News & Research

arXiv:2408.00057v3 Announce Type: replace-cross Abstract: Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in utilizing machine learning and deep learning techniques for unsupervised learning of protein representations. However, these approaches often focus solely on the amino acid sequence of proteins and lack factual knowledge about proteins and their interactions, thus limiting their performance. In this study, we present GOProteinGNN, a novel architecture that enhances protein language models by integrating protein knowledge graph information during the creation of amino acid level representations. Our approach allows for the integration of information at both the individual amino acid level and the entire protein level, enabling a comprehensive and effective learning process through graph-based learnin

arXiv:2605.28124v1 Announce Type: new Abstract: The goal of this work is to reduce the effect of photon noise in dental cone-beam CT reconstruction. We consider an inverse problem formulation and develop a databased prior. To this end, we simulate fan-beam acquisitions and add photon noise to the projection data. The prior is obtained by training a gradient-step denoiser using reconstructed simulated acquisitions. The trained model is integrated into a plug-and-play gradient-step algorithm to reconstruct images from simulated projections. Experiments on synthetic data demonstrate the denoising capabilities of the trained model, while qualitative evaluations on real images showcase the algorithm's performance and generalization ability.

arXiv:2605.28390v1 Announce Type: new Abstract: Test-time skill evolving is regarded as a new paradigm for enhancing deployed agentic systems. Existing works mainly focus on hard-coded skill evolving strategies or parametric learning that rely on expensive parameter updates in the underlying LLMs. In this paper, we demonstrate that test-time refinement of the skill evolving framework itself is necessary for continuous improvement of the agent systems in different downstream scenarios, and lightweight algorithmic adaptation is feasible. Specifically, we propose HiSME, a lightweight hierarchical skill meta-evolving solution that jointly optimizes skills and the skill evolving strategy by learning meta-skills from agents' task execution traces. Experiments on diverse agentic benchmarks show that meta-evolving can produce a higher-quality skill library than pure skill evolving and can derive diverse meta-skills for different scenarios, thereby facilitating future continual experience learn

arXiv:2605.28517v1 Announce Type: cross Abstract: Stochastic gradient descent with momentum (SGDM) is one of the most widely used optimization algorithms in machine learning. While optimization properties of SGDM have been extensively studied in the literature, it remains insufficiently understood whether and when SGDM can generalize well to unseen data. In particular, it has been conjectured that while momentum accelerates training, it may degrade generalization. In this paper, we close this gap by developing a comprehensive generalization analysis of SGDM through the lens of algorithmic stability. More specifically, we introduce a generalized SGDM framework that encompasses both Polyak's and Nesterov's momentum schemes, and establish tight on-average model stability bounds for smooth and convex problems. Notably, the obtained bounds exploit small optimization error bounds along the trajectory, apply to any momentum parameter in the interval $[0, 1)$, and do not require the commonly a

arXiv:2605.27813v1 Announce Type: cross Abstract: Text-to-image diffusion models generate images through an iterative denoising process, so internal neural layers produce trajectories of activations rather than single static representations. Sparse autoencoders (SAEs) have recently been used to decompose diffusion activations into interpretable feature directions, but most approaches analyze activations at individual timesteps or condition on time rather than learning directly from full activation trajectories. In this work, we introduce residualized temporal SAEs for diffusion activation trajectories. We collect activations across denoising time, fit linear predictors between neighboring timesteps, and represent each trajectory using an initial activation together with residual components not explained by these linear dynamics. Training an SAE on this residualized representation encourages sparse latents to capture structure beyond what is linearly predictable. The residualized decode

arXiv:2605.28483v1 Announce Type: new Abstract: Linking learning resources to a structured competency framework is key to enabling competency-based search and curriculum analytics in Learning Management Systems (LMS). However, manual tagging is labor-intensive, and fully automatic methods often lack transparency. In this paper, we present an end-to-end alignment pipeline that uses a large language model (LLM) as a constrained, evidence-producing tagger. LMS resources -both instructional content and assessments -are first segmented into meaningful pedagogical fragments. For each fragment, a small set of candidate competencies is retrieved from structured competency profiles enriched with graph-based context. The LLM then selects the most relevant competencies from this set and provides supporting evidence spans from the fragment text. These predictions are refined using the structure of the competency graph and aggregated at the resource level. We evaluate our approach on a dataset buil

arXiv:2605.28500v1 Announce Type: cross Abstract: Large language models have shown impressive capabilities in code generation, yet they often produce functionally incorrect code. Uncertainty quantification (UQ) methods have emerged as a promising approach for detecting hallucinations in natural language generation, but their effectiveness for code generation tasks remains underexplored. We systematically evaluate how UQ techniques transfer to code generation across three programming languages, five LLMs, and over 1,700 problems. We find that some token-probability-based methods generalize effectively without modification, while sampling-based methods relying on natural language inference (NLI) fail because NLI models cannot distinguish functionally different code, causing most responses to collapse into a single semantic cluster. To address this, we introduce functional equivalence methods, a family of code-specific methods that replace NLI-based semantic equivalence with an LLM-based

arXiv:2605.28164v1 Announce Type: cross Abstract: Evolutionary computation offers a variety of tools to solve complex real-world optimization problems. However, research often focuses on smaller, simplified problems and optimization algorithms that sometimes miss expectations in real-world scenarios. Additionally, trust in the applied algorithm and the solutions it provides is often essential in such settings, but requires an understanding of the search process itself. This leads to evolutionary computation often not being seriously considered by practitioners in many application contexts, among them physics-based modeling. In this article, techniques from evolutionary computation are detailed that can alleviate these problems. First, five real-world physics-based optimization problems are introduced and described by domain experts. For each of these, the requirements for the evolutionary algorithm regarding performance and explainability to increase trust and usability are presented.

