for early AD diagnosis. AD diagnosis increasingly relies on multimodal data such as clinical assessments, structural Magnetic Resonance Imaging (MRI), and Positron Emission Tomography (PET) imaging. However, MRI and PET acquisition remain costly and not universally accessible, making full-modality inference impractical in real-world clinical workflows. We propose ProMUSE, a Progressive Multi-modal Uncertainty Guided Staged Evidential Network that adaptively determines when additional modalities are necessary, helping reduce the overall cost of data acquisition while maintaining accuracy. ProMUSE first performs evidential classification using low-cost clinical data and quantifies uncertainty via a Dirichlet-based subjective logic model. When uncertainty exceeds a learned threshold, ProMUSE progressively incorporates MRI or PET features, fusing modality-wise belief and uncertainty through Dempster-Shafer theory to obtain a calibrated multimodal prediction. This staged acquisition strategy enables accurate diagnosis while minimizing reliance on expensive imaging. Experiments on ADNI, AIBL, and OASIS across CN-AD, CN-MCI, and MCI-AD tasks demonstrate that ProMUSE achieves competitive or superior accuracy compared to full-modality baselines while reducing MRI/PET usage by 50-90%, yielding substantial cost savings. These results highlight ProMUSE as a practical, uncertainty-aware, and resource-efficient solution for real-world AD screening.

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

Probing Low Frame Rate Degradation in Neural Audio Codecs

arXiv:2606.16969v1 Announce Type: cross Abstract: Low frame rates in neural audio codecs are attractive for autoregressive speech synthesis, where the generation cost scales linearly with the sequence length. Recent work has demonstrated that codecs can operate at 12.5 Hz and below, but the mechanisms underlying low frame rate degradation remain insufficiently understood. We investigate these mechanisms through a controlled frame rate ablation. We reproduce a quality cliff at 6.25 Hz reported in previous works and evaluate candidate explanations: phonemic collisions and codebook saturation, neither of which shows evidence of a fundamental barrier. The cliff is instead caused by suboptimal training configuration: fixed clip duration during training yields too few tokens at low frame rates, starving the decoder of inter-token context. Once corrected, WER degrades smoothly with phonemic load down to 3.1 Hz and 1.6 Hz, suggesting the inference-time efficiency gains of low frame rate codecs are more accessible than previously assumed.

04.
arXiv (quant-ph) 2026-06-12

A ribbon ZX calculus for gauge theory

arXiv:2606.13551v1 Announce Type: cross Abstract: ZX calculus provides a graphical formalism for reasoning about quantum processes, built from two interacting Frobenius algebras associated with the Z and X bases of a qubit. While it has found widespread application in quantum information and computing, its relationship to quantum field theory has only recently begun to be explored. In this work, we further develop this connection by providing a generalization of ZX calculus to two-dimensional Yang Mills theory with a compact gauge group. The key observation is that both frameworks can be organized around the Hopf Frobenius algebraic structure associated with a group algebra, which can in turn be described by the diagrammatics of two dimensional topological quantum field theory. Given the well known relationship between gauge theory and gravity in two and three dimensions, our work paves the way for applications of ZX to low dimensional gravity.

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

Sovereign Execution Brokers: Enforcing Certificate-Bound Authority in Agentic Control Planes

arXiv:2606.20520v1 Announce Type: cross Abstract: Autonomous agents are increasingly connected to cloud, deployment, and data-control workflows, but production mutation authority should not reside inside non-deterministic reasoning processes. Existing access-control mechanisms authorize identities, while assurance layers certify proposed actions; neither alone provides a mandatory enforcement point for certified authority at the moment of mutation. This paper introduces the Sovereign Execution Broker (SEB), a runtime enforcement boundary for certificate-bound agentic infrastructure. SEB consumes certificates issued by the Sovereign Assurance Boundary (SAB), verifies that the requested mutation matches the certified execution contract, checks validity windows, policy epochs, revocation epochs, and live-state drift, mints scoped execution identity, invokes infrastructure APIs, and records signed decision and outcome records. By separating proposal, admission, and execution, SEB turns certified authority into a short-lived, revocable, auditable runtime capability, provided that production mutation APIs reject non-broker identities. We present the SEB execution model, certificate and replay-verification predicates, scoped identity semantics, bypass-prevention deployment patterns, failure behavior, and a concrete prototype implementation. We evaluate the prototype on AWS and Kubernetes clusters, measuring latency overheads, revocation propagation, drift detection, and security under fault injection.

