arXiv subjects

Siwei Chen

Publications and source records attributed to Siwei Chen.

At least 19 recordsLinked to original sources

arXiv2026

Multi-mode fiber enabled multi-wavelength optical trapping and dynamic manipulation

Optical fiber tweezers offer distinct advantages for long-distance manipulation, compact integration, and minimally invasive operation in biological environments. However, most optical fiber tweezers rely on single-mode fibers (SMFs), which are constrained by limited optical mode diversity and reduced control flexibility. Although multi-mode fibers (MMFs) support a wider spectrum of propagation modes, their inherent mixed guided modes with low coherence become a long-standing limitation for the design of focused trapping configurations. To address these limitations, we propose and experimentally validate a fully MMF-based optical tweezer system integrated with a micro-lens structure fabricated on the fiber facet, enabling stable optical trapping across multiple wavelengths and dynamic manipulation of trapped cells. Employing 532 nm continuous-wave and 800 nm femtosecond lasers, we demonstrate that both light sources can generate tightly focused optical spots through the micro-lens with a high numerical aperture (NA>0.7), achieving robust trapping and axial dynamic manipulation of cells. Compared with conventional SMF-based tweezers, this approach leverages the broadband and multi-mode properties of MMFs, allows for wavelength-flexible and dynamically adjustable trapping of cells, and paves the way for lab-on-fiber biophotonic platforms with potential applications such as interventional manipulation, cell sorting, and cellular fluorescence analysis.

physics.optics↗

arXiv2026

QLPO: Quadrant-weighted Sampling for Length-aware Policy Optimization

Recent large reasoning models often develop long chain-of-thought responses during reinforcement learning (RL), resulting in high inference latency and deployment cost. Existing methods for response length control typically rely on explicit length penalties or additional control modules, which require careful tuning and may compromise reasoning quality. We propose Quadrant-weighted Sampling for Length-aware Policy Optimization (QLPO), a simple resampling-based variant of GRPO that introduces implicit length control without modifying the reward function. QLPO first over-generates candidate responses and then resamples the training group by preserving the empirical correct/incorrect ratio while favoring short correct responses and long incorrect responses. This reshapes the training distribution and implicitly encourages shorter model outputs. Across models ranging from 1.5B to 32B parameters, including both base models and strong reasoning models, QLPO consistently improves the accuracy-length trade-off. It reduces response length by 30% to 70% while preserving reasoning performance. These results suggest that structured resampling provides an effective and robust approach to efficient reasoning.

cs.AI↗

arXiv2026

Quantum Sampling Architecture for Protein Structure Reconstruction on Utility-Scale Hardware

Predicting the structure of short peptides in protein binding pockets remains difficult because this regime requires physics-based conformational search, yet existing methods do not provide a practical way to carry out that search on current hardware. We present QSAD, a quantum-classical framework that reformulates peptide structure prediction as amino-acid-level Hamiltonian sampling and replaces iterative optimization with non-iterative Hamiltonian evolution. Executed entirely on IBM Heron R2 across 101 binding-pocket peptides (5-18 residues), QSAD improves prediction accuracy by 27-71% over all evaluated AI and quantum baselines while maintaining the lowest variance across tested lengths. QSAD also tolerates noise levels 3-5x beyond typical hardware error rates, where iterative methods fail, and reduces mean quantum execution time by 27x relative to VQE. The sampled ensemble further supports approximate reconstruction of protein energy landscapes. These results establish coarse-grained quantum sampling as a practical computational path for structure prediction in regimes where data-driven methods lack sufficient signal.

cs.ET↗

arXiv2026

DARTS: Distribution-Aware Active Rollout Trajectory Shaping for Accelerating LLM Reinforcement Learning

Reinforcement Learning (RL) has become pivotal for improving model capabilities yet suffers from rollout efficiency bottlenecks due to the long-tail response length distribution. While existing works mitigate the impact of long tails via prompt-level tail scheduling, we focus on the root source of inefficiency: the distribution itself. Specifically, we characterize the long-tail distribution at a finer granularity, identifying intra-prompt long tails, and revealing that they frequently consist of ineffective verbosity. To address this, we propose a novel paradigm of active distribution shaping to shape the rollout distribution towards conciseness and certainty, thereby fundamentally resolving tail-induced overheads. We achieve this through a distribution-aware trajectory sampling mechanism, which selects trajectories from a redundant exploration space for each prompt, and an adaptive redundancy allocation scheme to maximize both shaping effectiveness and system efficiency. Experiments demonstrate significant acceleration over state-of-the-art systems by up to 1.77x without compromising model performance.

