arXiv subjects

Lei Xu

Publications and source records attributed to Lei Xu.

At least 91 records · Page 5Linked to original sources

arXiv2025

Generative design and validation of therapeutic peptides for glioblastoma based on a potential target ATP5A

Glioblastoma (GBM) remains the most aggressive tumor, urgently requiring novel therapeutic strategies. Here, we present a dry-to-wet framework combining generative modeling and experimental validation to optimize peptides targeting ATP5A, a potential peptide-binding protein for GBM. Our framework introduces the first lead-conditioned generative model, which focuses exploration on geometrically relevant regions around lead peptides and mitigates the combinatorial complexity of de novo methods. Specifically, we propose POTFlow, a \underline{P}rior and \underline{O}ptimal \underline{T}ransport-based \underline{Flow}-matching model for peptide optimization. POTFlow employs secondary structure information (e.g., helix, sheet, loop) as geometric constraints, which are further refined by optimal transport to produce shorter flow paths. With this design, our method achieves state-of-the-art performance compared with five popular approaches. When applied to GBM, our method generates peptides that selectively inhibit cell viability and significantly prolong survival in a patient-derived xenograft (PDX) model. As the first lead peptide-conditioned flow matching model, POTFlow holds strong potential as a generalizable framework for therapeutic peptide design.

q-bio.BM↗

arXiv2025

Communication-Efficient Distributed Online Nonconvex Optimization with Time-Varying Constraints

This paper considers distributed online nonconvex optimization with time-varying inequality constraints over a network of agents, where the nonconvex local loss and convex local constraint functions can vary arbitrarily across iterations. For a time-varying directed graph, we propose two distributed bandit online primal--dual algorithm with compressed communication to efficiently utilize communication resources in the one-point and two-point bandit feedback settings, respectively. To measure the performance of the proposed algorithms, we use a network regret metric grounded in the first-order optimality condition associated with the variational inequality. We show that the compressed algorithms establish sublinear network regret and cumulative constraint violation bounds. Moreover, the network cumulative constraint violation bounds are reduced under Slater's condition. Finally, a simulation example is presented to validate the theoretical results.

math.OC↗

arXiv2025

QuCoWE Quantum Contrastive Word Embeddings with Variational Circuits for NearTerm Quantum Devices

We present QuCoWE a framework that learns quantumnative word embeddings by training shallow hardwareefficient parameterized quantum circuits PQCs with a contrastive skipgram objective Words are encoded by datareuploading circuits with controlled ring entanglement similarity is computed via quantum state fidelity and passed through a logitfidelity head that aligns scores with the shiftedPMI scale of SGNSNoiseContrastive Estimation To maintain trainability we introduce an entanglementbudget regularizer based on singlequbit purity that mitigates barren plateaus On Text8 and WikiText2 QuCoWE attains competitive intrinsic WordSim353 SimLex999 and extrinsic SST2 TREC6 performance versus 50100d classical baselines while using fewer learned parameters per token All experiments are run in classical simulation we analyze depolarizingreadout noise and include errormitigation hooks zeronoise extrapolation randomized compiling to facilitate hardware deployment

quant-ph↗

arXiv2025

HPCAgentTester: A Multi-Agent LLM Approach for Enhanced HPC Unit Test Generation

Unit testing in High-Performance Computing (HPC) is critical but challenged by parallelism, complex algorithms, and diverse hardware. Traditional methods often fail to address non-deterministic behavior and synchronization issues in HPC applications. This paper introduces HPCAgentTester, a novel multi-agent Large Language Model (LLM) framework designed to automate and enhance unit test generation for HPC software utilizing OpenMP and MPI. HPCAgentTester employs a unique collaborative workflow where specialized LLM agents (Recipe Agent and Test Agent) iteratively generate and refine test cases through a critique loop. This architecture enables the generation of context-aware unit tests that specifically target parallel execution constructs, complex communication patterns, and hierarchical parallelism. We demonstrate HPCAgentTester's ability to produce compilable and functionally correct tests for OpenMP and MPI primitives, effectively identifying subtle bugs that are often missed by conventional techniques. Our evaluation shows that HPCAgentTester significantly improves test compilation rates and correctness compared to standalone LLMs, offering a more robust and scalable solution for ensuring the reliability of parallel software systems.

cs.DC↗

arXiv2025

Every Activation Boosted: Scaling General Reasoner to 1 Trillion Open Language Foundation