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

The Circumplex Degeneracy Behind the Rare-Class Limit in Affect Recognition

In-the-wild expression recognition persistently fails on a few rare emotions, and the standard explanation is class imbalance. Through a controlled multi-task study on two benchmarks, we show the failure is instead a property of affect geometry: the rare classes are degenerate on Russell's circumplex, and that degeneracy bounds what any loss or cost can achieve. Our instrument is a circumplex-cost optimal-transport term that prices expression confusions by their valence-arousal distance. The term improves the official score and expression macro-F1, but a control most studies omit shows the gain is not geometric: a uniform cost, equivalent to a generic confidence penalty, matches it on Aff-Wild2 (p=0.625) and significantly exceeds it on AffectNet (+0.057 over base, larger than the circumplex). What the geometry reshapes is the structure of the errors, making them affectively nearer the truth on Aff-Wild2 (p=0.031 against the uniform control), an effect that does not survive on AffectNet, where a visual confound at the far corner of the circumplex overwhelms it. The rare-class failure, by contrast, is stable across both datasets we examine: the degenerate pairs (anger-fear on Aff-Wild2, anger-contempt on AffectNet) resist frequency-based interventions, the transport term, and an action-unit-augmented cost built specifically to separate them. We conclude that progress on rare expressions requires representations that distinguish the classes, not supervision that reprices their confusions, and we provide the controls and metrics needed to tell the two apart.

07.
arXiv (CS.CL) 2026-06-17

When Multiple Scripts Matter: Evaluating ASR in Clinical Settings

Automatic speech recognition (ASR) in non-English clinical settings is challenged by multiscript variability, where the same term may appear in multiple valid orthographic forms. Conventional string-matching evaluation metrics often underestimate ASR performance by treating orthographic variants as errors. To address this issue, we introduce MultiClin, a clinical ASR benchmark designed to evaluate robustness to multiscript variability. Experiments across diverse ASR models show that multiscript-aware evaluation provides a fairer assessment of recognition quality than conventional single-reference evaluation. We further investigate the impact of script consistency during training and find that inconsistent script mappings increase orthographic uncertainty and hinder model convergence, with a balanced 50% mapping ratio producing the highest entropy. In contrast, script unification consistently yields the best ASR performance. Our dataset and code are publicly available at: https://github.com/aitrics-ronaldo/Interspeech_MultiClin.

08.
bioRxiv (Bioinfo) 2026-06-10

Pseudoperplexity Probes Memorization in Protein Language Models

Protein Language Models (pLMs) have significantly advanced computational biology. Yet their scale and reliance on redundant training data raise a fundamental question: do pLMs generalize the statistical grammar of proteins, or do they simply memorize their training data? To investigate this, we used pseudoperplexity as a probe for sequence-level memorization, comparing ProtT5's pseudoperplexity on a pre-training proxy dataset against a post-training holdout of genuinely novel sequences. To ensure a valid comparison, we matched the datasets by sequence length, cluster size, and taxonomic family. As a statistical baseline, we trained n-gram language models; analysis of higher-order n-gram composition and a statistically significant divergence in perplexity confirmed that the post-training sequences were genuinely novel at the local sequence level. ProtT5 showed a statistically significant difference in pseudoperplexity between seen and unseen sequences, though further analysis revealed this memorization signal to be modest. These findings suggest that ProtT5 exhibits detectable but limited memorization of its training data as measured by a pseudoperplexity-based probe.

09.
arXiv (CS.CV) 2026-06-16

HadBalance: A Plug-and-Play Unified Global Geometric Prior Framework for Generalizable Biomedical Segmentation