cs.LG↗

arXiv2026

From Precise to Random: A Systematic Differential Fault Analysis of the Lightweight Block Cipher Lilliput

At SAC 2013, Berger et al. first proposed the Extended Generalized Feistel Networks (EGFN) structure for the design of block ciphers with efficient diffusion. Later, based on the Type-2 EGFN, they instantiated a new lightweight block cipher named Lilliput (published in IEEE Transactions on Computers, Vol. 65, Issue 7, 2016). According to published cryptanalysis results, Lilliput is sufficiently secure against theoretical attacks such as differential, linear, boomerang, and integral attacks, which rely on the statistical properties of plaintext and ciphertext. However, there is a lack of analysis regarding its resistance to physical attacks in real-world scenarios, such as fault attacks. In this paper, we present the first systematic differential fault analysis (DFA) of Lilliput under three nibble-oriented fault models with progressively relaxed adversarial assumptions to comprehensively assess its fault resilience. In Model I (multi-round fixed-location), precise fault injections at specific rounds recover the master key with a 98% success rate using only 8 faults. Model II (single-round fixed-location) relaxes the multi-round requirement, demonstrating that 8 faults confined to a single round are still sufficient to achieve a 99% success rate by exploiting Lilliput's diffusion properties and DDT-based constraints. Model III (single-round random-location) further weakens the assumption by allowing faults to occur randomly among the eight rightmost branches of round 27. By uniquely identifying the fault location from ciphertext differences with high probability, the attack remains highly feasible, achieving over 99% success with 33 faults and exceeding 99.5% with 36 faults. Our findings reveal a significant vulnerability of Lilliput to practical fault attacks across different adversary capabilities in real-world scenarios, providing crucial insights for its secure implementation.

cs.CR↗

arXiv2026

Purified Two-Relaxation-Time Lattice Boltzmann Method: Removing Ghost Modes from TRT for Enhanced Stability

The two-relaxation-time (TRT) lattice Boltzmann model is widely adopted for its simplicity and tunable boundary accuracy. However, its collision operator relaxes the full symmetric non-equilibrium component, implicitly retaining non-hydrodynamic ghost modes that degrade stability at high Reynolds numbers. In this work, we establish a rigorous connection between ghost-mode filtering and regularization within the TRT framework. By decomposing the discrete velocity space into hydrodynamic and non-hydrodynamic subspaces, we prove that the TRT-regularized lattice Boltzmann (TRT-RLB) model is mathematically equivalent to the standard TRT model with ghost modes explicitly removed. This equivalence holds exactly for D2Q9 and D3Q19 lattices, where the symmetric and antisymmetric subspaces are completely spanned by the physically relevant Hermite modes and identifiable ghost modes. Based on this finding, we propose the Purified TRT (P-TRT) model, which achieves regularization-level stability through simple algebraic ghost-mode subtraction rather than expensive tensor projections. For D2Q9, the non-equilibrium collision cost is reduced from 180 to 52 floating-point operations per node, a 71% reduction. Linear stability analysis in moment space further reveals that the P-TRT operator annihilates the ghost eigenvalue, proving its spectral radius is bounded above by that of standard TRT and that stability is governed exclusively by hydrodynamic modes. Benchmarks including the double shear layer at Re up to 10^7, Taylor--Green vortex decay, force-driven Poiseuille flow, and creeping flow past a square cylinder confirm that P-TRT preserves the stability, second-order accuracy, and zero-slip boundary properties of TRT-RLB while retaining the simplicity of the TRT family.

