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The tensor-polarized structures of the deuteron can be probed through the proton-deuteron Drell-Yan process, where the proton is unpolarized and the deuteron is tensor-polarized. This measurement will be conducted at Fermilab in the near future. In this reaction, the twist-3 contribution is not negligible compared to the twist-2 contribution due to the limited invariant mass of the dilepton pair. We calculate the twist-3 contribution for the Drell-Yan cross section with a tensor-polarized deuteron target, preserving the U(1)-gauge invariance of the hadronic tensor. The cross sections and weighted cross sections are expressed in terms of the tensor-polarized parton distribution functions (PDFs), thus one can extract the PDFs $f_{1\scriptscriptstyle{LL}}$, $f_{\scriptscriptstyle{LT}}$, and $f^{(1)}_{\scriptscriptstyle{1LT}}$ from the experimental measurements of Drell-Yan process. Our study should be helpful to solve the puzzle in the tensor-polarized structures of the deuteron., Comment: 8 pages, 3 figures

In recent years, machine learning has demonstrated impressive capability in handling molecular science tasks. To support various molecular properties at scale, machine learning models are trained in the multi-task learning paradigm. Nevertheless, data of different molecular properties are often not aligned: some quantities, e.g. equilibrium structure, demand more cost to compute than others, e.g. energy, so their data are often generated by cheaper computational methods at the cost of lower accuracy, which cannot be directly overcome through multi-task learning. Moreover, it is not straightforward to leverage abundant data of other tasks to benefit a particular task. To handle such data heterogeneity challenges, we exploit the specialty of molecular tasks that there are physical laws connecting them, and design consistency training approaches that allow different tasks to exchange information directly so as to improve one another. Particularly, we demonstrate that the more accurate energy data can improve the accuracy of structure prediction. We also find that consistency training can directly leverage force and off-equilibrium structure data to improve structure prediction, demonstrating a broad capability for integrating heterogeneous data., Comment: Published as a conference paper at NeurIPS 2024

In this paper, we consider the subdivision map between two KLRW algebras of type $A^{(1)}_e$ and $A^{(1)}_{e+1}$. We show that the image of an idempotent indexed by a partition under this map is still an idempotent indexed by a partition, and give the form of this new partition. Moreover, we give an equality of some graded decomposition numbers., Comment: Comments welcomed

While recent large-scale text-to-speech (TTS) models have achieved significant progress, they still fall short in speech quality, similarity, and prosody. Considering speech intricately encompasses various attributes (e.g., content, prosody, timbre, and acoustic details) that pose significant challenges for generation, a natural idea is to factorize speech into individual subspaces representing different attributes and generate them individually. Motivated by it, we propose NaturalSpeech 3, a TTS system with novel factorized diffusion models to generate natural speech in a zero-shot way. Specifically, 1) we design a neural codec with factorized vector quantization (FVQ) to disentangle speech waveform into subspaces of content, prosody, timbre, and acoustic details; 2) we propose a factorized diffusion model to generate attributes in each subspace following its corresponding prompt. With this factorization design, NaturalSpeech 3 can effectively and efficiently model intricate speech with disentangled subspaces in a divide-and-conquer way. Experiments show that NaturalSpeech 3 outperforms the state-of-the-art TTS systems on quality, similarity, prosody, and intelligibility, and achieves on-par quality with human recordings. Furthermore, we achieve better performance by scaling to 1B parameters and 200K hours of training data., Comment: Achieving human-level quality and naturalness on multi-speaker datasets (e.g., LibriSpeech) in a zero-shot way

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in \url{https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling}., Comment: Survey Paper. 25 pages, 9 figures, and 3 tables

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including \emph{3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets}, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at \url{https://github.com/QizhiPei/BioT5}., Comment: Accepted by ACL 2024 (Findings)