We introduce Ling 2.0, a series reasoning-oriented language foundation built upon the principle that every activation boosts reasoning capability. Designed to scale from tens of billions to one trillion parameters under a unified Mixture-of-Experts (MoE) paradigm, Ling 2.0 emphasizes high sparsity, cross-scale consistency, and efficiency guided by empirical scaling laws. The series includes three non-thinking (instruct) models - Ling-mini-2.0, Ling-flash-2.0, and Ling-1T - ranging from 16B to 1T total parameters and achieving up to 7-fold active-compute efficiency compared with dense counterparts. Ling 2.0 integrates coordinated innovations across model architecture, pre-training, post-training, and infrastructure: a high-sparsity MoE with MTP for efficient reasoning, reasoning-oriented data and mid-training CoT activation, reinforcement-based fine-tuning (DFT, Evo-CoT), and full-scale FP8 training with fine-grained heterogeneous pipelines. At the trillion scale, Ling-1T establishes a new Pareto frontier of reasoning accuracy versus computational efficiency, demonstrating that sparse activation, when properly aligned with reasoning objectives, enables scalable and efficient intelligence. Collectively, Ling 2.0 provides a coherent, open, and efficient foundation for advancing future reasoning and thinking models, including the Ring series built upon the same base.

cs.CL↗

arXiv2025

Text to Sketch Generation with Multi-Styles

Recent advances in vision-language models have facilitated progress in sketch generation. However, existing specialized methods primarily focus on generic synthesis and lack mechanisms for precise control over sketch styles. In this work, we propose a training-free framework based on diffusion models that enables explicit style guidance via textual prompts and referenced style sketches. Unlike previous style transfer methods that overwrite key and value matrices in self-attention, we incorporate the reference features as auxiliary information with linear smoothing and leverage a style-content guidance mechanism. This design effectively reduces content leakage from reference sketches and enhances synthesis quality, especially in cases with low structural similarity between reference and target sketches. Furthermore, we extend our framework to support controllable multi-style generation by integrating features from multiple reference sketches, coordinated via a joint AdaIN module. Extensive experiments demonstrate that our approach achieves high-quality sketch generation with accurate style alignment and improved flexibility in style control. The official implementation of M3S is available at https://github.com/CMACH508/M3S.

cs.CV↗

arXiv2025

Prior-Guided Flow Matching for Target-Aware Molecule Design with Learnable Atom Number

Structure-based drug design (SBDD), aiming to generate 3D molecules with high binding affinity toward target proteins, is a vital approach in novel drug discovery. Although recent generative models have shown great potential, they suffer from unstable probability dynamics and mismatch between generated molecule size and the protein pockets geometry, resulting in inconsistent quality and off-target effects. We propose PAFlow, a novel target-aware molecular generation model featuring prior interaction guidance and a learnable atom number predictor. PAFlow adopts the efficient flow matching framework to model the generation process and constructs a new form of conditional flow matching for discrete atom types. A protein-ligand interaction predictor is incorporated to guide the vector field toward higher-affinity regions during generation, while an atom number predictor based on protein pocket information is designed to better align generated molecule size with target geometry. Extensive experiments on the CrossDocked2020 benchmark show that PAFlow achieves a new state-of-the-art in binding affinity (up to -8.31 Avg. Vina Score), simultaneously maintains favorable molecular properties.

cs.LG↗

arXiv2025

Intrinsic Non-linearity of Josephson Junctions as an Alternative Origin of the Missing First Shapiro Step

The missing first Shapiro step in microwave-irradiated Josephson junctions has been widely interpreted as a hallmark of Majorana bound states. However, conventional mechanisms like junction underdamping or Joule heating can produce similar signatures. Here, we demonstrate that the intrinsic non-linear current-voltage characteristic of low-to-moderate transparency junctions can also suppress the first step, accompanied by distinctive zigzag boundaries between the zeroth and first step at intermediate driving frequencies. Microwave measurements on Al/WTe2 junctions and numerical simulations of a non-linear resistively and capacitively shunted junction model reveal the first step collapse induced by switching jumps of current, together with zigzag features absent in scenarios solely driven by finite \b{eta} or Joule heating. This zigzag signature therefore provides a crucial diagnostic tool, emphasizing the necessity of comprehensive analysis of microwave spectra before attributing the absence of the first Shapiro step to Majorana physics.

cond-mat.mes-hall↗

arXiv2025

Hybrid Quantum-Classical Eigensolver with Real-Space Sampling and Symmetric Subspace Measurements