physics.flu-dyn↗

arXiv2025

Cryptanalysis of Gleeok-128

Gleeok is a family of low latency keyed pseudorandom functions (PRFs) consisting of three parallel SPN based permutations whose outputs are XORed to form the final value. Both Gleeok-128 and Gleeok-256 use a 256 bit key, with block sizes of 128 and 256 bits, respectively. Owing to its multi branch structure, evaluating security margins and mounting effective key recovery attacks present nontrivial challenges. This paper provides the first comprehensive third party cryptanalysis of Gleeok-128. We introduce a two stage MILP based framework for constructing branch wise and full cipher differential linear (DL) distinguishers, together with an integral based key recovery framework tailored to multi branch designs. Our DL analysis yields 7, 7, 8, and 4 round distinguishers for Branch 1, Branch 2, Branch 3, and Gleeok-128, respectively, with squared correlations approximately 2 to the power minus 88.12, 2 to the power minus 88.12, 2 to the power minus 38.73, and 2 to the power minus 49.04, outperforming those in the design document except for the full PRF case. By tightening algebraic degree bounds, we further derive 9, 9, and 7 round integral distinguishers for the three branches and a 7 round distinguisher for the full PRF, extending the designers results by 3, 3, and 2 rounds and by 2 rounds, respectively. These integral properties enable 7 round and 8 round key recovery attacks in the non full codebook and full codebook settings. In addition, we identify a flaw in the original linear security evaluation of Branch 3, showing that it can be distinguished over all 12 rounds with data complexity about 2 to the power 48. We also propose optimized linear layer parameters that significantly improve linear resistance without sacrificing diffusion. Our results advance the understanding of Gleeok-128 and provide general methods for analyzing multi branch symmetric designs.

cs.CR↗

arXiv2025

Enhancing Deep Learning-Based Rotational-XOR Attacks on Lightweight Block Ciphers Simon32/64 and Simeck32/64

At CRYPTO 2019, Gohr pioneered neural cryptanalysis by introducing differential-based neural distinguishers to attack Speck32/64, establishing a novel paradigm combining deep learning with differential cryptanalysis.Since then, constructing neural distinguishers has become a significant approach to achieving the deep learning-based cryptanalysis for block ciphers.This paper advances rotational-XOR (RX) attacks through neural networks, focusing on optimizing distinguishers and presenting key-recovery attacks for the lightweight block ciphers Simon32/64 and Simeck32/64.In particular, we first construct the fundamental data formats specially designed for training RX-neural distinguishers by refining the existing data formats for differential-neural distinguishers. Based on these data formats, we systematically identify optimal RX-differences with Hamming weights 1 and 2 that develop high-accuracy RX-neural distinguishers. Then, through innovative application of the bit sensitivity test, we achieve significant compression of data format without sacrificing the distinguisher accuracy. This optimization enables us to add more multi-ciphertext pairs into the data formats, further strengthening the performance of RX-neural distinguishers. As an application, we obtain 14- and 17-round RX-neural distinguishers for Simon32/64 and Simeck32/64, which improves the previous ones by 3 and 2 rounds, respectively.In addition, we propose two novel techniques, key bit sensitivity test and the joint wrong key response, to tackle the challenge of applying Bayesian's key-recovery strategy to the target cipher that adopts nonlinear key schedule in the related-key setting without considering of weak-key space. By this, we can straightforwardly mount a 17-round key-recovery attack on Simeck32/64 based on the improved 16-round RX-nerual distinguisher. To the best of our knowledge, the presented RX-neural......

cs.CR↗

arXiv2025

A Hybrid Quantum-AI Framework for Protein Structure Prediction on NISQ Devices

Variational quantum algorithms provide a direct, physics-based approach to protein structure prediction, but their accuracy is limited by the coarse resolution of the energy landscapes generated on current noisy devices. We propose a hybrid framework that combines quantum computation with deep learning, formulating structure prediction as a problem of energy fusion. Candidate conformations are obtained through the Variational Quantum Eigensolver (VQE) executed on IBM's 127-qubit superconducting processor, which defines a global yet low-resolution quantum energy surface. To refine these basins, secondary structure probabilities and dihedral angle distributions predicted by the NSP3 neural network are incorporated as statistical potentials. These additional terms sharpen the valleys of the quantum landscape, resulting in a fused energy function that enhances effective resolution and better distinguishes native-like structures. Evaluation on 375 conformations from 75 protein fragments shows consistent improvements over AlphaFold3, ColabFold, and quantum-only predictions, achieving a mean RMSD of 4.9 {\AA} with statistical significance (p < 0.001). The findings demonstrate that energy fusion offers a systematic method for combining data-driven models with quantum algorithms, improving the practical applicability of near-term quantum computing to molecular and structural biology.

