arXiv subjects

Tao Qin

Publications and source records attributed to Tao Qin.

At least 73 records · Page 4Linked to original sources

arXiv2022

Direct Molecular Conformation Generation

Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology. Previous methods usually first predict the interatomic distances, the gradients of interatomic distances or the local structures (e.g., torsion angles) of a molecule, and then reconstruct its 3D conformation. How to directly generate the conformation without the above intermediate values is not fully explored. In this work, we propose a method that directly predicts the coordinates of atoms: (1) the loss function is invariant to roto-translation of coordinates and permutation of symmetric atoms; (2) the newly proposed model adaptively aggregates the bond and atom information and iteratively refines the coordinates of the generated conformation. Our method achieves the best results on GEOM-QM9 and GEOM-Drugs datasets. Further analysis shows that our generated conformations have closer properties (e.g., HOMO-LUMO gap) with the groundtruth conformations. In addition, our method improves molecular docking by providing better initial conformations. All the results demonstrate the effectiveness of our method and the great potential of the direct approach. The code is released at https://github.com/DirectMolecularConfGen/DMCG

cs.AI↗

arXiv2022

An Adaptive Deep RL Method for Non-Stationary Environments with Piecewise Stable Context

One of the key challenges in deploying RL to real-world applications is to adapt to variations of unknown environment contexts, such as changing terrains in robotic tasks and fluctuated bandwidth in congestion control. Existing works on adaptation to unknown environment contexts either assume the contexts are the same for the whole episode or assume the context variables are Markovian. However, in many real-world applications, the environment context usually stays stable for a stochastic period and then changes in an abrupt and unpredictable manner within an episode, resulting in a segment structure, which existing works fail to address. To leverage the segment structure of piecewise stable context in real-world applications, in this paper, we propose a \textit{\textbf{Se}gmented \textbf{C}ontext \textbf{B}elief \textbf{A}ugmented \textbf{D}eep~(SeCBAD)} RL method. Our method can jointly infer the belief distribution over latent context with the posterior over segment length and perform more accurate belief context inference with observed data within the current context segment. The inferred belief context can be leveraged to augment the state, leading to a policy that can adapt to abrupt variations in context. We demonstrate empirically that SeCBAD can infer context segment length accurately and outperform existing methods on a toy grid world environment and Mujuco tasks with piecewise-stable context.

cs.LG↗

arXiv2022

TD3 with Reverse KL Regularizer for Offline Reinforcement Learning from Mixed Datasets

We consider an offline reinforcement learning (RL) setting where the agent need to learn from a dataset collected by rolling out multiple behavior policies. There are two challenges for this setting: 1) The optimal trade-off between optimizing the RL signal and the behavior cloning (BC) signal changes on different states due to the variation of the action coverage induced by different behavior policies. Previous methods fail to handle this by only controlling the global trade-off. 2) For a given state, the action distribution generated by different behavior policies may have multiple modes. The BC regularizers in many previous methods are mean-seeking, resulting in policies that select out-of-distribution (OOD) actions in the middle of the modes. In this paper, we address both challenges by using adaptively weighted reverse Kullback-Leibler (KL) divergence as the BC regularizer based on the TD3 algorithm. Our method not only trades off the RL and BC signals with per-state weights (i.e., strong BC regularization on the states with narrow action coverage, and vice versa) but also avoids selecting OOD actions thanks to the mode-seeking property of reverse KL. Empirically, our algorithm can outperform existing offline RL algorithms in the MuJoCo locomotion tasks with the standard D4RL datasets as well as the mixed datasets that combine the standard datasets.

stat.ML↗

arXiv2022

FastCorrect: Fast Error Correction with Edit Alignment for Automatic Speech Recognition

Error correction techniques have been used to refine the output sentences from automatic speech recognition (ASR) models and achieve a lower word error rate (WER) than original ASR outputs. Previous works usually use a sequence-to-sequence model to correct an ASR output sentence autoregressively, which causes large latency and cannot be deployed in online ASR services. A straightforward solution to reduce latency, inspired by non-autoregressive (NAR) neural machine translation, is to use an NAR sequence generation model for ASR error correction, which, however, comes at the cost of significantly increased ASR error rate. In this paper, observing distinctive error patterns and correction operations (i.e., insertion, deletion, and substitution) in ASR, we propose FastCorrect, a novel NAR error correction model based on edit alignment. In training, FastCorrect aligns each source token from an ASR output sentence to the target tokens from the corresponding ground-truth sentence based on the edit distance between the source and target sentences, and extracts the number of target tokens corresponding to each source token during edition/correction, which is then used to train a length predictor and to adjust the source tokens to match the length of the target sentence for parallel generation. In inference, the token number predicted by the length predictor is used to adjust the source tokens for target sequence generation. Experiments on the public AISHELL-1 dataset and an internal industrial-scale ASR dataset show the effectiveness of FastCorrect for ASR error correction: 1) it speeds up the inference by 6-9 times and maintains the accuracy (8-14% WER reduction) compared with the autoregressive correction model; and 2) it outperforms the popular NAR models adopted in neural machine translation and text edition by a large margin.