Precise biomedical image segmentation is crucial for clinical diagnosis. Geometric cues (e.g., boundary, shape, and topology) can improve structural consistency, yet most are task-specific and lack a unified geometric foundation that generalizes across organs and modalities. We are motivated by the observation that several medical segmentation targets can be approximated as globally near-convex shapes. A convex region is one in which any two interior points can be connected by a line segment entirely contained within the region. In practice, medical targets may exhibit small local concavities or boundary irregularities; we refer to such globally convex-like shapes as near-convex. Motivated by this, we derive Hadwiger Shape Priors from Hadwiger's theorem as an interpretable global regularizer using three 2D measures: area A, perimeter P, and Euler characteristic chi, enabling transfer across organs and modalities. However, because medical datasets are shape-heterogeneous, enforcing near-convex priors uniformly can over-regularize non-convex anatomy with significant concavities, washing out concavities and fine details and degrading segmentation accuracy. To address this challenge, we propose Conflict-Aware Objective Balancing (CAOB), which integrates shape priors with segmentation in a gradient-aware manner. For each prior, CAOB removes only the gradient component that conflicts with segmentation while preserving the remaining aligned component, and adaptively regulates objective influences to prevent prior dominance. This enables stable use of shape priors on shape-heterogeneous data without erasing genuine concavities or fine structural details. We call this plug-and-play framework HadBalance.

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

Expressivity of Quantum Reservoir Computers

arXiv:2501.15528v3 Announce Type: replace Abstract: Using Hamiltonian encoding to inject an input into parameterized quantum circuits (PQCs), the output of the PQC can be written as truncated Fourier series. In recent years, the expressivity of PQCs was established as the number of frequencies contained in this Fourier series. While this concept has also been applied to other quantum machine learning (QML) paradigms, a clear notion of expressivity for temporal information processing with quantum systems is still lacking. Here, we introduce such a notion to the field of quantum reservoir computing (QRC). We analytically derive an expression for the readouts showing that the output of a QRC can be interpreted as a multi-dimensional Fourier series. We give a formula for the growth of expressivity induced by the sequential information injection, which we corroborate with numerical simulations, calculating explicitly the number of multi-dimensional output functions which can be generated from the readouts. Our results show that the specific interplay between system size, input encoding, and memory time gives rise to a boundary on the system size beyond which it is obstructive to further increase the reservoir size in extreme scrambling systems. We propose a recipe for determining this maximal system size for a given QRC setup.

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

EiCAP: Beyond Fluency, Probing and Improving Emotional Intelligence in LLMs via Psychologically Grounded Multi-Turn Dialogue

Large Language Models increasingly serve in emotionally sensitive roles, including mental health support, education, and crisis response, yet they lack a principled framework for assessing or improving Emotional Intelligence (EI). We introduce EiCAP, a unified, psychologically grounded six-layer EI taxonomy operationalized into two complementary resources. EiCAP-Bench is a multi-turn, one-vs-three forced-choice evaluation suite with 3,174 probes across 24 subcategories and cross-turn dependencies that reflect real conversational EI demands. EiCAP-SFT is a 152,820-dialogue supervision corpus aligned to the same taxonomy, enabling controlled, interpretable fine-tuning. Two key findings emerge. First, generic conversational supervised fine-tuning does not confer EI: fine-tuning on UltraChat yields no significant gain in any of the 24 subcategories, with a macro score of 24.6%, near the chance level of 25%. Second, applying EI-grounded LoRA, using approximately 0.8% of parameters, directly to Qwen-2.5-7B-Base achieves significant gains in all 24 subcategories, reaching a macro score of 75.33%, a gain of 51.7 percentage points over Base and 37.1 percentage points over Instruct. Crucially, an ablation shows that the UltraChat pre-stage is counterproductive, reducing performance by 21.4 percentage points: direct EI-grounded training is both necessary and sufficient.

12.
arXiv (CS.CV) 2026-06-11

SpecLoR: Spectral Lookahead Rectification for Motion-Coherent Text-to-Video Generation

Flow Matching has enabled robust text-to-video generation via latent ODE sampling. However, velocity approximation and numerical discretization errors inevitably accumulate, causing sampling trajectories to drift. Consequently, generated videos often suffer from severe spatiotemporal inconsistencies. Nevertheless, directly correcting these drifted, noisy latents is challenging: (i) timestep-dependent noise obscures reliable structural cues; (ii) spatial interventions risk disrupting intricate local geometry while incurring heavy computational costs. To address this, we propose Spectral Lookahead Rectification (SpecLoR), a plug-and-play inference method that bypasses noise via lookahead prediction, and circumvents spatiotemporal entanglement by shifting corrections to the frequency domain, where universal statistical priors of natural videos are readily available. First, during early sampling stages, SpecLoR looks ahead to estimate the clean latent $z_{t,0}$ and computes its 3D spatiotemporal spectrum. Next, SpecLoR rectifies the amplitude spectrum to match the prior, leaving the phase intact. Finally, the corrected state is re-noised to resume ODE integration. Experiments on Wan2.2 demonstrate that SpecLoR significantly reduces physical artifacts and enhances motion coherence across multiple benchmarks with minimal computational overhead (4 additional NFEs).