Generalized distribution amplitudes (GDAs) of mesons can be probed by the reactions $e^- e^+ \to M_1 M_2 \gamma$, which are accessible at electron-positron colliders such as BESIII and Belle II. After discussing the neutral meson production case in the first paper of this series \cite{Pire:2023kng}, we discuss here the complementary case of the charged meson ($M^+ M^-$) production, where one can extract the complete information on GDAs from the interference of the amplitudes of the two competing processes where the photon is emitted either in the initial or in the final state. Considering the importance of the charged meson production, we present a complete expression for the interference term of the cross section which is experimentally accessible thanks to its charge conjugation specific property. We adopt two types of models for leading twist $\pi \pi$ GDAs to estimate the size of the interference term in the process $e^- e^+ \to \pi^+ \pi^- \gamma$ numerically, namely a model extracted from previous experimental results on $\gamma^* \gamma \to \pi^0 \pi^0$ at Belle and the asymptotic form predicted by QCD evolution equations. We include in the calculation the kinematical power suppressed (sometimes called kinematical higher-twist) corrections up to $1/Q^2$ for the helicity amplitudes. Both models of GDAs indicate that the kinematical corrections are not negligible for the interference term of the cross section measured at BESIII, thus it is necessary to include them if we try to extract the GDAs precisely. On the other side, the kinematical corrections are very tiny for the measurements at Belle II, and the leading twist-2 formula of the interference term will be good enough to describe the charge conjugation odd part of the differential cross section., Comment: 12 pages, 10 figures, accepted by Physical Review D

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose $\mathbf{FABind}$, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. $\mathbf{FABind}$ incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed $\mathbf{FABind}$ demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind, Comment: Accepted by Neural Information Processing Systems 2023 (NeurIPS 2023)

We investigate the magnetotransport of topological Dirac semimetals (DSMs) by taking into account the Lifshitz transition of the Fermi arc surface states. We demonstrate that a bulk momentum-dependent gap term, which is usually neglected in study of the bulk energy-band topology, can cause the Lifshitz transition by developing an additional Dirac cone for the surface to prevent the Fermi arcs from connecting the bulk Dirac points. As a result, the Weyl orbits can be turned off by the surface Dirac cone without destroying the bulk Dirac points. In response to the surface Lifshitz transition, the Weyl-orbit mechanism for the 3D quantum Hall effect (QHE) in topological DSMs will break down. The resulting quantized Hall plateaus can be thickness-dependent, similar to the Weyl-orbit mechanism, but their widths and quantized values become irregular. Accordingly, we propose that apart from the bulk Weyl nodes and Fermi arcs, the surface Lifshitz transition is also crucial for realizing stable Weyl orbits and 3D QHE in real materials., Comment: 7

There are three types of fragmentation functions (FFs) which are used to describe the twist-3 cross sections of the hard semi-inclusive processes under QCD collinear factorization, and they are called intrinsic, kinematical, and dynamical FFs. In this work, we investigate the theoretical relations among these FFs for a tensor-polarized spin-1 hadron. Three Lorentz-invariance relations (LIRs) are derived by using the identities between the nonlocal quark-quark and quark-gluon-quark operators, which guarantee the frame independence of the twist-3 spin observables. The QCD equation of motion (e.o.m.) relations are also presented for the tensor-polarized FFs. In addition, we also show that the intrinsic and kinematical twist-3 FFs can be decomposed into the contributions of twist-2 FFs and twist-3 three-parton FFs, and the latter are also called dynamical FFs. If one neglects the dynamical FFs, we can obtain relations which are analogous to the Wandzura-Wilczek (WW) relation. Then, the intrinsic and kinematical twist-3 FFs are expressed in terms of the leading-twist ones. Since the FFs of a spin-1 hadron can be measured at various experimental facilities in the near future, these theoretical relations will play an important role in the analysis of the collinear tensor-polarized FFs., Comment: 10 pages

