arXiv subjects

Liang Huang

Publications and source records attributed to Liang Huang.

At least 91 records · Page 5Linked to original sources

arXiv2020

ThreshKnot: Thresholded ProbKnot for Improved RNA Secondary Structure Prediction

RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures using base-pairing probabilities. Two examples of the latter group are the popular maximum expected accuracy (MEA) method and the ProbKnot method. ProbKnot is a fast heuristic that pairs nucleotides that are reciprocally most probable pairing partners, and unlike MEA, can also predict structures with pseudoknots. However, ProbKnot's full potential has been largely overlooked. In particular, when introduced, it did not have an MEA-like hyperparameter that can balance between positive predictive value (PPV) and sensitivity. We show that a simple thresholded version of ProbKnot, which we call ThreshKnot, leads to more accurate overall predictions by filtering out unlikely pairs whose probabilities fall under a given threshold. We also show that on three widely-used folding engines (RNAstructure, Vienna RNAfold, and CONTRAfold), ThreshKnot always outperforms the much more involved MEA algorithm in (1) its higher structure prediction accuracy, (2) its capability to predict pseudoknots, and (3) its faster runtime and easier implementation. This suggests that ThreshKnot should replace MEA as the default partition function-based structure prediction algorithm. ThreshKnot is already available in the widely used RNAstructure software package version 6.2 (released November 27, 2019): https://rna.urmc.rochester.edu/RNAstructure.html

q-bio.BM↗

arXiv2020

Quantum signatures of transitions from stable fixed points to limit cycles in optomechanical systems

Optomechanical systems, due to its inherent nonlinear optomechanical coupling, owns rich nonlinear dynamics of different types of motion. The interesting question is that whether there exist some common quantum features to infer the nonlinear dynamical transitions from one type to another. In this paper, we have studied the quantum signatures of transitions from stable fixed points to limit cycles in an optomechanical phonon laser system. Our calculations show that the entanglement of stable fixed points in the long run does not change with time, however, it will oscillate periodically with time at the mechanical vibration frequency for the limit cycles. Most strikingly, the entanglement quite close to the boundary line keeps as a constant, and it is very robust to the thermal phonon noise, as strong indications of this particular classical transitions.

quant-ph↗

arXiv2019

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and this slowness limits their use in genome-wide applications. Results: We present a novel alternative $O(n^3)$-time dynamic programming algorithm for RNA folding that is amenable to heuristics that make it run in $O(n)$ time and $O(n)$ space, while producing a high-quality approximation to the optimal solution. Inspired by incremental parsing for context-free grammars in computational linguistics, our alternative dynamic programming algorithm scans the sequence in a left-to-right (5'-to-3') direction rather than in a bottom-up fashion, which allows us to employ the effective beam pruning heuristic. Our work, though inexact, is the first RNA folding algorithm to achieve linear runtime (and linear space) without imposing constraints on the output structure. Surprisingly, our approximate search results in even higher overall accuracy on a diverse database of sequences with known structures. More interestingly, it leads to significantly more accurate predictions on the longest sequence families in that database (16S and 23S Ribosomal RNAs), as well as improved accuracies for long-range base pairs (500+ nucleotides apart), both of which are well known to be challenging for the current models. Availability: Our source code is available at https://github.com/LinearFold/LinearFold, and our webserver is at http://linearfold.org (sequence limit: 100,000nt).

q-bio.BM↗

arXiv2019

Data Augmentation for Deep Learning-based Radio Modulation Classification

Deep learning has recently been applied to automatically classify the modulation categories of received radio signals without manual experience. However, training deep learning models requires massive volume of data. An insufficient training data will cause serious overfitting problem and degrade the classification accuracy. To cope with small dataset, data augmentation has been widely used in image processing to expand the dataset and improve the robustness of deep learning models. However, in wireless communication areas, the effect of different data augmentation methods on radio modulation classification has not been studied yet. In this paper, we evaluate different data augmentation methods via a state-of-the-art deep learning-based modulation classifier. Based on the characteristics of modulated signals, three augmentation methods are considered, i.e., rotation, flip, and Gaussian noise, which can be applied in both training phase and inference phase of the deep learning algorithm. Numerical results show that all three augmentation methods can improve the classification accuracy. Among which, the rotation augmentation method outperforms the flip method, both of which achieve higher classification accuracy than the Gaussian noise method. Given only 12.5% of training dataset, a joint rotation and flip augmentation policy can achieve even higher classification accuracy than the baseline with initial 100% training dataset without augmentation. Furthermore, with data augmentation, radio modulation categories can be successfully classified using shorter radio samples, leading to a simplified deep learning model and shorter the classification response time.