13.
medRxiv (Medicine) 2026-06-22

The Protective Role of Belonging and Socioeconomic Status in Dropout Intent Among Minority Ethnic Students: A Mixed Methods Study

Improving minority ethnic student retention is a global higher education priority. This mixed-methods study investigated how institutional belonging and socioeconomic status interact to shape dropout intentions among minority university students in the UK (N = 182). Quantitative results revealed that perceived course difficulty and lower subjective socioeconomic status were the strongest predictors of dropout intent. While the interaction between socioeconomic status and difficulty was non-significant, qualitative accounts showed distinct structural vulnerabilities. Financial strain restricted social integration, turning socioeconomic disparities into campus isolation. Conversely, representative curricula, diverse peer networks, and stable cultural in-groups (e.g., religious affiliations, living in the parental home) functioned as essential psychological buffers against academic exhaustion and alienation. Universities must shift from transactional models to sustained structural equity to protect vulnerable student groups.

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

Multi-Rate Mixture of Experts for Accelerating Liquid Neural Network Training

arXiv:2606.12240v1 Announce Type: cross Abstract: Multivariate time-series data often exhibit complex temporal dependencies, irregular sampling, and heterogeneous dynamics across multiple time scales, making accurate sequence modeling particularly challenging. Traditional recurrent neural networks (RNNs), such as Long Short-Term Memory (LSTM) networks, operate in discrete time and may struggle to effectively capture continuous and irregular temporal behaviors. Liquid Neural Networks (LNNs) address some of these limitations through continuous-time dynamics, but standard LNN architectures typically rely on a single dynamical system, limiting their ability to model heterogeneous temporal patterns. To address these challenges, we propose a Multi-Rate Mixture-of-Experts (MR-MoE) framework built on top of Liquid Neural Networks. In the proposed architecture, multiple LNN-based experts operate at distinct time scales, enabling the model to explicitly separate fast-changing dynamics from slow-evolving temporal trends. A gating network further enables adaptive expert specialization based on input conditions. In addition, we incorporate both feature-level and temporal attention mechanisms to improve robustness, interpretability, and long-range dependency modeling. Feature-level attention suppresses noisy or irrelevant variables, while temporal attention selectively focuses on informative historical states. We evaluate the proposed framework on a complex multivariate time-series prediction task and compare it against strong baselines, including LSTM, monolithic LNN, and standard MoE models. Experimental results demonstrate that the proposed MR-MoE framework consistently achieves improved AUROC and AUPRC performance while maintaining favorable computational efficiency. These results highlight the effectiveness of combining continuous-time dynamics, multi-scale expert decomposition, and adaptive attention mechanisms for time-series modeling.

15.
arXiv (quant-ph) 2026-06-11

Mixed-State Topological Order under Coherent Noise

arXiv:2411.03441v2 Announce Type: replace Abstract: Mixed-state phases of matter under local decoherence have recently garnered significant attention due to the ubiquitous presence of noise in current quantum processors. One of the key issues is understanding how topological quantum memory is affected by realistic coherent noise, such as random rotation noise and amplitude-damping noise. In this work, we investigate the intrinsic error threshold of the two-dimensional toric code (TC), a paradigmatic topological quantum memory, under these types of coherent noise by employing both analytical and numerical methods based on the doubled-Hilbert-space formalism. A connection between the mixed-state phase of the decohered TC and a non-Hermitian Ashkin-Teller-type statistical-mechanics model is established, and the mixed-state phase diagrams under the coherent noise are obtained. We find remarkable stability of mixed-state topological order under random rotation noise with axes near the $Y$-axis of qubits. We also identify intriguing extended critical regions at the phase boundaries, highlighting a connection with non-Hermitian physics. We argue that these phase boundaries provide upper bounds for the intrinsic error threshold, beyond which quantum error correction becomes impossible. We complement these findings by estimating the error thresholds for random rotation noise under standard quantum error correction, thereby providing lower bounds on the intrinsic error threshold.