cs.CL↗

arXiv2022

FastCorrect 2: Fast Error Correction on Multiple Candidates for Automatic Speech Recognition

Error correction is widely used in automatic speech recognition (ASR) to post-process the generated sentence, and can further reduce the word error rate (WER). Although multiple candidates are generated by an ASR system through beam search, current error correction approaches can only correct one sentence at a time, failing to leverage the voting effect from multiple candidates to better detect and correct error tokens. In this work, we propose FastCorrect 2, an error correction model that takes multiple ASR candidates as input for better correction accuracy. FastCorrect 2 adopts non-autoregressive generation for fast inference, which consists of an encoder that processes multiple source sentences and a decoder that generates the target sentence in parallel from the adjusted source sentence, where the adjustment is based on the predicted duration of each source token. However, there are some issues when handling multiple source sentences. First, it is non-trivial to leverage the voting effect from multiple source sentences since they usually vary in length. Thus, we propose a novel alignment algorithm to maximize the degree of token alignment among multiple sentences in terms of token and pronunciation similarity. Second, the decoder can only take one adjusted source sentence as input, while there are multiple source sentences. Thus, we develop a candidate predictor to detect the most suitable candidate for the decoder. Experiments on our inhouse dataset and AISHELL-1 show that FastCorrect 2 can further reduce the WER over the previous correction model with single candidate by 3.2% and 2.6%, demonstrating the effectiveness of leveraging multiple candidates in ASR error correction. FastCorrect 2 achieves better performance than the cascaded re-scoring and correction pipeline and can serve as a unified post-processing module for ASR.

cs.CL↗

arXiv2022

BinauralGrad: A Two-Stage Conditional Diffusion Probabilistic Model for Binaural Audio Synthesis

Binaural audio plays a significant role in constructing immersive augmented and virtual realities. As it is expensive to record binaural audio from the real world, synthesizing them from mono audio has attracted increasing attention. This synthesis process involves not only the basic physical warping of the mono audio, but also room reverberations and head/ear related filtrations, which, however, are difficult to accurately simulate in traditional digital signal processing. In this paper, we formulate the synthesis process from a different perspective by decomposing the binaural audio into a common part that shared by the left and right channels as well as a specific part that differs in each channel. Accordingly, we propose BinauralGrad, a novel two-stage framework equipped with diffusion models to synthesize them respectively. Specifically, in the first stage, the common information of the binaural audio is generated with a single-channel diffusion model conditioned on the mono audio, based on which the binaural audio is generated by a two-channel diffusion model in the second stage. Combining this novel perspective of two-stage synthesis with advanced generative models (i.e., the diffusion models),the proposed BinauralGrad is able to generate accurate and high-fidelity binaural audio samples. Experiment results show that on a benchmark dataset, BinauralGrad outperforms the existing baselines by a large margin in terms of both object and subject evaluation metrics (Wave L2: 0.128 vs. 0.157, MOS: 3.80 vs. 3.61). The generated audio samples (https://speechresearch.github.io/binauralgrad) and code (https://github.com/microsoft/NeuralSpeech/tree/master/BinauralGrad) are available online.

eess.AS↗

arXiv2022

Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-design

Antibodies are versatile proteins that can bind to pathogens and provide effective protection for human body. Recently, deep learning-based computational antibody design has attracted popular attention since it automatically mines the antibody patterns from data that could be complementary to human experiences. However, the computational methods heavily rely on high-quality antibody structure data, which is quite limited. Besides, the complementarity-determining region (CDR), which is the key component of an antibody that determines the specificity and binding affinity, is highly variable and hard to predict. Therefore, the data limitation issue further raises the difficulty of CDR generation for antibodies. Fortunately, there exists a large amount of sequence data of antibodies that can help model the CDR and alleviate the reliance on structure data. By witnessing the success of pre-training models for protein modeling, in this paper, we develop the antibody pre-training language model and incorporate it into the (antigen-specific) antibody design model in a systemic way. Specifically, we first pre-train an antibody language model based on the sequence data, then propose a one-shot way for sequence and structure generation of CDR to avoid the heavy cost and error propagation from an autoregressive manner, and finally leverage the pre-trained antibody model for the antigen-specific antibody generation model with some carefully designed modules. Through various experiments, we show that our method achieves superior performances over previous baselines on different tasks, such as sequence and structure generation and antigen-binding CDR-H3 design.