Speech conveys more information than text, as the same word can be uttered in various voices to convey diverse information. Compared to traditional text-to-speech (TTS) methods relying on speech prompts (reference speech) for voice variability, using text prompts (descriptions) is more user-friendly since speech prompts can be hard to find or may not exist at all. TTS approaches based on the text prompt face two main challenges: 1) the one-to-many problem, where not all details about voice variability can be described in the text prompt, and 2) the limited availability of text prompt datasets, where vendors and large cost of data labeling are required to write text prompts for speech. In this work, we introduce PromptTTS 2 to address these challenges with a variation network to provide variability information of voice not captured by text prompts, and a prompt generation pipeline to utilize the large language models (LLM) to compose high quality text prompts. Specifically, the variation network predicts the representation extracted from the reference speech (which contains full information about voice variability) based on the text prompt representation. For the prompt generation pipeline, it generates text prompts for speech with a speech language understanding model to recognize voice attributes (e.g., gender, speed) from speech and a large language model to formulate text prompts based on the recognition results. Experiments on a large-scale (44K hours) speech dataset demonstrate that compared to the previous works, PromptTTS 2 generates voices more consistent with text prompts and supports the sampling of diverse voice variability, thereby offering users more choices on voice generation. Additionally, the prompt generation pipeline produces high-quality text prompts, eliminating the large labeling cost. The demo page of PromptTTS 2 is available online., Comment: Demo page: https://speechresearch.github.io/prompttts2

Retrosynthesis, which predicts the reactants of a given target molecule, is an essential task for drug discovery. In recent years, the machine learing based retrosynthesis methods have achieved promising results. In this work, we introduce RetroKNN, a local reaction template retrieval method to further boost the performance of template-based systems with non-parametric retrieval. We first build an atom-template store and a bond-template store that contain the local templates in the training data, then retrieve from these templates with a k-nearest-neighbor (KNN) search during inference. The retrieved templates are combined with neural network predictions as the final output. Furthermore, we propose a lightweight adapter to adjust the weights when combing neural network and KNN predictions conditioned on the hidden representation and the retrieved templates. We conduct comprehensive experiments on two widely used benchmarks, the USPTO-50K and USPTO-MIT. Especially for the top-1 accuracy, we improved 7.1% on the USPTO-50K dataset and 12.0% on the USPTO-MIT dataset. These results demonstrate the effectiveness of our method., Comment: AAAI-2023 camera ready

While Neural Machine Translation(NMT) has achieved great progress in recent years, it still suffers from inaccurate translation of entities (e.g., person/organization name, location), due to the lack of entity training instances. When we humans encounter an unknown entity during translation, we usually first look up in a dictionary and then organize the entity translation together with the translations of other parts to form a smooth target sentence. Inspired by this translation process, we propose an Extract-and-Attend approach to enhance entity translation in NMT, where the translation candidates of source entities are first extracted from a dictionary and then attended to by the NMT model to generate the target sentence. Specifically, the translation candidates are extracted by first detecting the entities in a source sentence and then translating the entities through looking up in a dictionary. Then, the extracted candidates are added as a prefix of the decoder input to be attended to by the decoder when generating the target sentence through self-attention. Experiments conducted on En-Zh and En-Ru demonstrate that the proposed method is effective on improving both the translation accuracy of entities and the overall translation quality, with up to 35% reduction on entity error rate and 0.85 gain on BLEU and 13.8 gain on COMET.