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

Faster Completion, Less Learning: Generative AI Reduced Study Time on Math Problems and the Knowledge They Build

arXiv:2605.21629v2 Announce Type: replace-cross Abstract: How much have students' ordinary learning processes shifted in response to generative AI, and how does that affect their durable learning outcomes? Self-report surveys show little change, while small-scale behavioral studies report widespread AI use without the scale or duration to measure learning consequences. We address both questions using a ten-year panel of $3.2$ million ALEKS learning interactions for investigating time-on-task, complemented by ALEKS PPL placement-assessment data for examining proctoring and learning outcomes, with a quasi-experimental design exploiting variation in tasks that are more susceptible to AI (text-based word problems) and less susceptible to AI (interactive graph-based problems). Learning time on AI-susceptible problems declines $2.8\%$ per quarter among college students after ChatGPT's release, cumulating to $26.9\%$ over eleven quarters; high-schoolers show $31.3\%$, middle-schoolers $9.0\%$, and Grade 5 students no detectable change. Among college students, the post-ChatGPT divergence vanishes entirely under proctoring, ruling out broad efficiency gains as the likely explanation. Logistic fixed-effects models on randomly assigned proctored retention items yield a $25\%$ cumulative decline in odds of correct response; the same estimator on non-proctored assessment produces a large opposite-signed increase – inconsistent with any platform, cohort, or curriculum explanation. These results are among the first large-scale behavioral and outcome evidence that generative AI has altered how students study and the knowledge they build – the population-level indicator of cognitive surrender, with direct implications for educational research, assessment governance, and AI policy.

17.
arXiv (CS.LG) 2026-06-11

Flow Matching with In-Context Priors for Out-of-Distribution Brain Dynamics

arXiv:2606.11833v1 Announce Type: new Abstract: Flow matching and diffusion models enable conditional generation across domains ranging from images to proteins, with recent extensions to out-of-distribution contexts. Yet generative models of neural time series have largely remained restricted to categorical conditioning, precluding compositional and zero-shot generalization. In this work, we propose a per-timestep conditioned diffusion transformer for generating realistic fMRI brain dynamics during unseen cognitive tasks by injecting both compositional language and optional spatial priors in-context. Such zero-shot generation could enable counterfactual neuroscience by supporting in-silico design and evaluation of novel cognitive experiments before empirical validation. Leveraging this model, we evaluate across hundreds of held-out task conditions and characterize predictive performance in relation to the training manifold. From language alone, the model recovers region-specific recruitment across tasks and held-out spatial activation patterns. Spatial priors, when available, complement the text pathway by anchoring generation in regions of task space where language alone degrades, while retaining the compositional structure needed for counterfactual task specification. To our knowledge this is the first generative model of whole-cortex fMRI dynamics for unseen cognitive tasks, advancing counterfactual neuroscience and data-driven experimental design.

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

Kolmogorov-Arnold Reservoir Computing

arXiv:2606.19984v1 Announce Type: new Abstract: Reservoir computing offers a lightweight framework for forecasting dynamical systems but may struggle to capture long-range dependencies due to limited representational capacity. Conventional reservoir computing recurrently uses trainable reservoirs with hyperparameter sensitivity, while the next-generation reservoir computing removes recurrence at the cost of rapidly growing feature dimensions. Here, we develop Kolmogorov-Arnold Reservoir Computing (KARC), which replaces reservoirs with explicit basis-function expansions inspired by the Kolmogorov-Arnold representation theorem. We rigorously show that KARC is a lightweight design of Kolmogorov-Arnold networks (KANs), preserving the potential expressive capacity of KANs while admitting efficient closed-form training of reservoir computing. At comparable cost, KARC outperforms existing reservoir computing methods on challenging benchmarks including partial differential equations. It can also be integrated with generative diffusion models for text-to-image generation. This work thus establishes a principled bridge between reservoir computing and KANs, enabling efficient and high-fidelity dynamical system forecasting.