We propose a hybrid quantum-classical eigensolver to address the computational challenges of simulating strongly correlated quantum many-body systems, where the exponential growth of the Hilbert space and extensive entanglement render classical methods intractable. Our approach combines real-space sampling of tensor-network-bridged quantum circuits with symmetric subspace measurements, effectively constraining the wavefunction within a substaintially reduced Hilbert space for efficient and scalable simulations of versatile target states. The system is partitioned into equal-sized subsystems, where quantum circuits capture local entanglement and tensor networks reconnect them to recover global correlations, thereby overcoming partition-induced limitations. Symmetric subspace measurements exploit point-group symmetries through a many-to-one mapping that aggregates equivalent real-space configurations into a single symmetric state, effectively enhancing real-space bipartition entanglement while elimilating redundant degrees of freedom. The tensor network further extends this connectivity across circuits, restoring global entanglement and correlation, while simultaneously enabling generative sampling for efficient optimization. As a proof of concept, we apply the method to the periodic $J_1\!-\!J_2$ antiferromagnetic Heisenberg model in one and two dimensions, incorporating translation, reflection, and inversion symmetries. With a small matrix product state bond dimension of up to 6, the method achieves an absolute energy error of $10^{-5}$ for a 64-site periodic chain and a $6\times6$ torus after bond-dimension extrapolation. These results validate the accuracy and efficiency of the hybrid eigensolver and demonstrate its strong potential for scalable quantum simulations of strongly correlated systems.

quant-ph↗

arXiv2025

Dual Data Alignment Makes AI-Generated Image Detector Easier Generalizable

Existing detectors are often trained on biased datasets, leading to the possibility of overfitting on non-causal image attributes that are spuriously correlated with real/synthetic labels. While these biased features enhance performance on the training data, they result in substantial performance degradation when applied to unbiased datasets. One common solution is to perform dataset alignment through generative reconstruction, matching the semantic content between real and synthetic images. However, we revisit this approach and show that pixel-level alignment alone is insufficient. The reconstructed images still suffer from frequency-level misalignment, which can perpetuate spurious correlations. To illustrate, we observe that reconstruction models tend to restore the high-frequency details lost in real images (possibly due to JPEG compression), inadvertently creating a frequency-level misalignment, where synthetic images appear to have richer high-frequency content than real ones. This misalignment leads to models associating high-frequency features with synthetic labels, further reinforcing biased cues. To resolve this, we propose Dual Data Alignment (DDA), which aligns both the pixel and frequency domains. Moreover, we introduce two new test sets: DDA-COCO, containing DDA-aligned synthetic images for testing detector performance on the most aligned dataset, and EvalGEN, featuring the latest generative models for assessing detectors under new generative architectures such as visual auto-regressive generators. Finally, our extensive evaluations demonstrate that a detector trained exclusively on DDA-aligned MSCOCO could improve across 8 diverse benchmarks by a non-trivial margin, showing a +7.2% on in-the-wild benchmarks, highlighting the improved generalizability of unbiased detectors. Our code is available at: https://github.com/roy-ch/Dual-Data-Alignment.

cs.CV↗

arXiv2025

Expertise need not monopolize: Action-Specialized Mixture of Experts for Vision-Language-Action Learning

Vision-Language-Action (VLA) models are experiencing rapid development and demonstrating promising capabilities in robotic manipulation tasks. However, scaling up VLA models presents several critical challenges: (1) Training new VLA models from scratch demands substantial computational resources and extensive datasets. Given the current scarcity of robot data, it becomes particularly valuable to fully leverage well-pretrained VLA model weights during the scaling process. (2) Real-time control requires carefully balancing model capacity with computational efficiency. To address these challenges, We propose AdaMoE, a Mixture-of-Experts (MoE) architecture that inherits pretrained weights from dense VLA models, and scales up the action expert by substituting the feedforward layers into sparsely activated MoE layers. AdaMoE employs a decoupling technique that decouples expert selection from expert weighting through an independent scale adapter working alongside the traditional router. This enables experts to be selected based on task relevance while contributing with independently controlled weights, allowing collaborative expert utilization rather than winner-takes-all dynamics. Our approach demonstrates that expertise need not monopolize. Instead, through collaborative expert utilization, we can achieve superior performance while maintaining computational efficiency. AdaMoE consistently outperforms the baseline model across key benchmarks, delivering performance gains of 1.8% on LIBERO and 9.3% on RoboTwin. Most importantly, a substantial 21.5% improvement in real-world experiments validates its practical effectiveness for robotic manipulation tasks.

cs.RO↗

arXiv2025

Intelligent4DSE: Optimizing High-Level Synthesis Design Space Exploration with Graph Neural Networks and Large Language Models