cs.ET↗

arXiv2025

Conditionally Whitened Generative Models for Probabilistic Time Series Forecasting

Probabilistic forecasting of multivariate time series is challenging due to non-stationarity, inter-variable dependencies, and distribution shifts. While recent diffusion and flow matching models have shown promise, they often ignore informative priors such as conditional means and covariances. In this work, we propose Conditionally Whitened Generative Models (CW-Gen), a framework that incorporates prior information through conditional whitening. Theoretically, we establish sufficient conditions under which replacing the traditional terminal distribution of diffusion models, namely the standard multivariate normal, with a multivariate normal distribution parameterized by estimators of the conditional mean and covariance improves sample quality. Guided by this analysis, we design a novel Joint Mean-Covariance Estimator (JMCE) that simultaneously learns the conditional mean and sliding-window covariance. Building on JMCE, we introduce Conditionally Whitened Diffusion Models (CW-Diff) and extend them to Conditionally Whitened Flow Matching (CW-Flow). Experiments on five real-world datasets with six state-of-the-art generative models demonstrate that CW-Gen consistently enhances predictive performance, capturing non-stationary dynamics and inter-variable correlations more effectively than prior-free approaches. Empirical results further demonstrate that CW-Gen can effectively mitigate the effects of distribution shift.

stat.ML↗

arXiv2025

An improved lattice Boltzmann method with a novel conservative boundary scheme for viscoelastic fluid flows

The high Weissenberg number problem has been a persistent challenge in the numerical simulation of viscoelastic fluid flows. This paper presents an improved lattice Boltzmann method for solving viscoelastic flow problems at high Weissenberg numbers. The proposed approach employs two independent two-relaxation-time regularized lattice Boltzmann models to solve the hydrodynamic field and conformation tensor field of viscoelastic fluid flows, respectively. The viscoelastic stress computed from the conformation tensor is directly embedded into the hydrodynamic field using a newly proposed local velocity discretization scheme, thereby avoiding spatial gradient calculations. The constitutive equations are treated as convection-diffusion equations and solved using an improved convection-diffusion model specifically designed for this purpose, incorporating a novel auxiliary source term that eliminates the need for spatial and temporal derivative computations. Additionally, a conservative non-equilibrium bounce-back (CNEBB) scheme is proposed for implementing solid wall boundary conditions in the constitutive equations. The robustness of the present algorithm is validated through a series of benchmark problems. The simplified four-roll mill problem demonstrates that the method effectively improves numerical accuracy and stability in bulk regions containing stress singularities. The Poiseuille flow problem validates the accuracy of the current algorithm with the CNEBB boundary scheme at extremely high Weissenberg numbers (tested up to Wi = 10,000). The flow past a circular cylinder problem confirms the superior stability and applicability of the algorithm for complex curved boundary problems compared to other existing common schemes.

physics.flu-dyn↗

arXiv2025

DISPROTBENCH: Uncovering the Functional Limits of Protein Structure Prediction Models in Intrinsically Disordered Regions

Intrinsically disordered regions (IDRs) play central roles in cellular function, yet remain poorly evaluated by existing protein structure prediction benchmarks. Current evaluations largely focus on well-folded domains, overlooking three fundamental challenges in realistic biological settings: the structural complexity of proteins, the resulting low availability of reliable ground truth, and prediction uncertainty that can propagate into high-risk downstream failures, such as in drug discovery, protein-protein interaction modeling, and functional annotation. We present DisProtBench, an IDR-centric benchmark that explicitly incorporates prediction uncertainty into the evaluation of protein structure prediction models (PSPMs). To address structural complexity and ground-truth scarcity, we curate and unify a large-scale, multi-modal dataset spanning disease-relevant IDRs, GPCR-ligand interactions, and multimeric protein complexes. To assess predictive uncertainty, we introduce Functional Uncertainty Sensitivity (FUS), a novel prediction uncertainty-stratified metric that quantifies downstream task performance under prediction uncertainty. Using this benchmark, we conduct a systematic evaluation of state-of-the-art PSPMs and reveal clear, task-dependent failure modes. Protein-protein interaction prediction degrades sharply in IDRs, while structure-based drug discovery remains comparatively robust. These effects are largely invisible to standard global accuracy metrics, which overestimate functional reliability under prediction uncertainty. We have open-sourced our benchmark and the codebase at https://github.com/Susan571/DisProtBench.

q-bio.BM↗

arXiv2025

Do Graph Diffusion Models Accurately Capture and Generate Substructure Distributions?