19.
bioRxiv (Bioinfo) 2026-06-12

DNA Compression with Genomic Language Models: Tokenization, Benchmarking, and an Information-Content Map

Lossless compression and probabilistic sequence modeling are two faces of the same coin: a model that assigns high probability to a sequence can encode it in few bits via arithmetic coding. We exploit this duality to evaluate genomic language models as compressors of DNA, using compression primarily as an objective probe of generative sequence modeling rather than as a deployable storage system. We release DNAGPT2, a family of ten GPT-2-small models pretrained for one epoch on a single A40 using the DNABERT2 multi-species corpus that differ only in byte-pair encoding vocabulary size. Coupled with arithmetic coding, the best model reaches 1.47 bits per base (bpb) on the T2T human genome, fourth in the Cobilab compression benchmark and ahead of every general-purpose compressor. Our results suggest that NLP-style tokenization choices may be suboptimal for DNA: a 32-token BPE vocabulary compresses better than larger vocabularies. We also find that, in this benchmark, published long-context genomic LMs underperform a much shorter-context BPE GPT-2; we discuss in Section 5 that this is not a controlled context-length ablation, since the compared models also differ in architecture, training data, parameter count, and tokenization. Finally, we compute a per-nucleotide information-content map of the human genome and show that exons, introns, intergenic regions, and Alu repeats have statistically distinct information profiles.

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

Edu-Theater: A Data-Efficient Agent Framework for Scalable Learner Behavior Simulation through Staging Roll-Call

arXiv:2606.15225v1 Announce Type: cross Abstract: Large-scale learner-task interaction data are crucial for intelligent educational systems but are costly to collect and constrained by privacy and learner engagement. Learner simulators play a critical role in simulating scalable learner behavior without the need for continuous involvement of real learners. However, existing methods are predominantly individual-centric, pairing a simulator with each learner to iteratively infer latent knowledge states from dense interaction histories, which is both data- and computation-intensive, and fragile in cold-start scenarios. We propose a cohort-aware roll-call simulation paradigm that first constructs cohort-level proficiency priors and refines individual learner states through a small number of targeted diagnostic queries. Based on this paradigm, we introduce Edu-Theater, an LLM-powered agent system that performs cohort-aware learner simulation via a teacher agent and retrospective roll-call probing over learner logs. Edu-Theater enables scalable future behavior simulation without the need for dense per-learner histories. Experiments on two real-world datasets demonstrate that Edu-Theater achieves higher simulation accuracy with significantly fewer LLM calls, producing synthetic data that enhances downstream applications such as adaptive testing.

21.
arXiv (CS.LG) 2026-06-12

Is Stochastic Gradient Descent Effective? A PDE Perspective on Machine Learning processes

arXiv:2501.08425v3 Announce Type: replace Abstract: In this paper we analyze the behaviour of the stochastic gradient descent (SGD), a widely used method in supervised learning for optimizing neural network weights via a minimization of non-convex loss functions. Since the pioneering work of E, Li and Tai (2017), the underlying structure of such processes can be understood via parabolic PDEs of Fokker-Planck type, which are at the core of our analysis. Even if Fokker-Planck equations have a long history and a extensive literature, almost nothing is known when the potential is non-convex or when the diffusion matrix is degenerate, and this is the main difficulty that we face in our analysis. We identify two different regimes: in the initial phase of SGD, the loss function drives the weights to concentrate around the nearest local minimum. We refer to this phase as the drift regime and we provide quantitative estimates on this concentration phenomenon. Next, we introduce the diffusion regime, where stochastic fluctuations help the learning process to escape suboptimal local minima. We analyze the Mean Exit Time (MET) and prove upper and lower bounds of the MET. Finally, we address the asymptotic convergence of SGD, for a non-convex cost function and a degenerate diffusion matrix, that do not allow to use the standard approaches, and require new techniques. For this purpose, we exploit two different methods: duality and entropy methods. We provide new results about the dynamics and effectiveness of SGD, offering a deep connection between stochastic optimization and PDE theory, and some answers and insights to basic questions in the Machine Learning processes: How long does SGD take to escape from a bad minimum? Do neural network parameters converge using SGD? How do parameters evolve in the first stage of training with SGD?

22.
bioRxiv (Bioinfo) 2026-06-17

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

Transfer RNA (tRNA) molecules serve as essential adapters during protein translation. While direct RNA sequencing (DRS) via Oxford Nanopore Technologies has emerged as a powerful platform for systematic tRNAome profiling, we currently lack a simple and robust statistical framework for nanopore tRNA data analyses. Here, we address this gap by developing AMaNITA (Abundance, Modifications, and Nanopore Intensity Toolbox Application), an end-to-end bioinformatic workflow that enables simplified, robust, and scalable analyses of nanopore native tRNA sequencing datasets. AMaNITA streamlines the entire analytical trajectory: from upstream processing (basecalling, mapping, filtering, batch effect correction) to downstream assessment of differential tRNA abundance and modification stoichiometry. The workflow generates an interactive HTML report for data exploration and analysis, allowing the user to download the source data files and resulting plots. AMaNITA can be executed using Singularity from the command line, without requiring installation of dependencies.