High-Level Synthesis (HLS) Design Space Exploration (DSE) is essential for generating hardware designs that balance performance, power, and area (PPA). To optimize this process, existing works often employs message-passing neural networks (MPNNs) to predict quality of results (QoR). These predictors serve as evaluators in the DSE process, effectively bypassing the time-consuming estimations traditionally required by HLS tools. However, existing models based on MPNNs struggle with over-smoothing and limited expressiveness. Additionally, while meta-heuristic algorithms are widely used in DSE, they typically require extensive domain-specific knowledge to design operators and time-consuming tuning. To address these limitations, we propose ECoGNNs-LLMMHs, a framework that integrates graph neural networks with task-adaptive message passing and large language model-enhanced meta-heuristic algorithms. Compared with state-of-the-art works, ECoGNN exhibits lower prediction error in the post-HLS prediction task, with the error reduced by 57.27\%. For post-implementation prediction tasks, ECoGNN demonstrates the lowest prediction errors, with average reductions of 17.6\% for flip-flop (FF) usage, 33.7\% for critical path (CP) delay, 26.3\% for power consumption, 38.3\% for digital signal processor (DSP) utilization, and 40.8\% for BRAM usage. LLMMH variants can generate superior Pareto fronts compared to meta-heuristic algorithms in terms of average distance from the reference set (ADRS) with average improvements of 87.47\%, respectively. Compared with the SOTA DSE approaches GNN-DSE and IRONMAN-PRO, LLMMH can reduce the ADRS by 68.17\% and 63.07\% respectively.

cs.LG↗

arXiv2025

Evaluating the Quality of Randomness and Entropy in Tasks Supported by Large Language Models

The rapid advancement of large language model (LLM) technology has led to diverse applications, many of which inherently require randomness, such as stochastic decision-making, gaming, scheduling, AI agents, and cryptography-related tasks. However, the capabilities of LLMs in handling randomness, particularly in generating and utilizing random numbers effectively, remain unclear. This paper investigates the capacity of LLMs for handling tasks that involve randomness through a series of experiments. We designed a set of experiments that consider various factors that can influence an LLM's performance in tasks involving randomness, such as accessibility to external tools, types of tasks, model states (fresh vs. non-fresh), and prompting strategies. The experiments cover a range of tasks, including generating random numbers, generating random strings such as passwords, shuffling items, and evaluating the quality of randomness using entropy and the NIST randomness test-suite. Our findings reveal that while LLMs can generate outputs that exhibit some degree of randomness, their performance is inconsistent and often deviates significantly from the expected behavior. The analysis of the experimental results highlights key limitations and areas where improvement is needed for the LLMs to effectively handle tasks involving randomness

cs.AI↗

arXiv2025

Adding All Flavors: A Hybrid Random Number Generator for dApps and Web3

Random numbers play a vital role in many decentralized applications (dApps), such as gaming and decentralized finance (DeFi) applications. Existing random number provision mechanisms can be roughly divided into two categories, on-chain, and off-chain. On-chain approaches usually rely on the blockchain as the major input and all computations are done by blockchain nodes. The major risk for this type of method is that the input itself is susceptible to the adversary's influence. Off-chain approaches, as the name suggested, complete the generation without the involvement of blockchain nodes and share the result directly with a dApp. These mechanisms usually have a strong security assumption and high complexity. To mitigate these limitations and provide a framework that allows a dApp to balance different factors involved in random number generation, we propose a hybrid random number generation solution that leverages IoT devices equipped with trusted execution environment (TEE) as the randomness sources, and then utilizes a set of cryptographic tools to aggregate the multiple sources and obtain the final random number that can be consumed by the dApp. The new approach only needs one honest random source to guarantee the unbiasedness of the final random number and a user can configure the system to tolerate malicious participants who can refuse to respond to avoid unfavored results. We also provide a concrete construction that can further reduce the on-chain computation complexity to lower the cost of the solution in practice. We evaluate the computation and gas costs to demonstrate the effectiveness of the improvement.

