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Liang Huang

Publications and source records attributed to Liang Huang.

At least 37 records · Page 2Linked to original sources

Citrus: Leveraging Expert Cognitive Pathways in a Medical Language Model for Advanced Medical Decision Support

Large language models (LLMs), particularly those with reasoning capabilities, have rapidly advanced in recent years, demonstrating significant potential across a wide range of applications. However, their deployment in healthcare, especially in disease reasoning tasks, is hindered by the challenge of acquiring expert-level cognitive data. In this paper, we introduce Citrus, a medical language model that bridges the gap between clinical expertise and AI reasoning by emulating the cognitive processes of medical experts. The model is trained on a large corpus of simulated expert disease reasoning data, synthesized using a novel approach that accurately captures the decision-making pathways of clinicians. This approach enables Citrus to better simulate the complex reasoning processes involved in diagnosing and treating medical conditions. To further address the lack of publicly available datasets for medical reasoning tasks, we release the last-stage training data, including a custom-built medical diagnostic dialogue dataset. This open-source contribution aims to support further research and development in the field. Evaluations using authoritative benchmarks such as MedQA, covering tasks in medical reasoning and language understanding, show that Citrus achieves superior performance compared to other models of similar size. These results highlight Citrus potential to significantly enhance medical decision support systems, providing a more accurate and efficient tool for clinical decision-making.

cs.AI↗

Advancing C-C Coupling of Electrocatalytic CO2 Reduction Reaction for C2+ Products

The production of multicarbon (C2+) products through electrocatalytic CO2 reduction reaction (CO2RR) is crucial to addressing global environmental challenges and advancing sustainable energy solutions. However, efficiently producing these high-value chemicals via C-C coupling reactions is a significant challenge. This requires catalysts with optimized surface configurations and electronic properties capable of breaking the scaling relations among various intermediates. In this report, we introduce the fundamentals of electrocatalytic CO2RR and the mechanism of C-C coupling. We examine the effects of catalytic surface interactions with key intermediates and reaction pathways, and discuss emerging strategies for enhancing C-C coupling reactions toward C2+ products. Despite varieties of these strategies, we summarize direct clues for the proper design of the catalyst for the electrocatalytic CO2RR towards C2+ products, aiming to provide valuable insights to broad readers in the field.

physics.chem-ph↗

Process Supervision-Guided Policy Optimization for Code Generation

Reinforcement learning (RL) with unit test feedback has enhanced large language models' (LLMs) code generation, but relies on sparse rewards provided only after complete code evaluation, limiting learning efficiency and incremental improvements. When generated code fails all unit tests, no learning signal is received, hindering progress on complex tasks. To address this, we propose a Process Reward Model (PRM) that delivers dense, line-level feedback on code correctness during generation, mimicking human code refinement and providing immediate guidance. We explore various strategies for training PRMs and integrating them into the RL framework, finding that using PRMs both as dense rewards and for value function initialization significantly boosts performance. Our experimental results also highlight the effectiveness of PRMs in enhancing RL-driven code generation, especially for long-horizon scenarios.

cs.AI↗

Sampling-based Continuous Optimization with Coupled Variables for RNA Design

The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as local search have been popular for this task, but by only exploring a fixed number of candidates. They can not keep up with the exponential growth of the design space, and often perform poorly on longer and harder-to-design structures. We instead formulate these discrete problems as continuous optimization, which starts with a distribution over all possible candidate sequences, and uses gradient descent to improve the expectation of an objective function. We define novel distributions based on coupled variables to rule out invalid sequences given the target structure and to model the correlation between nucleotides. To make it universally applicable to any objective function, we use sampling to approximate the expected objective function, to estimate the gradient, and to select the final candidate. Compared to the state-of-the-art methods, our work consistently outperforms them in key metrics such as Boltzmann probability, ensemble defect, and energy gap, especially on long and hard-to-design puzzles in the Eterna100 benchmark. Our code is available at: http://github.com/weiyutang1010/ncrna_design.

q-bio.BM↗

$q$-Breathers in the diatomic $β$-Fermi-Pasta-Ulam- Tsingou chains

$q$-Breathers (QBs) represent a quintessential phenomenon of energy localization, manifesting as stable periodic orbits exponentially localized in normal mode space. Their existence can hinder the thermalization process in nonlinear lattices. In this study, we employ the Newton's method to identify QB solutions in the diatomic Fermi-Pasta-Ulam-Tsingou chains and perform a comprehensive analysis of their linear stability. We derive an analytical expression for the instability thresholds of low-frequency QBs, which converges to the known results of monoatomic chains as the bandgap approaches zero. The expression reveals an inverse square relationship between instability thresholds and system size, as well as a quadratic dependence on the mass difference, both of which have been corroborated through extensive numerical simulations. Our results demonstrate that the presence of a bandgap can markedly enhance QB stability, providing a novel theoretical foundation and practical framework for controlling energy transport between modes in complex lattice systems. These results not only expand the applicability of QBs but also offer significant implications for understanding the thermalization dynamics in complex lattice structures, with wide potential applications in related low-dimensional materials.