q-bio.BM↗

arXiv2022

TeleMelody: Lyric-to-Melody Generation with a Template-Based Two-Stage Method

Lyric-to-melody generation is an important task in automatic songwriting. Previous lyric-to-melody generation systems usually adopt end-to-end models that directly generate melodies from lyrics, which suffer from several issues: 1) lack of paired lyric-melody training data; 2) lack of control on generated melodies. In this paper, we develop TeleMelody, a two-stage lyric-to-melody generation system with music template (e.g., tonality, chord progression, rhythm pattern, and cadence) to bridge the gap between lyrics and melodies (i.e., the system consists of a lyric-to-template module and a template-to-melody module). TeleMelody has two advantages. First, it is data efficient. The template-to-melody module is trained in a self-supervised way (i.e., the source template is extracted from the target melody) that does not need any lyric-melody paired data. The lyric-to-template module is made up of some rules and a lyric-to-rhythm model, which is trained with paired lyric-rhythm data that is easier to obtain than paired lyric-melody data. Second, it is controllable. The design of template ensures that the generated melodies can be controlled by adjusting the musical elements in template. Both subjective and objective experimental evaluations demonstrate that TeleMelody generates melodies with higher quality, better controllability, and less requirement on paired lyric-melody data than previous generation systems.

cs.SD↗

arXiv2022

Museformer: Transformer with Fine- and Coarse-Grained Attention for Music Generation

Symbolic music generation aims to generate music scores automatically. A recent trend is to use Transformer or its variants in music generation, which is, however, suboptimal, because the full attention cannot efficiently model the typically long music sequences (e.g., over 10,000 tokens), and the existing models have shortcomings in generating musical repetition structures. In this paper, we propose Museformer, a Transformer with a novel fine- and coarse-grained attention for music generation. Specifically, with the fine-grained attention, a token of a specific bar directly attends to all the tokens of the bars that are most relevant to music structures (e.g., the previous 1st, 2nd, 4th and 8th bars, selected via similarity statistics); with the coarse-grained attention, a token only attends to the summarization of the other bars rather than each token of them so as to reduce the computational cost. The advantages are two-fold. First, it can capture both music structure-related correlations via the fine-grained attention, and other contextual information via the coarse-grained attention. Second, it is efficient and can model over 3X longer music sequences compared to its full-attention counterpart. Both objective and subjective experimental results demonstrate its ability to generate long music sequences with high quality and better structures.

cs.SD↗

arXiv2022

Transcormer: Transformer for Sentence Scoring with Sliding Language Modeling

Sentence scoring aims at measuring the likelihood score of a sentence and is widely used in many natural language processing scenarios, like reranking, which is to select the best sentence from multiple candidates. Previous works on sentence scoring mainly adopted either causal language modeling (CLM) like GPT or masked language modeling (MLM) like BERT, which have some limitations: 1) CLM only utilizes unidirectional information for the probability estimation of a sentence without considering bidirectional context, which affects the scoring quality; 2) MLM can only estimate the probability of partial tokens at a time and thus requires multiple forward passes to estimate the probability of the whole sentence, which incurs large computation and time cost. In this paper, we propose \textit{Transcormer} -- a Transformer model with a novel \textit{sliding language modeling} (SLM) for sentence scoring. Specifically, our SLM adopts a triple-stream self-attention mechanism to estimate the probability of all tokens in a sentence with bidirectional context and only requires a single forward pass. SLM can avoid the limitations of CLM (only unidirectional context) and MLM (multiple forward passes) and inherit their advantages, and thus achieve high effectiveness and efficiency in scoring. Experimental results on multiple tasks demonstrate that our method achieves better performance than other language modelings.

cs.CL↗

arXiv2022

Towards Deployment-Efficient Reinforcement Learning: Lower Bound and Optimality

Deployment efficiency is an important criterion for many real-world applications of reinforcement learning (RL). Despite the community's increasing interest, there lacks a formal theoretical formulation for the problem. In this paper, we propose such a formulation for deployment-efficient RL (DE-RL) from an "optimization with constraints" perspective: we are interested in exploring an MDP and obtaining a near-optimal policy within minimal \emph{deployment complexity}, whereas in each deployment the policy can sample a large batch of data. Using finite-horizon linear MDPs as a concrete structural model, we reveal the fundamental limit in achieving deployment efficiency by establishing information-theoretic lower bounds, and provide algorithms that achieve the optimal deployment efficiency. Moreover, our formulation for DE-RL is flexible and can serve as a building block for other practically relevant settings; we give "Safe DE-RL" and "Sample-Efficient DE-RL" as two examples, which may be worth future investigation.