arXiv:2605.16578v3 Announce Type: replace-cross Abstract: Artificially generated speech is increasingly embedded in everyday life. Voice cloning in particular enables applications where identity preservation is important, such as completing a recording, dubbing in a new language, or preserving the voices of individuals with speech loss. However, in our work, we find that despite the term, voice cloning does not faithfully ''clone'' an individual's voice. Instead, we find that widely-used voice cloning models systematically apply style transfer to source voices. As rated by human annotators, cloned voices are perceived as more authoritative, warm, customer-service-like, and human-like compared to their sources. Human annotators also report greater trust in cloned voices than source voices, and a greater willingness to disclose sensitive personal information to them. Our work furthermore shows that voice cloning leads to homogenization of speaker characteristics, as measured by reduced v

arXiv:2605.28418v1 Announce Type: new Abstract: With the rise of tabular foundation models alongside traditional models still performing well on many tasks, choosing the right model for a tabular dataset remains difficult. We investigate whether dataset meta-features can explain performance gaps between model families on tabular prediction tasks. Using the TabArena benchmark results, we analyze dataset-level performance gaps and relate them to model-agnostic dataset descriptors. After strict statistical tests with false discovery control, we find that (1) for neural network vs. tree gaps, no meta-feature survives false discovery control, (2) for non-foundation vs. foundation model gaps, one association is robust but does not generalize when tested in leave-one-dataset-out prediction, and (3) for TabICLv2 vs. TabPFN-2.6, one robust association also improves held-out prediction. Furthermore, we conduct a leave-one-dataset-out analysis and find that meta-feature predictors fail to improve

arXiv:2605.27700v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used to generate scientific reports, but they can produce references that appear plausible while containing corrupted metadata or pointing to papers that do not exist. We introduce CiteCheck, a hybrid framework for citation hallucination detection that verifies whether a citation corresponds to a real scholarly work and whether its metadata is faithful to that work. CiteCheck retrieves candidate publications from external scholarly sources, compares the citation against the retrieved candidate using a structured LLM verifier, and maps verifier scores into three labels: Exact, Minor, and Major. We also construct a 982-citation physics benchmark with controlled corruptions that capture both subtle metadata drift and fully fabricated references. On the held-out test set, CiteCheck achieves 88.7 macro-F1 and 88.9% accuracy, outperforming GPT, Claude, and Gemini baselines, including web-search an

arXiv:2605.28044v1 Announce Type: new Abstract: Cited RAG evaluation often treats visible sources as a grounding signal, but a real, topically relevant citation can still under-warrant the attached wording. We study this diagnostic failure as citation laundering: a related source is presented as warrant for an over-strong claim. We introduce FORCEBENCH, a contrastive stress test for evidence-force calibration. Each item holds a cited passage fixed and pairs an evidence-calibrated claim with a localized force-raised variant across five operational axes: relation, modality, scope, temporal validity, and numeric specificity. A calibrated evaluator should score the evidence-calibrated claim higher. Headline experiments use a fixed, locality-filtered 198-pair evaluation set. A citation-presence sanity check is uninformative by design; token and entity overlap still violate monotonicity on 32.8--36.4% of pairs. Across four reported model judges, standard generic support prompting is insuffic

arXiv:2605.10583v2 Announce Type: replace Abstract: Despite extensive research on computed tomography (CT) denoising, few studies exploit projection-domain data characteristics to mitigate noise correlation. To bridge this gap, this work proposes FrequencyCT, the first zero-shot self-supervised method for pseudo-sample generation in the frequency domain for low-dose CT denoising. Specifically, by exploiting the distinct frequency-domain distributions of noise and true signal, a regional low-frequency anchoring technique is proposed. Applying phase-preserving noise and mask perturbations to the high-frequency region generates pseudo-samples for self-supervision. Driven by the exponential correlation between noise variance of noisy projections and the underlying true signal, consistent data truncation is applied to the generated samples to stabilize optimization gradients. Evaluation results on multiple public and real datasets confirm the clinical application potential of this research,

arXiv:2605.28683v1 Announce Type: new Abstract: Existing benchmarks have laid the foundation for travel planning agents by establishing API-centric paradigms. However, as the capabilities of Autonomous Agents continue to advance, their evaluation must evolve beyond simple tool execution toward handling the inherent complexities of the open web. Current benchmarks bypass core cognitive hurdles: they fail to account for information noise, ignore multi-source factual contradictions, and overlook the necessity of grounding visual perception into logical planning. We introduce VeriTrip, a verifiable benchmark designed to meet the increasing demands for agent robustness and reliability. VeriTrip shifts the evaluation focus to evidence-grounded reasoning over unstructured multimodal web corpora. It establishes a Multimodal Retrieval Base (MRB) derived from real-world sources, forcing agents to autonomously orchestrate queries across heterogeneous data. A synchronized Verifiable Knowledge Base

arXiv:2605.28565v1 Announce Type: cross Abstract: Users of search-augmented LLMs rely on citations as evidence that responses are grounded in real sources, and rarely verify the cited pages themselves. Millions of queries per day now pass through these systems, making citation quality a silent determinant of whether users are informed or misled-yet existing benchmarks each address one facet in isolation, leaving the joint structure that determines citation trustworthiness unmeasured. We construct CITETRACE, a large-scale dataset that traces the full citation chain from user query through retrieved source to generated answer: 11,200 real-world queries from 28 communities paired with 112,000 responses from ten models across five providers, yielding 761,495 evaluable citation pairs. We design a three-dimension evaluation framework that scores each citation on intent-purpose alignment, source suitability, and answer-source fidelity, using expert-validated predefined matrices and a five-lev