cond-mat.stat-mech↗

Geometry-induced wavefunction collapse

When a quantum particle moves in a curved space, a geometric potential can arise. In spite of a long history of extensive theoretical studies, to experimentally observe the geometric potential remains to be a challenge. What are the physically observable consequences of such a geometric potential? Solving the Schrodinger equation on a truncated conic surface, we uncover a class of quantum scattering states that bear a strong resemblance with the quasi-resonant states associated with atomic collapse about a Coulomb impurity, a remarkable quantum phenomenon in which an infinite number of quasi-resonant states emerge. A characteristic defining feature of such collapse states is the infinite oscillations of the local density of states (LDOS) about the zero energy point separating the scattering from the bound states. The emergence of such states in the curved (Riemannian) space requires neither a relativistic quantum mechanism nor any Coulomb impurity: they have zero angular momentum and their origin is purely geometrical - henceforth the term geometry-induced wavefunction collapse. We establish the collapsing nature of these states through a detailed comparative analysis of the behavior of the LDOS for both the zero and finite angular-momentum states as well as the corresponding classical picture. Potential experimental schemes to realize the geometry-induced collapse states are articulated. Not only has our study uncovered an intrinsic connection between the geometric potential and atomic collapse, it also provides a method to experimentally observe and characterize geometric potentials arising from different subfields of physics. For example, in nanoscience and nanotechnology, curved geometry has become increasingly common. Our finding suggests that wavefunction collapse should be an important factor of consideration in designing and developing nanodevices.

quant-ph↗

Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of folding into a target structure, little attention has been given to the identification of undesignable structures according to the minimum free energy (MFE) criterion under the Turner model. In this paper, we address this gap by first introducing mathematical theorems outlining sufficient conditions for recognizing undesignable structures, then proposing efficient algorithms, guided by these theorems, to verify the undesignability of RNA structures. Through the application of these theorems and algorithms to the Eterna100 puzzles, we demonstrate the ability to efficiently establish that 15 of the puzzles indeed fall within the category of undesignable structures. In addition, we provide specific insights from the study of undesignability, in the hope that it will enable more understanding of RNA folding and RNA design.

q-bio.BM↗

Attention-based SIC Ordering and Power Allocation for Non-orthogonal Multiple Access Networks

Non-orthogonal multiple access (NOMA) emerges as a superior technology for enhancing spectral efficiency compared to orthogonal multiple access. In NOMA networks, successive interference cancellation (SIC) plays a crucial role in decoding user signals sequentially. The challenge lies in the joint optimization of SIC ordering and power allocation, due to the factorial nature of ordering combinations. This study introduces an innovative solution, the Attention-based SIC Ordering and Power Allocation (ASOPA) framework, targeting an uplink NOMA network with dynamic SIC ordering. ASOPA aims to maximize weighted proportional fairness by employing deep reinforcement learning, strategically decomposing the problem into two manageable subproblems: SIC ordering optimization and optimal power allocation. Our approach utilizes an attention-based neural network, which processes instantaneous channel gains and user weights to determine the SIC decoding sequence for each user. Once the SIC ordering is established, the power allocation subproblem transforms into a convex optimization problem, enabling efficient calculation. Extensive simulations validate ASOPA's efficacy, demonstrating a performance closely paralleling the exhaustive method, with over 97% confidence in normalized network utility. Notably, ASOPA maintains a low execution latency of approximately 50 milliseconds in a ten-user NOMA network, aligning with static SIC ordering algorithms. Furthermore, ASOPA demonstrates superior performance in various NOMA network configurations, including scenarios with imperfect channel state information, multiple base stations, and multiple-antenna setups. Such results underscore ASOPA's robustness and effectiveness, highlighting its ability to excel across various NOMA network environments. The complete source code for ASOPA is accessible at https://github.com/Jil-Menzerna/ASOPA.

cs.NI↗

LinearAlifold: Linear-Time Consensus Structure Prediction for RNA Alignments

Predicting the consensus structure of a set of aligned RNA homologs is a convenient method to find conserved structures in an RNA genome, which has many applications including viral diagnostics and therapeutics. However, the most commonly used tool for this task, RNAalifold, is prohibitively slow for long sequences, due to a cubic scaling with the sequence length, taking over a day on 400 SARS-CoV-2 and SARS-related genomes (~30,000nt). We present LinearAlifold, a much faster alternative that scales linearly with both the sequence length and the number of sequences, based on our work LinearFold that folds a single RNA in linear time. Our work is orders of magnitude faster than RNAalifold (0.7 hours on the above 400 genomes, or ~36$\times$ speedup) and achieves higher accuracies when compared to a database of known structures. More interestingly, LinearAlifold's prediction on SARS-CoV-2 correlates well with experimentally determined structures, substantially outperforming RNAalifold. Finally, LinearAlifold supports two energy models (Vienna and BL*) and four modes: minimum free energy (MFE), maximum expected accuracy (MEA), ThreshKnot, and stochastic sampling, each of which takes under an hour for hundreds of SARS-CoV variants. Our resource is at: https://github.com/LinearFold/LinearAlifold (code) and http://linearfold.org/linear-alifold (server).