We outline the physics opportunities provided by the Electron Ion Collider (EIC). These include the study of the parton structure of the nucleon and nuclei, the onset of gluon saturation, the production of jets and heavy flavor, hadron spectroscopy and tests of fundamental symmetries. We review the present status and future challenges in EIC theory that have to be addressed in order to realize this ambitious and impactful physics program, including how to engage a diverse and inclusive workforce. In order to address these many-fold challenges, we propose a coordinated effort involving theory groups with differing expertise is needed. We discuss the scientific goals and scope of such an EIC Theory Alliance., Comment: 44 pages, ReVTeX, White Paper on EIC Theory Alliance

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text. Briefly, we detect the molecule names in each sequence and replace them to the corresponding SMILES. In this way, the SMILES could leverage the information from surrounding text, and vice versa. The above wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem are all fed into a language model for pre-training. Experimental results demonstrate that MolXPT outperforms strong baselines of molecular property prediction on MoleculeNet, performs comparably to the best model in text-molecule translation while using less than half of its parameters, and enables zero-shot molecular generation without finetuning., Comment: Accepted to ACL 2023; add more details about MoleculeNet finetune

Transformer networks have become the preferred architecture for many tasks due to their state-of-the-art performance. However, the optimal way to implement residual connections in Transformer, which are essential for effective training, is still debated. Two widely used variants are the Post-Layer-Normalization (Post-LN) and Pre-Layer-Normalization (Pre-LN) Transformers, which apply layer normalization after each residual block's output or before each residual block's input, respectively. While both variants enjoy their advantages, they also suffer from severe limitations: Post-LN causes gradient vanishing issue that hinders training deep Transformers, and Pre-LN causes representation collapse issue that limits model capacity. In this paper, we propose ResiDual, a novel Transformer architecture with Pre-Post-LN (PPLN), which fuses the connections in Post-LN and Pre-LN together and inherits their advantages while avoids their limitations. We conduct both theoretical analyses and empirical experiments to verify the effectiveness of ResiDual. Theoretically, we prove that ResiDual has a lower bound on the gradient to avoid the vanishing issue due to the residual connection from Pre-LN. Moreover, ResiDual also has diverse model representations to avoid the collapse issue due to the residual connection from Post-LN. Empirically, ResiDual outperforms both Post-LN and Pre-LN on several machine translation benchmarks across different network depths and data sizes. Thanks to the good theoretical and empirical performance, ResiDual Transformer can serve as a foundation architecture for different AI models (e.g., large language models). Our code is available at https://github.com/microsoft/ResiDual.

Traveling Salesman Problem (TSP), as a classic routing optimization problem originally arising in the domain of transportation and logistics, has become a critical task in broader domains, such as manufacturing and biology. Recently, Deep Reinforcement Learning (DRL) has been increasingly employed to solve TSP due to its high inference efficiency. Nevertheless, most of existing end-to-end DRL algorithms only perform well on small TSP instances and can hardly generalize to large scale because of the drastically soaring memory consumption and computation time along with the enlarging problem scale. In this paper, we propose a novel end-to-end DRL approach, referred to as Pointerformer, based on multi-pointer Transformer. Particularly, Pointerformer adopts both reversible residual network in the encoder and multi-pointer network in the decoder to effectively contain memory consumption of the encoder-decoder architecture. To further improve the performance of TSP solutions, Pointerformer employs both a feature augmentation method to explore the symmetries of TSP at both training and inference stages as well as an enhanced context embedding approach to include more comprehensive context information in the query. Extensive experiments on a randomly generated benchmark and a public benchmark have shown that, while achieving comparative results on most small-scale TSP instances as SOTA DRL approaches do, Pointerformer can also well generalize to large-scale TSPs., Comment: Accepted by AAAI 2023, February 2023

Scaling text-to-speech (TTS) to large-scale, multi-speaker, and in-the-wild datasets is important to capture the diversity in human speech such as speaker identities, prosodies, and styles (e.g., singing). Current large TTS systems usually quantize speech into discrete tokens and use language models to generate these tokens one by one, which suffer from unstable prosody, word skipping/repeating issue, and poor voice quality. In this paper, we develop NaturalSpeech 2, a TTS system that leverages a neural audio codec with residual vector quantizers to get the quantized latent vectors and uses a diffusion model to generate these latent vectors conditioned on text input. To enhance the zero-shot capability that is important to achieve diverse speech synthesis, we design a speech prompting mechanism to facilitate in-context learning in the diffusion model and the duration/pitch predictor. We scale NaturalSpeech 2 to large-scale datasets with 44K hours of speech and singing data and evaluate its voice quality on unseen speakers. NaturalSpeech 2 outperforms previous TTS systems by a large margin in terms of prosody/timbre similarity, robustness, and voice quality in a zero-shot setting, and performs novel zero-shot singing synthesis with only a speech prompt. Audio samples are available at https://speechresearch.github.io/naturalspeech2., Comment: A large-scale text-to-speech and singing voice synthesis system with latent diffusion models. Update: NaturalSpeech 2 extension to voice conversion and speech enhancement