Diffusion models have gained popularity in graph generation tasks; however, the extent of their expressivity concerning the graph distributions they can learn is not fully understood. Unlike models in other domains, popular backbones for graph diffusion models, such as Graph Transformers, do not possess universal expressivity to accurately model the distribution scores of complex graph data. Our work addresses this limitation by focusing on the frequency of specific substructures as a key characteristic of target graph distributions. When evaluating existing models using this metric, we find that they fail to maintain the distribution of substructure counts observed in the training set when generating new graphs. To address this issue, we establish a theoretical connection between the expressivity of Graph Neural Networks (GNNs) and the overall performance of graph diffusion models, demonstrating that more expressive GNN backbones can better capture complex distribution patterns. By integrating advanced GNNs into the backbone architecture, we achieve significant improvements in substructure generation.

cs.LG↗

arXiv2024

Magnetic Switching in Monolayer 2D Diluted Magnetic Semiconductors via Spin-to- Spin Conversion

The integration of two-dimensional (2D) van der Waals (vdW) magnets with topological insulators or heavy metals holds great potential for realizing next-generation spintronic memory devices. However, achieving high-efficiency SOT switching of monolayer vdW magnets at room temperature poses a significant challenge, particularly without an external magnetic field. Here, we show field-free, deterministic, and nonvolatile SOT switching of perpendicular magnetization in the monolayer, diluted magnetic semiconductor (DMS), Fe-doped MoS2(Fe:MoS2) at up to 380 K with a current density of $7\times10^4 A cm^{-2}$. The in situ doping of Fe into monolayer MoS2 via chemical vapor deposition and the geometry-induced strain in the crystal break the rotational switching symmetry in Fe:MoS2, promoting field-free SOT switching by generating out-of-plane spins via spin-to-spin conversion. An apparent anomalous Hall effect (AHE) loop shift at a zero in-plane magnetic field verifies the existence of z spins in Fe:MoS2, inducing an antidamping-like torque that facilitates field-free SOT switching. A strong topological Hall effect (THE) was also observed, attributed to the interfacial Dzyaloshinskii-Moriya interaction (DMI), reducing the energy barrier for SOT switching. This field-free SOT application using a 2D ferromagnetic monolayer provides a new pathway for developing highly power-efficient spintronic memory devices.

cond-mat.mes-hall↗

arXiv2024

Beyond Sight: Towards Cognitive Alignment in LVLM via Enriched Visual Knowledge

Does seeing always mean knowing? Large Vision-Language Models (LVLMs) integrate separately pre-trained vision and language components, often using CLIP-ViT as vision backbone. However, these models frequently encounter a core issue of "cognitive misalignment" between the vision encoder (VE) and the large language model (LLM). Specifically, the VE's representation of visual information may not fully align with LLM's cognitive framework, leading to a mismatch where visual features exceed the language model's interpretive range. To address this, we investigate how variations in VE representations influence LVLM comprehension, especially when the LLM faces VE-Unknown data-images whose ambiguous visual representations challenge the VE's interpretive precision. Accordingly, we construct a multi-granularity landmark dataset and systematically examine the impact of VE-Known and VE-Unknown data on interpretive abilities. Our results show that VE-Unknown data limits LVLM's capacity for accurate understanding, while VE-Known data, rich in distinctive features, helps reduce cognitive misalignment. Building on these insights, we propose Entity-Enhanced Cognitive Alignment (EECA), a method that employs multi-granularity supervision to generate visually enriched, well-aligned tokens that not only integrate within the LLM's embedding space but also align with the LLM's cognitive framework. This alignment markedly enhances LVLM performance in landmark recognition. Our findings underscore the challenges posed by VE-Unknown data and highlight the essential role of cognitive alignment in advancing multimodal systems.

cs.CV↗

arXiv2024

WHALES: A Multi-Agent Scheduling Dataset for Enhanced Cooperation in Autonomous Driving