q-bio.BM↗

Observation of Quantized Klein Tunneling in a Dielectric Resonator Chain

We present the first experimental observation of quantized Klein tunneling in a bounded Dirac system, implemented by a dimer chain of dielectric microwave resonators. Both the unusual quantized levels and corresponding spinor states hybridized from distinct particle and hole wavefunctions are measured. All observations are in quantitative agreement with the hitherto-untested prediction of Dirac equation. Our results make an important step to realize and understand the particle-hole physics of Klein tunneling in bounded Dirac systems, and also shed light on potential applications for manipulating particle-hole hybridized spinor waves.

quant-ph↗

Symmetry Hierarchy and Thermalization Frustration in Graphene Nanoresonators

As the essential cause of the intrinsic dissipation that limits the quality of graphene nanoresonators, intermodal energy transfer is also a key issue in thermalization dynamics. Typically systems with larger initial energy demand shorter time to be thermalized. However, we find quantitatively that instead of becoming shorter, the equipartition time of the graphene nanoresonator can increase abruptly by one order of magnitude. This thermalization frustration emerges due to the partition of the normal modes based on the hierarchical symmetry, and a sensitive on-off switching of the energy flow channels between symmetry classes controlled by Mathieu instabilities. The results uncover the decisive roles of symmetry in the thermalization at the nanoscale, and may also lead to strategies for improving the performance of graphene nanoresonators.

cond-mat.stat-mech↗

Messenger RNA Design via Expected Partition Function and Continuous Optimization

The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop a general framework for this optimization based on a generalization of classical partition function which we call "expected partition function". The basic idea is to start with a distribution over all possible candidate sequences, and extend the objective function from a sequence to a distribution. We then use gradient descent-based optimization methods to improve the extended objective function, and the distribution will gradually shrink towards a one-hot sequence (i.e., a single sequence). As a case study, we consider the important problem of mRNA design with wide applications in vaccines and therapeutics. While the recent work of LinearDesign can efficiently optimize mRNAs for minimum free energy (MFE), optimizing for ensemble free energy is much harder and likely intractable. Our approach can consistently improve over the LinearDesign solution in terms of ensemble free energy, with bigger improvements on longer sequences.

q-bio.BM↗

Damping Separation of Finite Open Systems in Gravity-Related Experiments in the Free Molecular Flow Regime

The residual gas damping of the test mass (TM) in the free molecular flow regime is studied in the finite open systems for high-precision gravity-related experiments. Through strict derivation, we separate the damping coefficients for two finite open systems, i.e., the bi-plate system and the sensor core system, into base damping and diffusion damping. This elucidates the relationship between the free damping in the infinite gas volume and the proximity damping in the constrained volume, unifies them into one microscopic picture, and allows us to point out three pathways of energy dissipation in the bi-plate gap. We also provide the conditions that need to be met to achieve this separation. In applications, for space gravitational wave detection, our results for the residual gas damping coefficient for the 4TM torsion balance experiment is the closest one to the experimental and simulation data compared to previous models. For the LISA mission, our estimation for residual gas acceleration noise at the sensitive axis is consistent with the simulation result, within about $5\%$ difference. In addition, in the test of the gravitational inverse-square law, our results suggest that the constraint on the distance between TM and the conducting membrane can be reduced by about $28\%$.

gr-qc↗

Symmetry dictated universal helicity redistribution of Dirac fermions in transport

Helicity is a fundamental property of Dirac fermions. Yet, the general rule of how it changes in transport is still lacking. We uncover, theoretically, the universal spinor state transformation and consequently helicity redistribution rule in two cases of transport through potentials of electrostatic and mass types, respectively. The former is dictated by Lorentz boost and its complex counterpart in Klein tunneling regime, which establishes miraculously a unified yet latent connection between helicity, Klein tunneling, and Lorentz boost. The latter is governed by an abstract rotation group we construct, which reduces to SO(2) when acting on the plane of effective mass and momentum. They generate invariant submanifolds, i.e., leaves, that foliate the Hilbert space of Dirac spinors. Our results provide a basis for unified understanding of helicity transport, and may open a new window for exotic helicity-based physics and applications in mesoscopic systems.