We carry out the calculation of kinematical higher-twist corrections to the cross section of $\gamma^* \to M_1 M_2 \gamma$ up to twist 4, where $M_i$ is a scalar or pseudoscalar neutral meson. The three independant helicity amplitudes are presented in terms of the twist-2 generalized distribution amplitudes (GDAs), which are important non-perturbative quantities for understanding the 3D structure of hadrons. Since this process can be measured by BESIII in $e^+ e^-$ collisions, we perform the numerical estimate of the kinematical higher-twist corrections by using the kinematics of BESIII. We adopt the $\pi \pi$ GDA extracted from Belle measurements and the asymptotic $\pi \pi$ GDA to study the size of the kinematical corrections in the case of pion meson pair, and a model $\eta \eta$ GDA is used to see the impact of target mass corrections $\mathcal O(m^2/s)$ for $\gamma^* \to \eta \eta \gamma$. Our results show that the kinematical higher-twist corrections account for $\sim 20\%$ of the cross sections at BESIII on the average, and it is necessary to include them if one tries to extract GDAs from experimental measurements precisely. We also comment the case of $\pi^0 \eta$ production which is important for the search of hybrid mesons., Comment: 13 pages, 7 figures, title changed, added comment on $\pi \eta$ production, published in PRD107(2023), 114014

We study the energy-momentum tensor of spin-$0$ and spin-$\frac{1}{2}$ hadrons in momentum space. We parametrize this object in terms of so-called gravitational transverse-momentum distributions, and we identify in the quark sector the relations between the latter and the usual transverse-momentum distributions. Focusing on particular components of the energy-momentum tensor, we study momentum densities, flux of inertia and stress distribution in momentum space, revealing part of the wealth of physical information that can be gained from higher-twist transverse-momentum distributions., Comment: 9 pages, 4 figures

Transformer-based autoregressive (AR) methods have achieved appealing performance for varied sequence-to-sequence generation tasks, e.g., neural machine translation, summarization, and code generation, but suffer from low inference efficiency. To speed up the inference stage, many non-autoregressive (NAR) strategies have been proposed in the past few years. Among them, the conditional masked language model (CMLM) is one of the most versatile frameworks, as it can support many different sequence generation scenarios and achieve very competitive performance on these tasks. In this paper, we further introduce a simple yet effective adaptive masking over masking strategy to enhance the refinement capability of the decoder and make the encoder optimization easier. Experiments on \textbf{3} different tasks (neural machine translation, summarization, and code generation) with \textbf{15} datasets in total confirm that our proposed simple method achieves significant performance improvement over the strong CMLM model. Surprisingly, our proposed model yields state-of-the-art performance on neural machine translation (\textbf{34.62} BLEU on WMT16 EN$\to$RO, \textbf{34.82} BLEU on WMT16 RO$\to$EN, and \textbf{34.84} BLEU on IWSLT De$\to$En) and even better performance than the \textbf{AR} Transformer on \textbf{7} benchmark datasets with at least \textbf{2.2$\times$} speedup. Our code is available at GitHub., Comment: Accepted by AAAI2023