cs.LG↗

arXiv2022

MeloForm: Generating Melody with Musical Form based on Expert Systems and Neural Networks

Human usually composes music by organizing elements according to the musical form to express music ideas. However, for neural network-based music generation, it is difficult to do so due to the lack of labelled data on musical form. In this paper, we develop MeloForm, a system that generates melody with musical form using expert systems and neural networks. Specifically, 1) we design an expert system to generate a melody by developing musical elements from motifs to phrases then to sections with repetitions and variations according to pre-given musical form; 2) considering the generated melody is lack of musical richness, we design a Transformer based refinement model to improve the melody without changing its musical form. MeloForm enjoys the advantages of precise musical form control by expert systems and musical richness learning via neural models. Both subjective and objective experimental evaluations demonstrate that MeloForm generates melodies with precise musical form control with 97.79% accuracy, and outperforms baseline systems in terms of subjective evaluation score by 0.75, 0.50, 0.86 and 0.89 in structure, thematic, richness and overall quality, without any labelled musical form data. Besides, MeloForm can support various kinds of forms, such as verse and chorus form, rondo form, variational form, sonata form, etc.

cs.SD↗

arXiv2022

Tailoring Molecules for Protein Pockets: a Transformer-based Generative Solution for Structured-based Drug Design

Structure-based drug design is drawing growing attentions in computer-aided drug discovery. Compared with the virtual screening approach where a pre-defined library of compounds are computationally screened, de novo drug design based on the structure of a target protein can provide novel drug candidates. In this paper, we present a generative solution named TamGent (Target-aware molecule generator with Transformer) that can directly generate candidate drugs from scratch for a given target, overcoming the limits imposed by existing compound libraries. Following the Transformer framework (a state-of-the-art framework in deep learning), we design a variant of Transformer encoder to process 3D geometric information of targets and pre-train the Transformer decoder on 10 million compounds from PubChem for candidate drug generation. Systematical evaluation on candidate compounds generated for targets from DrugBank shows that both binding affinity and drugability are largely improved. TamGent outperforms previous baselines in terms of both effectiveness and efficiency. The method is further verified by generating candidate compounds for the SARS-CoV-2 main protease and the oncogenic mutant KRAS G12C. The results show that our method not only re-discovers previously verified drug molecules , but also generates novel molecules with better docking scores, expanding the compound pool and potentially leading to the discovery of novel drugs.

q-bio.BM↗

arXiv2022

FastSpeech 2: Fast and High-Quality End-to-End Text to Speech

Non-autoregressive text to speech (TTS) models such as FastSpeech can synthesize speech significantly faster than previous autoregressive models with comparable quality. The training of FastSpeech model relies on an autoregressive teacher model for duration prediction (to provide more information as input) and knowledge distillation (to simplify the data distribution in output), which can ease the one-to-many mapping problem (i.e., multiple speech variations correspond to the same text) in TTS. However, FastSpeech has several disadvantages: 1) the teacher-student distillation pipeline is complicated and time-consuming, 2) the duration extracted from the teacher model is not accurate enough, and the target mel-spectrograms distilled from teacher model suffer from information loss due to data simplification, both of which limit the voice quality. In this paper, we propose FastSpeech 2, which addresses the issues in FastSpeech and better solves the one-to-many mapping problem in TTS by 1) directly training the model with ground-truth target instead of the simplified output from teacher, and 2) introducing more variation information of speech (e.g., pitch, energy and more accurate duration) as conditional inputs. Specifically, we extract duration, pitch and energy from speech waveform and directly take them as conditional inputs in training and use predicted values in inference. We further design FastSpeech 2s, which is the first attempt to directly generate speech waveform from text in parallel, enjoying the benefit of fully end-to-end inference. Experimental results show that 1) FastSpeech 2 achieves a 3x training speed-up over FastSpeech, and FastSpeech 2s enjoys even faster inference speed; 2) FastSpeech 2 and 2s outperform FastSpeech in voice quality, and FastSpeech 2 can even surpass autoregressive models. Audio samples are available at https://speechresearch.github.io/fastspeech2/.

