arXiv subjects

Liangyu Li

Publications and source records attributed to Liangyu Li.

11 recordsLinked to original sources

arXiv2026

Motif-Vocab: StatisticallyCalibrated Transcription-Factor-Identity Tokenization forGenomic Language Models

Tokenization is a central design choice in genomic language models, yet most deoxyribonucleic acid (DNA) tokenizers use characters, fixed-length k-mers, or frequency-derived subwords without explicitly using prior information about the specificity of DNA-binding regulatory factors. We introduce Motif-Vocab, a biologically informed tokenizer that scans both DNA strands for statistically calibrated motif matches, emits transcription-factor (TF) identity tokens, and applies nucleotide, $k$-mer, or byte-pair encoding (BPE) to unmatched sequence. Motif-specific null distributions put position-weight matrices (PWMs) of different lengths and degeneracy on a common significance scale; deterministic overlap rules make the representation reproducible. In controlled Bidirectional Encoder Representations from Transformers (BERT) pretraining on two billion base pairs, real motif libraries outperform randomized-motif controls on 54 of 55 in-scope downstream tasks. On a motif-disjoint recognition task derived from DART-Eval Task 2, TF-specific tokens improve macro-F1 by 0.040 over a position-matched generic motif token and by 0.033 over a matched no-motif tokenizer (95\% bootstrap confidence interval: 0.027--0.038). Motif tokens also receive stronger attribution and produce larger occlusion effects than shuffled controls. Dense no-motif tokenizers remain strong general-purpose baselines, including a near-tie on the five-task BERT-base panel. Thus, Motif-Vocab is not a universal accuracy replacement; it is a targeted, interpretable inductive bias for motif-sensitive genomic modeling.

q-bio.GN↗

arXiv2026

World Model Control by Trajectory Reachability Metrics

Latent world models can learn representations that contain information needed for control, while the downstream controller may still rank candidate actions poorly when it relies on terminal latent distance alone. We study this failure in a fixed encoder and introduce trajectory reachability metrics (TRM), a small temporal pairwise cost trained from logged trajectories and used to rank predicted endpoints of a candidate action sequence against a goal. In the TwoRoom evaluation on 100 episodes from a high distance range, the original controller with LeWorldModel reaches 7.0% mean success. Temporal TRM trained after excluding all evaluation episodes reaches 96.7%, shuffled label controls stay at 0.0%, and TRM also improves PLDM from 32.7% to 84.0%. TopoNav, a separate pixel navigation task, shows the same link between repaired ranking and closed loop control. The selection audit with shared candidates (SASC) and rowspace interventions show that the gain comes from reweighting latent directions carrying the action decision. The XY rowspace contributes less than 1% of terminal latent MSE but carries most of the information needed for control. Coverage and boundary tests define the scope. Balanced doorway coverage restores a 0.0% coverage failure to 100.0% success, while an unseen wall orientation and contact rich PushT expose layout, dynamics, and recovery limits.

cs.LG↗

arXiv2026

Action from Adjacent Set in Physical Space Outperforms the Best Prediction in World Models

Controllers based on sampling and latent world models assign a predicted terminal cost to each candidate action sequence, choose the minimum, execute its first action block, and replan. This rule can fail even when the terminal cost perfectly and accurately reflects the true task objective in the physical world. Residual prediction error can give an infeasible sequence an anomalously low cost, and a larger proposal pool gives such errors more chances to outrank feasible alternatives. We call this conditional failure proposal overgeneration. In Cube candidate execution audits, increasing the total proposal budget from 72 to 288 reduces the feasibility of selection by minimum latent cost from .375 to .062 for position targets and from .344 to .031 for targets defined by position and yaw, although every larger pool contains a feasible sequence. We introduce Adjacent Set Action Reconstruction (ASAR). Among proposals with low cost, ASAR identifies an adjacent set using standardized early action prefixes and reconstructs a full action sequence through locally weighted aggregation with a light anchor from the sequence with minimum cost. On a Carry and Release evaluation set of 75 queries, Kernel ASAR improves event completion success over matching selection by 28.0, 24.0, and 18.7 percentage points under latent cost and by 18.7, 20.0, and 17.3 points under a trajectory reachability cost at 72, 144, and 288 proposals. Analysis of finite proposal pools characterizes selection risk from the lower tail, separation by a related radius support statistic, and sequence containment under an explicit local feasibility condition.