eess.SP↗

arXiv2019

Machine Translation in Pronunciation Space

The research in machine translation community focus on translation in text space. However, humans are in fact also good at direct translation in pronunciation space. Some existing translation systems, such as simultaneous machine translation, are inherently more natural and thus potentially more robust by directly translating in pronunciation space. In this paper, we conduct large scale experiments on a self-built dataset with about $20$M En-Zh pairs of text sentences and corresponding pronunciation sentences. We proposed three new categories of translations: $1)$ translating a pronunciation sentence in source language into a pronunciation sentence in target language (P2P-Tran), $2)$ translating a text sentence in source language into a pronunciation sentence in target language (T2P-Tran), and $3)$ translating a pronunciation sentence in source language into a text sentence in target language (P2T-Tran), and compare them with traditional text translation (T2T-Tran). Our experiments clearly show that all $4$ categories of translations have comparable performances, with small and sometimes ignorable differences.

cs.CL↗

arXiv2019

Simpler and Faster Learning of Adaptive Policies for Simultaneous Translation

Simultaneous translation is widely useful but remains challenging. Previous work falls into two main categories: (a) fixed-latency policies such as Ma et al. (2019) and (b) adaptive policies such as Gu et al. (2017). The former are simple and effective, but have to aggressively predict future content due to diverging source-target word order; the latter do not anticipate, but suffer from unstable and inefficient training. To combine the merits of both approaches, we propose a simple supervised-learning framework to learn an adaptive policy from oracle READ/WRITE sequences generated from parallel text. At each step, such an oracle sequence chooses to WRITE the next target word if the available source sentence context provides enough information to do so, otherwise READ the next source word. Experiments on German<->English show that our method, without retraining the underlying NMT model, can learn flexible policies with better BLEU scores and similar latencies compared to previous work.

cs.CL↗

arXiv2019

Speculative Beam Search for Simultaneous Translation

Beam search is universally used in full-sentence translation but its application to simultaneous translation remains non-trivial, where output words are committed on the fly. In particular, the recently proposed wait-k policy (Ma et al., 2019a) is a simple and effective method that (after an initial wait) commits one output word on receiving each input word, making beam search seemingly impossible. To address this challenge, we propose a speculative beam search algorithm that hallucinates several steps into the future in order to reach a more accurate decision, implicitly benefiting from a target language model. This makes beam search applicable for the first time to the generation of a single word in each step. Experiments over diverse language pairs show large improvements over previous work.

cs.CL↗

arXiv2019

Remote blind state preparation with weak coherent pulses in the field

Quantum computing has seen tremendous progress in the past years. Due to the implementation complexity and cost, the future path of quantum computation is strongly believed to delegate computational tasks to powerful quantum servers on cloud. Universal blind quantum computing (UBQC) provides the protocol for the secure delegation of arbitrary quantum computations, and it has received significant attention. However, a great challenge in UBQC is how to transmit quantum state over long distance securely and reliably. Here, we solve this challenge by proposing and demonstrating a resource-efficient remote blind qubit preparation (RBQP) protocol with weak coherent pulses for the client to produce, using a compact and low-cost laser. We demonstrate the protocol in field, experimentally verifying the protocol over 100-km fiber. Our experiment uses a quantum teleportation setup in telecom wavelength and generates $1000$ secure qubits with an average fidelity of $(86.9\pm1.5)\%$, which exceeds the quantum no-cloning fidelity of equatorial qubit states. The results prove the feasibility of UBQC over long distances, and thus serving as a key milestone towards secure cloud quantum computing.

quant-ph↗

arXiv2019

Experimental investigation of the fluctuations in nonchaotic scattering in microwave billiards

