Sampling-based Continuous Optimization with Coupled Variables for RNA DesignWei Yu Tang, Ning Dai, Tianshuo Zhou et al.
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.
21.6AIOct 23, 2024
Process Supervision-Guided Policy Optimization for Code GenerationNing Dai, Zheng Wu, Renjie Zheng et al.
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.
Messenger RNA Design via Expected Partition Function and Continuous OptimizationNing Dai, Wei Yu Tang, Tianshuo Zhou et al.
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.
31.7CLJun 11, 2021
Direct Simultaneous Speech-to-Text Translation Assisted by Synchronized Streaming ASRJunkun Chen, Mingbo Ma, Renjie Zheng et al.
Simultaneous speech-to-text translation is widely useful in many scenarios. The conventional cascaded approach uses a pipeline of streaming ASR followed by simultaneous MT, but suffers from error propagation and extra latency. To alleviate these issues, recent efforts attempt to directly translate the source speech into target text simultaneously, but this is much harder due to the combination of two separate tasks. We instead propose a new paradigm with the advantages of both cascaded and end-to-end approaches. The key idea is to use two separate, but synchronized, decoders on streaming ASR and direct speech-to-text translation (ST), respectively, and the intermediate results of ASR guide the decoding policy of (but is not fed as input to) ST. During training time, we use multitask learning to jointly learn these two tasks with a shared encoder. En-to-De and En-to-Es experiments on the MuSTC dataset demonstrate that our proposed technique achieves substantially better translation quality at similar levels of latency.
5.5CLFeb 10, 2021
Fused Acoustic and Text Encoding for Multimodal Bilingual Pretraining and Speech TranslationRenjie Zheng, Junkun Chen, Mingbo Ma et al.
Recently, representation learning for text and speech has successfully improved many language related tasks. However, all existing methods suffer from two limitations: (a) they only learn from one input modality, while a unified representation for both speech and text is needed by tasks such as end-to-end speech translation, and as a result,(b) they can not exploit various large-scale text and speech data and their performance is limited by the scarcity of parallel speech translation data.To address these problems, we propose a Fused Acoustic and Text Masked Language Model (FAT-MLM) which jointly learns a unified representation for both acoustic and text input from various types of corpora including parallel data for speech recognition and machine translation, and even pure speech and text data. Within this cross-modal representation learning framework, we further present an end-to-end model for Fused Acoustic and Text Speech Translation (FAT-ST). Experiments on three translation directions show that by fine-tuning from FAT-MLM, our proposed speech translation models substantially improve translation quality by up to +5.9 BLEU.
Context-aware Stand-alone Neural Spelling CorrectionXiangci Li, Hairong Liu, Liang Huang
Existing natural language processing systems are vulnerable to noisy inputs resulting from misspellings. On the contrary, humans can easily infer the corresponding correct words from their misspellings and surrounding context. Inspired by this, we address the stand-alone spelling correction problem, which only corrects the spelling of each token without additional token insertion or deletion, by utilizing both spelling information and global context representations. We present a simple yet powerful solution that jointly detects and corrects misspellings as a sequence labeling task by fine-turning a pre-trained language model. Our solution outperforms the previous state-of-the-art result by 12.8% absolute F0.5 score.
27.0CLOct 21, 2020
Improving Simultaneous Translation by Incorporating Pseudo-References with Fewer ReorderingsJunkun Chen, Renjie Zheng, Atsuhito Kita et al.
Simultaneous translation is vastly different from full-sentence translation, in the sense that it starts translation before the source sentence ends, with only a few words delay. However, due to the lack of large-scale, high-quality simultaneous translation datasets, most such systems are still trained on conventional full-sentence bitexts. This is far from ideal for the simultaneous scenario due to the abundance of unnecessary long-distance reorderings in those bitexts. We propose a novel method that rewrites the target side of existing full-sentence corpora into simultaneous-style translation. Experiments on Zh->En and Ja->En simultaneous translation show substantial improvements (up to +2.7 BLEU) with the addition of these generated pseudo-references.
31.2CLMay 2, 2020
Opportunistic Decoding with Timely Correction for Simultaneous TranslationRenjie Zheng, Mingbo Ma, Baigong Zheng et al.
Simultaneous translation has many important application scenarios and attracts much attention from both academia and industry recently. Most existing frameworks, however, have difficulties in balancing between the translation quality and latency, i.e., the decoding policy is usually either too aggressive or too conservative. We propose an opportunistic decoding technique with timely correction ability, which always (over-)generates a certain mount of extra words at each step to keep the audience on track with the latest information. At the same time, it also corrects, in a timely fashion, the mistakes in the former overgenerated words when observing more source context to ensure high translation quality. Experiments show our technique achieves substantial reduction in latency and up to +3.1 increase in BLEU, with revision rate under 8% in Chinese-to-English and English-to-Chinese translation.