eess.AS↗

arXiv2022

Analyzing and Mitigating Interference in Neural Architecture Search

Weight sharing is a popular approach to reduce the cost of neural architecture search (NAS) by reusing the weights of shared operators from previously trained child models. However, the rank correlation between the estimated accuracy and ground truth accuracy of those child models is low due to the interference among different child models caused by weight sharing. In this paper, we investigate the interference issue by sampling different child models and calculating the gradient similarity of shared operators, and observe: 1) the interference on a shared operator between two child models is positively correlated with the number of different operators; 2) the interference is smaller when the inputs and outputs of the shared operator are more similar. Inspired by these two observations, we propose two approaches to mitigate the interference: 1) MAGIC-T: rather than randomly sampling child models for optimization, we propose a gradual modification scheme by modifying one operator between adjacent optimization steps to minimize the interference on the shared operators; 2) MAGIC-A: forcing the inputs and outputs of the operator across all child models to be similar to reduce the interference. Experiments on a BERT search space verify that mitigating interference via each of our proposed methods improves the rank correlation of super-pet and combining both methods can achieve better results. Our discovered architecture outperforms RoBERTa$_{\rm base}$ by 1.1 and 0.6 points and ELECTRA$_{\rm base}$ by 1.6 and 1.1 points on the dev and test set of GLUE benchmark. Extensive results on the BERT compression, reading comprehension and ImageNet task demonstrate the effectiveness and generality of our proposed methods.

cs.CL↗

arXiv2022

Mixed-Phoneme BERT: Improving BERT with Mixed Phoneme and Sup-Phoneme Representations for Text to Speech

Recently, leveraging BERT pre-training to improve the phoneme encoder in text to speech (TTS) has drawn increasing attention. However, the works apply pre-training with character-based units to enhance the TTS phoneme encoder, which is inconsistent with the TTS fine-tuning that takes phonemes as input. Pre-training only with phonemes as input can alleviate the input mismatch but lack the ability to model rich representations and semantic information due to limited phoneme vocabulary. In this paper, we propose MixedPhoneme BERT, a novel variant of the BERT model that uses mixed phoneme and sup-phoneme representations to enhance the learning capability. Specifically, we merge the adjacent phonemes into sup-phonemes and combine the phoneme sequence and the merged sup-phoneme sequence as the model input, which can enhance the model capacity to learn rich contextual representations. Experiment results demonstrate that our proposed Mixed-Phoneme BERT significantly improves the TTS performance with 0.30 CMOS gain compared with the FastSpeech 2 baseline. The Mixed-Phoneme BERT achieves 3x inference speedup and similar voice quality to the previous TTS pre-trained model PnG BERT

eess.AS↗

arXiv2022

Inspector: Pixel-Based Automated Game Testing via Exploration, Detection, and Investigation

Deep reinforcement learning (DRL) has attracted much attention in automated game testing. Early attempts rely on game internal information for game space exploration, thus requiring deep integration with games, which is inconvenient for practical applications. In this work, we propose using only screenshots/pixels as input for automated game testing and build a general game testing agent, Inspector, that can be easily applied to different games without deep integration with games. In addition to covering all game space for testing, our agent tries to take human-like behaviors to interact with key objects in a game, since some bugs usually happen in player-object interactions. Inspector is based on purely pixel inputs and comprises three key modules: game space explorer, key object detector, and human-like object investigator. Game space explorer aims to explore the whole game space by using a curiosity-based reward function with pixel inputs. Key object detector aims to detect key objects in a game, based on a small number of labeled screenshots. Human-like object investigator aims to mimic human behaviors for investigating key objects via imitation learning. We conduct experiments on two popular video games: Shooter Game and Action RPG Game. Experiment results demonstrate the effectiveness of Inspector in exploring game space, detecting key objects, and investigating objects. Moreover, Inspector successfully discovers two potential bugs in those two games. The demo video of Inspector is available at https://github.com/Inspector-GameTesting/Inspector-GameTesting.

cs.AI↗

arXiv2022

Unified 2D and 3D Pre-Training of Molecular Representations

Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of all atoms. We note that most previous work handles 2D and 3D information separately, while jointly leveraging these two sources may foster a more informative representation. In this work, we explore this appealing idea and propose a new representation learning method based on a unified 2D and 3D pre-training. Atom coordinates and interatomic distances are encoded and then fused with atomic representations through graph neural networks. The model is pre-trained on three tasks: reconstruction of masked atoms and coordinates, 3D conformation generation conditioned on 2D graph, and 2D graph generation conditioned on 3D conformation. We evaluate our method on 11 downstream molecular property prediction tasks: 7 with 2D information only and 4 with both 2D and 3D information. Our method achieves state-of-the-art results on 10 tasks, and the average improvement on 2D-only tasks is 8.3%. Our method also achieves significant improvement on two 3D conformation generation tasks.

cs.LG↗