We report on the experimental investigation of the properties of the eigenvalues and wavefunctions and the fluctuation properties of the scattering matrix of closed and open billiards, respectively, of which the classical dynamics undergoes a transition from integrable via almost integrable to fully chaotic. To realize such a system we chose a billiard with a 60 degree sector shape of which the classical dynamics is integrable, and introduced circular scatterers of varying number, size and position. The spectral properties of generic quantum systems of which the classical counterpart is either integrable or chaotic are universal and well understood. If, however, the classical dynamics is pseudo-integrable or almost-integrable, they exhibit a non-universal intermediate statistics, for which analytical results are known only in a few cases, like, e.g., if it corresponds to semi-Poisson statistics. Since the latter is, above all, clearly distinguishable from those of integrable and chaotic systems our aim was to design a billiard with these features which indeed is achievable by adding just one scatterer of appropriate size and position to the sector billiard. We demonstrate that, while the spectral properties of almost-integrable billiards are sensitive to the classical dynamics, this is not the case for the distribution of the wavefunction components, which was analysed in terms of the strength distribution, and the fluctuation properties of the scattering matrix which coincide with those of typical, fully chaotic systems.

quant-ph↗

arXiv2019

STACL: Simultaneous Translation with Implicit Anticipation and Controllable Latency using Prefix-to-Prefix Framework

Simultaneous translation, which translates sentences before they are finished, is useful in many scenarios but is notoriously difficult due to word-order differences. While the conventional seq-to-seq framework is only suitable for full-sentence translation, we propose a novel prefix-to-prefix framework for simultaneous translation that implicitly learns to anticipate in a single translation model. Within this framework, we present a very simple yet surprisingly effective wait-k policy trained to generate the target sentence concurrently with the source sentence, but always k words behind. Experiments show our strategy achieves low latency and reasonable quality (compared to full-sentence translation) on 4 directions: zh<->en and de<->en.

cs.CL↗

arXiv2019

Learning to Stop in Structured Prediction for Neural Machine Translation

Beam search optimization resolves many issues in neural machine translation. However, this method lacks principled stopping criteria and does not learn how to stop during training, and the model naturally prefers the longer hypotheses during the testing time in practice since they use the raw score instead of the probability-based score. We propose a novel ranking method which enables an optimal beam search stopping criteria. We further introduce a structured prediction loss function which penalizes suboptimal finished candidates produced by beam search during training. Experiments of neural machine translation on both synthetic data and real languages (German-to-English and Chinese-to-English) demonstrate our proposed methods lead to better length and BLEU score.

cs.CL↗

arXiv2019

Simultaneous Translation with Flexible Policy via Restricted Imitation Learning

Simultaneous translation is widely useful but remains one of the most difficult tasks in NLP. Previous work either uses fixed-latency policies, or train a complicated two-staged model using reinforcement learning. We propose a much simpler single model that adds a `delay' token to the target vocabulary, and design a restricted dynamic oracle to greatly simplify training. Experiments on Chinese<->English simultaneous translation show that our work leads to flexible policies that achieve better BLEU scores and lower latencies compared to both fixed and RL-learned policies.

cs.CL↗

arXiv2019

Robust Machine Translation with Domain Sensitive Pseudo-Sources: Baidu-OSU WMT19 MT Robustness Shared Task System Report

This paper describes the machine translation system developed jointly by Baidu Research and Oregon State University for WMT 2019 Machine Translation Robustness Shared Task. Translation of social media is a very challenging problem, since its style is very different from normal parallel corpora (e.g. News) and also include various types of noises. To make it worse, the amount of social media parallel corpora is extremely limited. In this paper, we use a domain sensitive training method which leverages a large amount of parallel data from popular domains together with a little amount of parallel data from social media. Furthermore, we generate a parallel dataset with pseudo noisy source sentences which are back-translated from monolingual data using a model trained by a similar domain sensitive way. We achieve more than 10 BLEU improvement in both En-Fr and Fr-En translation compared with the baseline methods.

cs.CL↗

arXiv2019

Robust Neural Machine Translation with Joint Textual and Phonetic Embedding

Neural machine translation (NMT) is notoriously sensitive to noises, but noises are almost inevitable in practice. One special kind of noise is the homophone noise, where words are replaced by other words with similar pronunciations. We propose to improve the robustness of NMT to homophone noises by 1) jointly embedding both textual and phonetic information of source sentences, and 2) augmenting the training dataset with homophone noises. Interestingly, to achieve better translation quality and more robustness, we found that most (though not all) weights should be put on the phonetic rather than textual information. Experiments show that our method not only significantly improves the robustness of NMT to homophone noises, but also surprisingly improves the translation quality on some clean test sets.