31.4CLApr 27, 2020
Simultaneous Translation Policies: From Fixed to AdaptiveBaigong Zheng, Kaibo Liu, Renjie Zheng et al.
Adaptive policies are better than fixed policies for simultaneous translation, since they can flexibly balance the tradeoff between translation quality and latency based on the current context information. But previous methods on obtaining adaptive policies either rely on complicated training process, or underperform simple fixed policies. We design an algorithm to achieve adaptive policies via a simple heuristic composition of a set of fixed policies. Experiments on Chinese -> English and German -> English show that our adaptive policies can outperform fixed ones by up to 4 BLEU points for the same latency, and more surprisingly, it even surpasses the BLEU score of full-sentence translation in the greedy mode (and very close to beam mode), but with much lower latency.
30.6CLSep 4, 2019
Simpler and Faster Learning of Adaptive Policies for Simultaneous TranslationBaigong Zheng, Renjie Zheng, Mingbo Ma et al.
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.
31.0CLApr 1, 2019
Learning to Stop in Structured Prediction for Neural Machine TranslationMingbo Ma, Renjie Zheng, Liang Huang
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.
32.0CLSep 9, 2018
Speeding Up Neural Machine Translation Decoding by Cube PruningWen Zhang, Liang Huang, Yang Feng et al.
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.
32.0CLAug 31, 2018
Ensemble Sequence Level Training for Multimodal MT: OSU-Baidu WMT18 Multimodal Machine Translation System ReportRenjie Zheng, Yilin Yang, Mingbo Ma et al.
This paper describes multimodal machine translation systems developed jointly by Oregon State University and Baidu Research for WMT 2018 Shared Task on multimodal translation. In this paper, we introduce a simple approach to incorporate image information by feeding image features to the decoder side. We also explore different sequence level training methods including scheduled sampling and reinforcement learning which lead to substantial improvements. Our systems ensemble several models using different architectures and training methods and achieve the best performance for three subtasks: En-De and En-Cs in task 1 and (En+De+Fr)-Cs task 1B.
32.4CLAug 28, 2018
Breaking the Beam Search Curse: A Study of (Re-)Scoring Methods and Stopping Criteria for Neural Machine TranslationYilin Yang, Liang Huang, Mingbo Ma
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.
32.1CLAug 28, 2018
Multi-Reference Training with Pseudo-References for Neural Translation and Text GenerationRenjie Zheng, Mingbo Ma, Liang Huang
Neural text generation, including neural machine translation, image captioning, and summarization, has been quite successful recently. However, during training time, typically only one reference is considered for each example, even though there are often multiple references available, e.g., 4 references in NIST MT evaluations, and 5 references in image captioning data. We first investigate several different ways of utilizing multiple human references during training. But more importantly, we then propose an algorithm to generate exponentially many pseudo-references by first compressing existing human references into lattices and then traversing them to generate new pseudo-references. These approaches lead to substantial improvements over strong baselines in both machine translation (+1.5 BLEU) and image captioning (+3.1 BLEU / +11.7 CIDEr).
32.1CLAug 27, 2018
Large Margin Neural Language ModelJiaji Huang, Yi Li, Wei Ping et al.
We propose a large margin criterion for training neural language models. Conventionally, neural language models are trained by minimizing perplexity (PPL) on grammatical sentences. However, we demonstrate that PPL may not be the best metric to optimize in some tasks, and further propose a large margin formulation. The proposed method aims to enlarge the margin between the "good" and "bad" sentences in a task-specific sense. It is trained end-to-end and can be widely applied to tasks that involve re-scoring of generated text. Compared with minimum-PPL training, our method gains up to 1.1 WER reduction for speech recognition and 1.0 BLEU increase for machine translation.
32.0CLMay 17, 2018
Linear-Time Constituency Parsing with RNNs and Dynamic ProgrammingJuneki Hong, Liang Huang
Recently, span-based constituency parsing has achieved competitive accuracies with extremely simple models by using bidirectional RNNs to model "spans". However, the minimal span parser of Stern et al (2017a) which holds the current state of the art accuracy is a chart parser running in cubic time, $O(n^3)$, which is too slow for longer sentences and for applications beyond sentence boundaries such as end-to-end discourse parsing and joint sentence boundary detection and parsing. We propose a linear-time constituency parser with RNNs and dynamic programming using graph-structured stack and beam search, which runs in time $O(n b^2)$ where $b$ is the beam size. We further speed this up to $O(n b\log b)$ by integrating cube pruning. Compared with chart parsing baselines, this linear-time parser is substantially faster for long sentences on the Penn Treebank and orders of magnitude faster for discourse parsing, and achieves the highest F1 accuracy on the Penn Treebank among single model end-to-end systems.