cs.CR↗

arXiv2025

Possible Observation of Quadrupole Waves in Spin Nematics

Discovery of new states of matter is a key objective in modern condensed matter physics, which often leads to revolutionary technological advancements such as superconductivity. Quantum spin nematic, a ``hidden order'' that evades conventional magnetic probes, is one such state. Na$_2$BaNi(PO$_4$)$_2$ is a potential spin nematic material, suggested by the observation of a two-magnon Bose-Einstein condensation from above the saturation field. However, direct confirmation of the spin nematicity remains elusive. This Letter presents inelastic neutron scattering spectra from the putative spin nematic phases of Na$_2$BaNi(PO$_4$)$_2$, revealing low-energy quadrupole waves that are absent in the neighboring conventional magnetic phases. A spin-one model quantitatively captures the full details of the spin excitation spectra across all low-temperature phases, providing direct evidence of the spin nematic orders. Additionally, we show evidence of the three-magnon continuum and two-magnon bound states in the $1/3$-magnetization plateau, revealing condensation of the two-magnon bound state as the origin of the low-field spin nematic supersolid phase.

cond-mat.str-el↗

arXiv2025

Adaptive LLM-Symbolic Reasoning via Dynamic Logical Solver Composition

Neuro-symbolic NLP methods aim to leverage the complementary strengths of large language models and formal logical solvers. However, current approaches are mostly static in nature, i.e., the integration of a target solver is predetermined at design time, hindering the ability to employ diverse formal inference strategies. To address this, we introduce an adaptive, multi-paradigm, neuro-symbolic inference framework that: (1) automatically identifies formal reasoning strategies from problems expressed in natural language; and (2) dynamically selects and applies specialized formal logical solvers via autoformalization interfaces. Extensive experiments on individual and multi-paradigm reasoning tasks support the following conclusions: LLMs are effective at predicting the necessary formal reasoning strategies with an accuracy above 90 percent. This enables flexible integration with formal logical solvers, resulting in our framework outperforming competing baselines by 27 percent and 6 percent compared to GPT-4o and DeepSeek-V3.1, respectively. Moreover, adaptive reasoning can even positively impact pure LLM methods, yielding gains of 10, 5, and 6 percent on zero-shot, CoT, and symbolic CoT settings with GPT-4o. Finally, although smaller models struggle with adaptive neuro-symbolic reasoning, post-training offers a viable path to improvement. Overall, this work establishes the foundations for adaptive LLM-symbolic reasoning, offering a path forward for unifying material and formal inferences on heterogeneous reasoning challenges.

cs.CL↗

arXiv2025

Distributed Constrained Online Nonconvex Optimization with Compressed Communication

This paper considers distributed online nonconvex optimization with time-varying inequality constraints over a network of agents. For a time-varying graph, we propose a distributed online primal-dual algorithm with compressed communication to efficiently utilize communication resources. We show that the proposed algorithm establishes an $\mathcal{O}( {{T^{\max \{ {1 - {θ_1},{θ_1}} \}}}} )$ network regret bound and an $\mathcal{O}( {T^{1 - {θ_1}/2}} )$ network cumulative constraint violation bound, where $T$ is the number of iterations and ${θ_1} \in ( {0,1} )$ is a user-defined trade-off parameter. When Slater's condition holds (i.e, there is a point that strictly satisfies the inequality constraints at all iterations), the network cumulative constraint violation bound is reduced to $\mathcal{O}( {T^{1 - {θ_1}}} )$. These bounds are comparable to the state-of-the-art results established by existing distributed online algorithms with perfect communication for distributed online convex optimization with (time-varying) inequality constraints. Finally, a simulation example is presented to validate the theoretical results.

math.OC↗

arXiv2025

LGE-Guided Cross-Modality Contrastive Learning for Gadolinium-Free Cardiomyopathy Screening in Cine CMR

Cardiomyopathy, a principal contributor to heart failure and sudden cardiac mortality, demands precise early screening. Cardiac Magnetic Resonance (CMR), recognized as the diagnostic 'gold standard' through multiparametric protocols, holds the potential to serve as an accurate screening tool. However, its reliance on gadolinium contrast and labor-intensive interpretation hinders population-scale deployment. We propose CC-CMR, a Contrastive Learning and Cross-Modal alignment framework for gadolinium-free cardiomyopathy screening using cine CMR sequences. By aligning the latent spaces of cine CMR and Late Gadolinium Enhancement (LGE) sequences, our model encodes fibrosis-specific pathology into cine CMR embeddings. A Feature Interaction Module concurrently optimizes diagnostic precision and cross-modal feature congruence, augmented by an uncertainty-guided adaptive training mechanism that dynamically calibrates task-specific objectives to ensure model generalizability. Evaluated on multi-center data from 231 subjects, CC-CMR achieves accuracy of 0.943 (95% CI: 0.886-0.986), outperforming state-of-the-art cine-CMR-only models by 4.3% while eliminating gadolinium dependency, demonstrating its clinical viability for wide range of populations and healthcare environments.

cs.CV↗