cs.CL↗

arXiv2018

A network approach to quantifying radiotherapy effect on cancer: Radiosensitive gene group centrality

Radiotherapy plays a vital role in cancer treatment, for which accurate prognosis is important for guiding sequential treatment and improving the curative effect for patients. An issue of great significance in radiotherapy is to assess tumor radiosensitivity for devising the optimal treatment strategy. Previous studies focused on gene expression in cells closely associated with radiosensitivity, but factors such as the response of a cancer patient to irradiation and the patient survival time are largely ignored. For clinical cancer treatment, a specific pre-treatment indicator taking into account cancer cell type and patient radiosensitivity is of great value but it has been missing. Here, we propose an effective indicator for radiosensitivity: radiosensitive gene group centrality (RSGGC), which characterizes the importance of the group of genes that are radiosensitive in the whole gene correlation network. We demonstrate, using both clinical patient data and experimental cancer cell lines, which RSGGC can provide a quantitative estimate of the effect of radiotherapy, with factors such as the patient survival time and the survived fraction of cancer cell lines under radiotherapy fully taken into account. Our main finding is that, for patients with a higher RSGGC score before radiotherapy, cancer treatment tends to be more effective. The RSGGC can have significant applications in clinical prognosis, serving as a key measure to classifying radiosensitive and radioresistant patients.

q-bio.QM↗

arXiv2018

Breaking the Beam Search Curse: A Study of (Re-)Scoring Methods and Stopping Criteria for Neural Machine Translation

Beam search is widely used in neural machine translation, and usually improves translation quality compared to greedy search. It has been widely observed that, however, beam sizes larger than 5 hurt translation quality. We explain why this happens, and propose several methods to address this problem. Furthermore, we discuss the optimal stopping criteria for these methods. Results show that our hyperparameter-free methods outperform the widely-used hyperparameter-free heuristic of length normalization by +2.0 BLEU, and achieve the best results among all methods on Chinese-to-English translation.

cs.CL↗

arXiv2018

Transport signatures of relativistic quantum scars in a graphene cavity

We study a relativistic quantum cavity system realized by etching out from a graphene sheet by quantum transport measurements and theoretical calculations. The conductance of the graphene cavity has been measured as a function of the back gate voltage (or the Fermi energy) and the magnetic field applied perpendicular to the graphene sheet, and characteristic conductance contour patterns are observed in the measurements. In particular, two types of high conductance contour lines, i.e., straight and parabolic-like high conductance contour lines, are found in the measurements. The theoretical calculations are performed within the framework of tight-binding approach and Green's function formalism. Similar characteristic high conductance contour features as in the experiments are found in the calculations. The wave functions calculated at points selected along a straight conductance contour line are found to be dominated by a chain of scars of high probability distributions arranged as a necklace following the shape of cavity and the current density distributions calculated at these point are dominated by an overall vortex in the cavity. These characteristics are found to be insensitive to increasing magnetic field. However, the wave function probability distributions and the current density distributions calculated at points selected along a parabolic-like contour line show a clear dependence on increasing magnetic field, and the current density distributions at these points are characterized by the complex formation of several localized vortices in the cavity. Our work brings a new insight into quantum chaos in relativistic particle systems and would greatly stimulate experimental and theoretical efforts towards this still emerging field.

cond-mat.mes-hall↗

arXiv2018

Speeding Up Neural Machine Translation Decoding by Cube Pruning

Although neural machine translation has achieved promising results, it suffers from slow translation speed. The direct consequence is that a trade-off has to be made between translation quality and speed, thus its performance can not come into full play. We apply cube pruning, a popular technique to speed up dynamic programming, into neural machine translation to speed up the translation. To construct the equivalence class, similar target hidden states are combined, leading to less RNN expansion operations on the target side and less \$\mathrm{softmax}\$ operations over the large target vocabulary. The experiments show that, at the same or even better translation quality, our method can translate faster compared with naive beam search by \$3.3\times\$ on GPUs and \$3.5\times\$ on CPUs.

cs.CL↗