Cooperative perception research is hindered by the limited availability of datasets that capture the complexity of real-world Vehicle-to-Everything (V2X) interactions, particularly under dynamic communication constraints. To address this gap, we introduce WHALES (Wireless enhanced Autonomous vehicles with Large number of Engaged agents), the first large-scale V2X dataset explicitly designed to benchmark communication-aware agent scheduling and scalable cooperative perception. WHALES introduces a new benchmark that enables state-of-the-art (SOTA) research in communication-aware cooperative perception, featuring an average of 8.4 cooperative agents per scene and 2.01 million annotated 3D objects across diverse traffic scenarios. It incorporates detailed communication metadata to emulate real-world communication bottlenecks, enabling rigorous evaluation of scheduling strategies. To further advance the field, we propose the Coverage-Aware Historical Scheduler (CAHS), a novel scheduling baseline that selects agents based on historical viewpoint coverage, improving perception performance over existing SOTA methods. WHALES bridges the gap between simulated and real-world V2X challenges, providing a robust framework for exploring perception-scheduling co-design, cross-data generalization, and scalability limits. The WHALES dataset and code are available at https://github.com/chensiweiTHU/WHALES.

cs.CV↗

arXiv2024

Emergent Topological Hall Effect in Fe-doped Monolayer WSe2

The topological Hall effect (THE) has attracted great attention since it provides an important probe of the interaction between electron and topological spin textures. THE has been considered an experimental signature of the topological spin texture of skyrmions. While THE has been widely reported in chiral magnets, oxide heterostructures, and hybrid systems such as ferromagnet/heavy metal and ferromagnet/topological insulators, the study of monolayer structures is lacking, hindering the understanding of noncollinear spin textures at the atomically thin scale. Here, we show a discernible THE via proximity coupling of Fe-doped monolayer WSe2 (Fe:WSe2) synthesized using chemical vapor deposition on a Pt Hall bar. Multiple characterization methods were employed to demonstrate that Fe atoms substitutionally replace W atoms, making a two-dimensional (2D) van der Waals (vdW) dilute magnetic semiconductor (DMS) at room temperature. Distinct from the intrinsic anomalous Hall effect, we found the transverse Hall resistivity of Fe:WSe2 displaying two additional dip/peak features in the temperature-dependent measurements, consistent with the contribution of THE. The topological Hall effect is attributed to the magnetic skyrmions that emerge from the Dzyaloshinskii-Moriya interactions at the Fe:WSe2 and Pt interface. Our work shows that a DMS synthesized from 2D vdW transition metal dichalcogenides is promising for realizing magnetic skyrmions and spintronic applications.

physics.atom-ph↗

arXiv2024

Enhancing the MILP/MIQCP-based Automatic Search for Differential-Linear Distinguishers of Simon-Like Ciphers

In this paper, we propose an improved method based on Mixed-Integer Linear Programming/Mixed-Integer Quadratic Constraint Programming (MILP/MIQCP) to automatically find better differential-linear (DL) distinguishers for the all members of Simon and Simeck block cipher families. To be specific, we first give the completely precise MILP model to describe the linear part, and explain how to utilize the general expressions of \textsf{Gurobi} solver to model the propagation of continuous difference for the middle part in a quite easy way. Secondly, in order to solve the MILP/MIQCP model in a reasonable time, we propose two heuristic strategies based on the divide-and-conquer idea to speed up the search process. Thirdly, we introduce the transforming technique, which exploits the clustering effect on DL trails, to improve the estimated correlation of the DL approximation. We apply our method to Simon and Simeck block cipher families. Consequently, we find the 14/17/21/26-round theoretical DL distinguishers of Simon32/48/64/96, which extend the previous longest ones of Simon32/48/96 by one round and Simon64 by two rounds, respectively. For Simeck, we do not explore longer distinguishers compared to the currently best results, but refresh all the results of Zhou et al. (the first work to automate finding DL distinguishers for Simon-like ciphers using MILP/MIQCP). Besides, in order to validate the correctness of these distinguishers, the experimental verifications are conducted on Simon32/Simeck32 and Simon48/Simeck48. The results show that our theoretical estimations on correlations are very close to the experimental ones, which can be regarded as a concrete support for the effectiveness of our method.

cs.CR↗