cs.RO↗

arXiv2026

AutoRefine: Compiling Trajectories into Validated Typed Agent Artifacts

Large language model agents repeatedly encounter related tasks, yet systems that learn from trajectories commit every lesson to one predefined artifact form. A local constraint, a reusable procedure, and a delegated objective require different amounts of runtime ownership, so one form either under-specifies the correction or wraps it in execution machinery it does not need. We present AutoRefine, which treats trajectory learning as typed artifact compilation. It contrasts failed against successful trajectories to derive a type-neutral, evidence-linked intervention specification, then compiles that specification into the first Rule, Skill, or bounded Subagent that closes it under a runtime-relative ownership order: the selected schema must own every specified observation, state variable, dependent decision, and completion condition. Validation is stated in the same terms: a type-specific contract gate tests whether the generated object realizes its declared boundary, and a replay gate admits it only when it improves the correction cases linked to its source failures without regression on preservation cases. With GPT-5.6-terra as the shared backbone, AutoRefine records the highest success on ALFWorld, ScienceWorld, TravelPlanner, and SpreadsheetBench, and ties the best result on SkillCraft; on TravelPlanner it reaches 80.56% success against 50.0% for the strongest baseline. Removing boundary closure or replay validation costs 15.00 and 16.11 percentage points, the two largest losses among our construction and admission policies. In a longitudinal TravelPlanner stream, the repository holds 89--91% held-out success after 60 learning tasks with no net loss on previously solved tasks, and frozen repositories improve all 25 evaluated source--target pairs, more within a domain (14.20 points on average) than across domains (6.99).

cs.AI↗

arXiv2026

Revisiting Cross-Attention Mechanisms: Leveraging Beneficial Noise for Domain-Adaptive Learning

Unsupervised Domain Adaptation (UDA) seeks to transfer knowledge from a labeled source domain to an unlabeled target domain but often suffers from severe domain and scale gaps that degrade performance. Existing cross-attention-based transformers can align features across domains, yet they struggle to preserve content semantics under large appearance and scale variations. To explicitly address these challenges, we introduce the concept of beneficial noise, which regularizes cross-attention by injecting controlled perturbations, encouraging the model to ignore style distractions and focus on content. We propose the Domain-Adaptive Cross-Scale Matching (DACSM) framework, which consists of a Domain-Adaptive Transformer (DAT) for disentangling domain-shared content from domain-specific style, and a Cross-Scale Matching (CSM) module that adaptively aligns features across multiple resolutions. DAT incorporates beneficial noise into cross-attention, enabling progressive domain translation with enhanced robustness, yielding content-consistent and style-invariant representations. Meanwhile, CSM ensures semantic consistency under scale changes. Extensive experiments on VisDA-2017, Office-Home, and DomainNet demonstrate that DACSM achieves state-of-the-art performance, with up to +2.3% improvement over CDTrans on VisDA-2017. Notably, DACSM achieves a +5.9% gain on the challenging "truck" class of VisDA, evidencing the strength of beneficial noise in handling scale discrepancies. These results highlight the effectiveness of combining domain translation, beneficial-noise-enhanced attention, and scale-aware alignment for robust cross-domain representation learning.

cs.CV↗

arXiv2026

A Deep-Learning-Boosted Framework for Quantum Sensing with Nitrogen-Vacancy Centers in Diamond