De novo molecular generation is an essential task for science discovery. Recently, fragment-based deep generative models have attracted much research attention due to their flexibility in generating novel molecules based on existing molecule fragments. However, the motif vocabulary, i.e., the collection of frequent fragments, is usually built upon heuristic rules, which brings difficulties to capturing common substructures from large amounts of molecules. In this work, we propose a new method, MiCaM, to generate molecules based on mined connection-aware motifs. Specifically, it leverages a data-driven algorithm to automatically discover motifs from a molecule library by iteratively merging subgraphs based on their frequency. The obtained motif vocabulary consists of not only molecular motifs (i.e., the frequent fragments), but also their connection information, indicating how the motifs are connected with each other. Based on the mined connection-aware motifs, MiCaM builds a connection-aware generator, which simultaneously picks up motifs and determines how they are connected. We test our method on distribution-learning benchmarks (i.e., generating novel molecules to resemble the distribution of a given training set) and goal-directed benchmarks (i.e., generating molecules with target properties), and achieve significant improvements over previous fragment-based baselines. Furthermore, we demonstrate that our method can effectively mine domain-specific motifs for different tasks.

Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design. Recently, the combination of ML-based single-step reaction predictors with multi-step planners has led to promising results. However, the single-step predictors are mostly trained offline to optimize the single-step accuracy, without considering complete routes. Here, we leverage reinforcement learning (RL) to improve the single-step predictor, by using a tree-shaped MDP to optimize complete routes. Specifically, we propose a novel online training algorithm, called Planning with Dual Value Networks (PDVN), which alternates between the planning phase and updating phase. In PDVN, we construct two separate value networks to predict the synthesizability and cost of molecules, respectively. To maintain the single-step accuracy, we design a two-branch network structure for the single-step predictor. On the widely-used USPTO dataset, our PDVN algorithm improves the search success rate of existing multi-step planners (e.g., increasing the success rate from 85.79% to 98.95% for Retro*, and reducing the number of model calls by half while solving 99.47% molecules for RetroGraph). Additionally, PDVN helps find shorter synthesis routes (e.g., reducing the average route length from 5.76 to 4.83 for Retro*, and from 5.63 to 4.78 for RetroGraph). Our code is available at \url{https://github.com/DiXue98/PDVN}., Comment: Accepted to ICML 2023

Nearest neighbor machine translation augments the Autoregressive Translation~(AT) with $k$-nearest-neighbor retrieval, by comparing the similarity between the token-level context representations of the target tokens in the query and the datastore. However, the token-level representation may introduce noise when translating ambiguous words, or fail to provide accurate retrieval results when the representation generated by the model contains indistinguishable context information, e.g., Non-Autoregressive Translation~(NAT) models. In this paper, we propose a novel $n$-gram nearest neighbor retrieval method that is model agnostic and applicable to both AT and NAT models. Specifically, we concatenate the adjacent $n$-gram hidden representations as the key, while the tuple of corresponding target tokens is the value. In inference, we propose tailored decoding algorithms for AT and NAT models respectively. We demonstrate that the proposed method consistently outperforms the token-level method on both AT and NAT models as well on general as on domain adaptation translation tasks. On domain adaptation, the proposed method brings $1.03$ and $2.76$ improvements regarding the average BLEU score on AT and NAT models respectively.

Machine learning methods for conditional data generation usually build a mapping from source conditional data X to target data Y. The target Y (e.g., text, speech, music, image, video) is usually high-dimensional and complex, and contains information that does not exist in source data, which hinders effective and efficient learning on the source-target mapping. In this paper, we present a learning paradigm called regeneration learning for data generation, which first generates Y' (an abstraction/representation of Y) from X and then generates Y from Y'. During training, Y' is obtained from Y through either handcrafted rules or self-supervised learning and is used to learn X-->Y' and Y'-->Y. Regeneration learning extends the concept of representation learning to data generation tasks, and can be regarded as a counterpart of traditional representation learning, since 1) regeneration learning handles the abstraction (Y') of the target data Y for data generation while traditional representation learning handles the abstraction (X') of source data X for data understanding; 2) both the processes of Y'-->Y in regeneration learning and X-->X' in representation learning can be learned in a self-supervised way (e.g., pre-training); 3) both the mappings from X to Y' in regeneration learning and from X' to Y in representation learning are simpler than the direct mapping from X to Y. We show that regeneration learning can be a widely-used paradigm for data generation (e.g., text generation, speech recognition, speech synthesis, music composition, image generation, and video generation) and can provide valuable insights into developing data generation methods.