23.
arXiv (CS.LG) 2026-06-17

Questioning the Coverage-Length Metric in Conformal Prediction: When Shorter Intervals Are Not Better

arXiv:2601.21455v2 Announce Type: replace-cross Abstract: Conformal prediction(CP) has become a cornerstone of distribution-free uncertainty quantification, conventionally evaluated by its coverage and interval length. This work critically examines the sufficiency of these standard metrics. We demonstrate that the interval length might be deceptively improved through a counter-intuitive approach termed Prejudicial Trick(PT), while the coverage remains valid. Specifically, for any given test sample, PT probabilistically returns an interval, which is either null or constructed using an adjusted confidence level, thereby preserving marginal coverage. While PT potentially yields a deceptively lower interval length, it introduces practical vulnerabilities: the same input can yield completely different prediction intervals across repeated runs of the algorithm. We formally derive the conditions under which PT achieves these misleading improvements and provide extensive empirical evidence across various regression and classification tasks. Furthermore, we introduce a new metric interval stability which helps detect whether a new CP method implicitly improves the length based on such PT-like techniques. Code is available at https://github.com/benben-cd/PT-Conformal-Prediction.

24.
PLOS Computational Biology 2026-06-22

Ten simple rules for making the supplement increase your paper’s impact

作者:

by Volker Grimm, Uta Berger, Stefano Mammola Have you ever lost hours navigating supplementary materials—clicking between the main text and dozens of auxiliary files only to encounter broken links, illegible figures, and undefined variables and acronyms? If so, you’re not alone. What should support scientific communication has instead become an obstacle: supplementary information (SI) increasingly suffers from inconsistent formatting, poor accessibility, and fragmented organization that impedes rather than advances understanding. This is disheartening since the SI, if used effectively, has the power to enhance transparency, credibility, and reproducibility of research. Therefore, we propose 10 simple rules to help authors design SI that genuinely increase the impact of their research. The rules emphasize treating SI with the same care as the main text, using it strategically to support the scientific narrative while preserving clarity and focus. Key recommendations include creating a single, well-structured, self-contained SI master document; ensuring explicit cross-referencing between the main text and SI; making SI machine-readable; and avoiding the misuse of SI as a substitute for proper data repositories. We also highlight the importance of creativity in choosing appropriate formats and strict adherence to journal-specific guidelines. Finally, when available, we advocate the use of standardized templates to improve consistency, readability, and reuse across studies. By following these rules, authors can substantially increase the scientific impact of their work while at the same time contributing to more sustainable research practices.

25.
arXiv (CS.CL) 2026-06-18

PragReST: Self-Reinforcing Counterfactual Reasoning for Pragmatic Language Understanding

Natural language understanding often depends on meanings that are implied rather than explicitly stated, requiring pragmatic reasoning. Despite strong performance on math and logical reasoning, large language models (LLMs) still struggle with making pragmatic inferences, often choosing literal interpretations. To improve LLM pragmatic reasoning, we introduce PragReST, a self-supervised framework that constructs pragmatic QA data, generates counterfactual reasoning traces, and trains models to internalize them through supervised fine-tuning and reinforcement learning, without human-labeled training data or distillation from a stronger teacher. Across four pragmatic benchmarks (PragMega, Ludwig, MetoQA, and AltPrag), PragReST improves over backbone models, task-specific pragmatic tuning baselines, and non-counterfactual variants of the same pipeline. On accuracy-based benchmarks, PragReST improves over the instruct backbone by 5.37 and 5.50% (absolute) for Qwen3-8B and Qwen3-14B, respectively. Our error analysis and ablations underscore the importance of counterfactual reasoning: PragReST primarily reduces errors caused by failures to contrast observed utterances with plausible alternatives, and removing counterfactual reasoning substantially reduces performance. Moreover, our training preserves out-of-domain performance on general-knowledge and mathematical reasoning benchmarks.