Nitrogen-vacancy (NV) centers in diamond are a versatile quantum sensing platform for high sensitivity measurements of magnetic fields, temperature and strain with nanoscale spatial resolution. A common bottleneck is the analysis of optically detected magnetic resonance (ODMR) spectra, where target quantities are encoded in resonance features. Conventional nonlinear fitting is often computationally expensive, sensitive to initialization, and prone to failure at low signal-to-noise ratio (SNR). Here we introduce a robust, efficient machine learning (ML) framework for real-time ODMR analysis based on a one-dimensional convolutional neural network (1D-CNN). The model performs direct parameter inference without initial guesses or iterative optimization, and is naturally parallelizable on graphics processing units (GPU) for high-throughput processing. We validate the approach on both synthetic and experimental datasets, showing improved throughput, accuracy and robustness than standard nonlinear fitting, with the largest gains in the low-SNR regime. We further validate our methods in two representative sensing applications: diagnosing intracellular temperature changes using nanodiamond probes and widefield magnetic imaging of superconducting vortices in a high-temperature superconductor. This deep-learning inference framework enables fast and reliable extraction of physical parameters from complex ODMR data and provides a scalable route to real-time quantum sensing and imaging.

quant-ph↗

arXiv2025

PCaM: A Progressive Focus Attention-Based Information Fusion Method for Improving Vision Transformer Domain Adaptation

Unsupervised Domain Adaptation (UDA) aims to transfer knowledge from a labeled source domain to an unlabeled target domain. Recent UDA methods based on Vision Transformers (ViTs) have achieved strong performance through attention-based feature alignment. However, we identify a key limitation: foreground object mismatch, where the discrepancy in foreground object size and spatial distribution across domains weakens attention consistency and hampers effective domain alignment. To address this issue, we propose the Progressive Focus Cross-Attention Mechanism (PCaM), which progressively filters out background information during cross-attention, allowing the model to focus on and fuse discriminative foreground semantics across domains. We further introduce an attentional guidance loss that explicitly directs attention toward task-relevant regions, enhancing cross-domain attention consistency. PCaM is lightweight, architecture-agnostic, and easy to integrate into existing ViT-based UDA pipelines. Extensive experiments on Office-Home, DomainNet, VisDA-2017, and remote sensing datasets demonstrate that PCaM significantly improves adaptation performance and achieves new state-of-the-art results, validating the effectiveness of attention-guided foreground fusion for domain adaptation.

cs.LG↗

arXiv2024

Must: Maximizing Latent Capacity of Spatial Transcriptomics Data

Spatial transcriptomics (ST) technologies have revolutionized the study of gene expression patterns in tissues by providing multimodality data in transcriptomic, spatial, and morphological, offering opportunities for understanding tissue biology beyond transcriptomics. However, we identify the modality bias phenomenon in ST data species, i.e., the inconsistent contribution of different modalities to the labels leads to a tendency for the analysis methods to retain the information of the dominant modality. How to mitigate the adverse effects of modality bias to satisfy various downstream tasks remains a fundamental challenge. This paper introduces Multiple-modality Structure Transformation, named MuST, a novel methodology to tackle the challenge. MuST integrates the multi-modality information contained in the ST data effectively into a uniform latent space to provide a foundation for all the downstream tasks. It learns intrinsic local structures by topology discovery strategy and topology fusion loss function to solve the inconsistencies among different modalities. Thus, these topology-based and deep learning techniques provide a solid foundation for a variety of analytical tasks while coordinating different modalities. The effectiveness of MuST is assessed by performance metrics and biological significance. The results show that it outperforms existing state-of-the-art methods with clear advantages in the precision of identifying and preserving structures of tissues and biomarkers. MuST offers a versatile toolkit for the intricate analysis of complex biological systems.