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., Comment: NeurIPS 2022

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., Comment: Accepted by ICDM-22 (Best Student Paper Runner-Up Awards)

Error correction in automatic speech recognition (ASR) aims to correct those incorrect words in sentences generated by ASR models. Since recent ASR models usually have low word error rate (WER), to avoid affecting originally correct tokens, error correction models should only modify incorrect words, and therefore detecting incorrect words is important for error correction. Previous works on error correction either implicitly detect error words through target-source attention or CTC (connectionist temporal classification) loss, or explicitly locate specific deletion/substitution/insertion errors. However, implicit error detection does not provide clear signal about which tokens are incorrect and explicit error detection suffers from low detection accuracy. In this paper, we propose SoftCorrect with a soft error detection mechanism to avoid the limitations of both explicit and implicit error detection. Specifically, we first detect whether a token is correct or not through a probability produced by a dedicatedly designed language model, and then design a constrained CTC loss that only duplicates the detected incorrect tokens to let the decoder focus on the correction of error tokens. Compared with implicit error detection with CTC loss, SoftCorrect provides explicit signal about which words are incorrect and thus does not need to duplicate every token but only incorrect tokens; compared with explicit error detection, SoftCorrect does not detect specific deletion/substitution/insertion errors but just leaves it to CTC loss. Experiments on AISHELL-1 and Aidatatang datasets show that SoftCorrect achieves 26.1% and 9.4% CER reduction respectively, outperforming previous works by a large margin, while still enjoying fast speed of parallel generation., Comment: AAAI 2023

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.

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., Comment: Accepted by the Thirty-sixth Conference on Neural Information Processing Systems (NeurIPS 2022)

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e., BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large scale biomedical literature. We evaluate BioGPT on six biomedical NLP tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms. Code is available at https://github.com/microsoft/BioGPT., Comment: Published at Briefings in Bioinformatics. Code is available at https://github.com/microsoft/BioGPT

We estimate kinematical higher-twist (up to twist 4) corrections to the $\gamma^*(q_1) \gamma(q_2) \to M(p_1) \bar{M}(p_2)$ amplitudes at large $Q^2=-q_1^2$ and small $s=(q_1+q_2)^2$, where $M$ is a scalar or pseudoscalar meson. This process is known to factorize at leading twist into a perturbatively calculable coefficient function and generalized distribution amplitudes (GDAs). The kinematical higher-twist contributions of order $s/Q^2$ and $m^2/Q^2$ turn out to be important in the cross section, considering the kinematics accessible at Belle and Belle II. We present numerical estimates for the cross section for $\gamma^* \gamma \to \pi^0 \pi^0$ with the $\pi \pi$ GDA extracted from Belle measurements and with the asymptotic $\pi \pi$ GDA as inputs to study the magnitude of the kinematical corrections. To see how the target mass corrections of order $m^2/Q^2$ affect the cross section, we also perform the calculation for $\gamma^* \gamma \to \eta \eta$ by using a model $\eta \eta$ GDA.In the range $s> 1$ GeV$^2$, the kinematical higher-twist corrections account for $\sim 15 \%$ of the total cross section, an effect which is not negligible. Since $\pi \pi$ GDAs are the best way to access the pion energy-momentum tensor (EMT), our study demonstrates that an accurate evaluation of EMT form factors requires the inclusion of kinematical higher-twist contributions., Comment: 17 pages, 7 figures

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.

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.