cond-mat.mes-hall↗

LinearSankoff: Linear-time Simultaneous Folding and Alignment of RNA Homologs

The classical Sankoff algorithm for the simultaneous folding and alignment of homologous RNA sequences is highly influential, but it suffers from two major limitations in efficiency and modeling power. First, it takes $O(n^6)$ for two sequences where n is the average sequence length. Most implementations and variations reduce the runtime to $O(n^3)$ by restricting the alignment search space, but this is still too slow for long sequences such as full-length viral genomes. On the other hand, the Sankoff algorithm and all its existing implementations use a rather simplistic alignment model, which can result in poor alignment accuracy. To address these problems, we propose LinearSankoff, which seamlessly integrates the original Sankoff algorithm with a powerful Hidden Markov Model-based alignment module. This extension substantially improves alignment quality, which in turn benefits secondary structure prediction quality, confirmed over a diverse set of RNA families. LinearSankoff also applies beam search heuristics and the A$^\star$-like algorithm to achieve that runtime scales linearly with sequence length. LinearSankoff is the first linear-time algorithm for simultaneous folding and alignment, and the first such algorithm to scale to coronavirus genomes (n $\approx$ 30,000nt). It only takes 10 minutes for a pair of SARS-CoV-2 and SARS-related genomes, and outperforms previous work at identifying crucial conserved structures between the two genomes.

q-bio.BM↗

Experimental full network nonlocality with independent sources and strict locality constraints

Nonlocality arising in networks composed of several independent sources gives rise to phenomena radically different from that in standard Bell scenarios. Over the years, the phenomenon of network nonlocality in the entanglement-swapping scenario has been well investigated and demonstrated. However, it is known that violations of the so-called bilocality inequality used in previous experimental demonstrations cannot be used to certify the non-classicality of their sources. This has put forward a stronger concept for nonlocality in networks, called full network nonlocality. Here, we experimentally observe full network nonlocal correlations in a network where the source-independence, locality, and measurement-independence loopholes are closed. This is ensured by employing two independent sources, rapid setting generation, and space-like separations of relevant events. Our experiment violates known inequalities characterizing non-full network nonlocal correlations by over five standard deviations, certifying the absence of classical sources in the realization.

quant-ph↗

ERNIE-SAT: Speech and Text Joint Pretraining for Cross-Lingual Multi-Speaker Text-to-Speech

Speech representation learning has improved both speech understanding and speech synthesis tasks for single language. However, its ability in cross-lingual scenarios has not been explored. In this paper, we extend the pretraining method for cross-lingual multi-speaker speech synthesis tasks, including cross-lingual multi-speaker voice cloning and cross-lingual multi-speaker speech editing. We propose a speech-text joint pretraining framework, where we randomly mask the spectrogram and the phonemes given a speech example and its transcription. By learning to reconstruct the masked parts of the input in different languages, our model shows great improvements over speaker-embedding-based multi-speaker TTS methods. Moreover, our framework is end-to-end for both the training and the inference without any finetuning effort. In cross-lingual multi-speaker voice cloning and cross-lingual multi-speaker speech editing tasks, our experiments show that our model outperforms speaker-embedding-based multi-speaker TTS methods.

eess.AS↗

LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules

Many ncRNAs function through RNA-RNA interactions. Fast and reliable RNA structure prediction with consideration of RNA-RNA interaction is useful. Some existing tools are less accurate due to omitting the competing of intermolecular and intramolecular base pairs, or focus more on predicting the binding region rather than predicting the complete secondary structure of two interacting strands. Vienna RNAcofold, which reduces the problem into the classical single sequence folding by concatenating two strands, scales in cubic time against the combined sequence length, and is slow for long sequences. To address these issues, we present LinearCoFold, which predicts the complete minimum free energy structure of two strands in linear runtime, and LinearCoPartition, which calculates the cofolding partition function and base pairing probabilities in linear runtime. LinearCoFold and LinearCoPartition follows the concatenation strategy of RNAcofold, but are orders of magnitude faster than RNAcofold. For example, on a sequence pair with combined length of 26,190 nt, LinearCoFold is 86.8x faster than RNAcofold MFE mode (0.6 minutes vs. 52.1 minutes), and LinearCoPartition is 642.3x faster than RNAcofold partition function mode (1.8 minutes vs. 1156.2 minutes). Different from the local algorithms, LinearCoFold and LinearCoPartition are global cofolding algorithms without restriction on base pair length. Surprisingly, LinearCoFold and LinearCoPartition's predictions have higher PPV and sensitivity of intermolecular base pairs. Furthermore, we apply LinearCoFold to predict the RNA-RNA interaction between SARS-CoV-2 gRNA and human U4 snRNA, which has been experimentally studied, and observe that LinearCoFold's prediction correlates better to the wet lab results.

q-bio.BM↗