cs.CE↗

arXiv2023

Decoding the Mechanisms of Reversibility Loss in Rechargeable Zinc-Air Batteries

Attaining high reversibility of electrodes and electrolyte is essential for the longevity of secondary batteries. Rechargeable zinc-air batteries (RZABs), however, encounter drastic irreversible changes in the zinc anodes and air cathodes during cycling. To uncover the mechanisms of reversibility loss in RZABs, we investigate the evolution of zinc anode, alkaline electrolyte, and air electrode through experiments and first-principles calculations. Morphology diagrams of zinc anodes under versatile operating conditions reveal that the nano-sized mossy zinc dominates the later cycling stage. Such anodic change is induced by the increased zincate concentration due to hydrogen evolution, which is catalyzed by the mossy structure and results in oxide passivation on electrodes, and eventually leads to low true Coulombic efficiencies and short lifespans of batteries. Inspired by these findings, we finally present a novel overcharge-cycling protocol to compensate the Coulombic efficiency loss caused by hydrogen evolution and significantly extend the battery life.

cond-mat.mtrl-sci↗

arXiv2023

Pressure-induced superconductivity in quasi-one-dimensional semimetal $\mathrm{Ta}_2 \mathrm{PdSe}_6$

Here we report the discovery of pressure-induced superconductivity in quasi-one-dimensional $\mathrm{Ta}_2 \mathrm{PdSe}_6$, through a combination of electrical transport, synchrotron x-ray diffraction, and theoretical calculations. Our transport measurements show that the superconductivity appears at a critical pressure $P_{\mathrm{c}} \sim 18.3$ GPa and is robust upon further compression up to $62.6$ GPa. The estimated upper critical field $μ_0 H_{\mathrm{c} 2}(0)$ in the pressurized $\mathrm{Ta}_2 \mathrm{PdSe}_6$ is much lower than the Pauli limiting field, in contrast to the case in its isostructural analogs $M_2 \mathrm{Pd}_{\mathrm{x}} X_5$ $(M=\mathrm{Nb}$, Ta; $X=\mathrm{S}, \mathrm{Se})$. Concomitant with the occurrence of superconductivity, anomalies in pressuredependent transport properties are observed, including sign reversal of Hall coefficient, abnormally enhanced resistance, and dramatically suppressed magnetoresistance. Meanwhile, room-temperature synchrotron x-ray diffraction experiments reveal the stability of the pristine monoclinic structure (space group $C 2 / m$ ) upon compression. Combined with the density functional theory calculations, we argue that a pressure-induced Lifshitz transition could be the electronic origin of the emergent superconductivity in $\mathrm{Ta}_2 \mathrm{PdSe}_6$.

cond-mat.supr-con↗

arXiv2022

EVNet: An Explainable Deep Network for Dimension Reduction

Dimension reduction (DR) is commonly utilized to capture the intrinsic structure and transform high-dimensional data into low-dimensional space while retaining meaningful properties of the original data. It is used in various applications, such as image recognition, single-cell sequencing analysis, and biomarker discovery. However, contemporary parametric-free and parametric DR techniques suffer from several significant shortcomings, such as the inability to preserve global and local features and the pool generalization performance. On the other hand, regarding explainability, it is crucial to comprehend the embedding process, especially the contribution of each part to the embedding process, while understanding how each feature affects the embedding results that identify critical components and help diagnose the embedding process. To address these problems, we have developed a deep neural network method called EVNet, which provides not only excellent performance in structural maintainability but also explainability to the DR therein. EVNet starts with data augmentation and a manifold-based loss function to improve embedding performance. The explanation is based on saliency maps and aims to examine the trained EVNet parameters and contributions of components during the embedding process. The proposed techniques are integrated with a visual interface to help the user to adjust EVNet to achieve better DR performance and explainability. The interactive visual interface makes it easier to illustrate the data features, compare different DR techniques, and investigate DR. An in-depth experimental comparison shows that EVNet consistently outperforms the state-of-the-art methods in both performance measures and explainability.

cs.LG↗