Chang Su

Matthew Brendel, Chang Su, Zilong Bai et al.

Single-cell RNA-sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states and phenotypes, and has helped elucidate biological processes, such as those occurring during development of complex organisms and improved our understanding of disease states, such as cancer, diabetes, and COVID, among others. Deep learning, a recent advance of artificial intelligence that has been used to address many problems involving large datasets, has also emerged as a promising tool for scRNA-seq data analysis, as it has a capacity to extract informative, compact features from noisy, heterogeneous, and high-dimensional scRNA-seq data to improve downstream analysis. The present review aims at surveying recently developed deep learning techniques in scRNA-seq data analysis, identifying key steps within the scRNA-seq data analysis pipeline that have been advanced by deep learning, and explaining the benefits of deep learning over more conventional analysis tools. Finally, we summarize the challenges in current deep learning approaches faced within scRNA-seq data and discuss potential directions for improvements in deep algorithms for scRNA-seq data analysis.

Zhongkai Hao, Jiachen Yao, Chang Su et al.

While significant progress has been made on Physics-Informed Neural Networks (PINNs), a comprehensive comparison of these methods across a wide range of Partial Differential Equations (PDEs) is still lacking. This study introduces PINNacle, a benchmarking tool designed to fill this gap. PINNacle provides a diverse dataset, comprising over 20 distinct PDEs from various domains, including heat conduction, fluid dynamics, biology, and electromagnetics. These PDEs encapsulate key challenges inherent to real-world problems, such as complex geometry, multi-scale phenomena, nonlinearity, and high dimensionality. PINNacle also offers a user-friendly toolbox, incorporating about 10 state-of-the-art PINN methods for systematic evaluation and comparison. We have conducted extensive experiments with these methods, offering insights into their strengths and weaknesses. In addition to providing a standardized means of assessing performance, PINNacle also offers an in-depth analysis to guide future research, particularly in areas such as domain decomposition methods and loss reweighting for handling multi-scale problems and complex geometry. To the best of our knowledge, it is the largest benchmark with a diverse and comprehensive evaluation that will undoubtedly foster further research in PINNs.

Yilun Liu, Shimin Tao, Xiaofeng Zhao et al.

Instruction tuning is crucial for enabling Language Learning Models (LLMs) in responding to human instructions. The quality of instruction pairs used for tuning greatly affects the performance of LLMs. However, the manual creation of high-quality instruction datasets is costly, leading to the adoption of automatic generation of instruction pairs by LLMs as a popular alternative. To ensure the high quality of LLM-generated instruction datasets, several approaches have been proposed. Nevertheless, existing methods either compromise dataset integrity by filtering a large proportion of samples, or are unsuitable for industrial applications. In this paper, instead of discarding low-quality samples, we propose CoachLM, a novel approach to enhance the quality of instruction datasets through automatic revisions on samples in the dataset. CoachLM is trained from the samples revised by human experts and significantly increases the proportion of high-quality samples in the dataset from 17.7% to 78.9%. The effectiveness of CoachLM is further assessed on various real-world instruction test sets. The results show that CoachLM improves the instruction-following capabilities of the instruction-tuned LLM by an average of 29.9%, which even surpasses larger LLMs with nearly twice the number of parameters. Furthermore, CoachLM is successfully deployed in a data management system for LLMs at Huawei, resulting in an efficiency improvement of up to 20% in the cleaning of 40k real-world instruction pairs. We release various assets of CoachLM, including the training data, code and test set (https://github.com/lunyiliu/CoachLM).

Jiachen Yao, Chang Su, Zhongkai Hao et al.

Physics-informed Neural Networks (PINNs) have recently achieved remarkable progress in solving Partial Differential Equations (PDEs) in various fields by minimizing a weighted sum of PDE loss and boundary loss. However, there are several critical challenges in the training of PINNs, including the lack of theoretical frameworks and the imbalance between PDE loss and boundary loss. In this paper, we present an analysis of second-order non-homogeneous PDEs, which are classified into three categories and applicable to various common problems. We also characterize the connections between the training loss and actual error, guaranteeing convergence under mild conditions. The theoretical analysis inspires us to further propose MultiAdam, a scale-invariant optimizer that leverages gradient momentum to parameter-wisely balance the loss terms. Extensive experiment results on multiple problems from different physical domains demonstrate that our MultiAdam solver can improve the predictive accuracy by 1-2 orders of magnitude compared with strong baselines.

Xinyue Hu, Lin Gu, Kazuma Kobayashi et al.

Medical visual question answering (VQA) aims to answer clinically relevant questions regarding input medical images. This technique has the potential to improve the efficiency of medical professionals while relieving the burden on the public health system, particularly in resource-poor countries. Existing medical VQA methods tend to encode medical images and learn the correspondence between visual features and questions without exploiting the spatial, semantic, or medical knowledge behind them. This is partially because of the small size of the current medical VQA dataset, which often includes simple questions. Therefore, we first collected a comprehensive and large-scale medical VQA dataset, focusing on chest X-ray images. The questions involved detailed relationships, such as disease names, locations, levels, and types in our dataset. Based on this dataset, we also propose a novel baseline method by constructing three different relationship graphs: spatial relationship, semantic relationship, and implicit relationship graphs on the image regions, questions, and semantic labels. The answer and graph reasoning paths are learned for different questions.

Ailin Huang, Ang Li, Aobo Kong et al.

We introduce Step 3.5 Flash, a sparse Mixture-of-Experts (MoE) model that bridges frontier-level agentic intelligence and computational efficiency. We focus on what matters most when building agents: sharp reasoning and fast, reliable execution. Step 3.5 Flash pairs a 196B-parameter foundation with 11B active parameters for efficient inference. It is optimized with interleaved 3:1 sliding-window/full attention and Multi-Token Prediction (MTP-3) to reduce the latency and cost of multi-round agentic interactions. To reach frontier-level intelligence, we design a scalable reinforcement learning framework that combines verifiable signals with preference feedback, while remaining stable under large-scale off-policy training, enabling consistent self-improvement across mathematics, code, and tool use. Step 3.5 Flash demonstrates strong performance across agent, coding, and math tasks, achieving 85.4% on IMO-AnswerBench, 86.4% on LiveCodeBench-v6 (2024.08-2025.05), 88.2% on tau2-Bench, 69.0% on BrowseComp (with context management), and 51.0% on Terminal-Bench 2.0, comparable to frontier models such as GPT-5.2 xHigh and Gemini 3.0 Pro. By redefining the efficiency frontier, Step 3.5 Flash provides a high-density foundation for deploying sophisticated agents in real-world industrial environments.

Chang Guo, Juyuan Zhang, Chang Su et al.

Propagation models are essential for modeling and simulating dynamic processes such as epidemics and information diffusion. However, existing tools struggle to scale to large-scale graphs that emerge across social networks, epidemic networks and so on, due to limited algorithmic efficiency, weak scalability, and high communication overhead. We present FS_GPlib, a unified library that enables efficient, high-fidelity propagation modeling on Web-scale graphs. FS_GPlib introduces a dual-acceleration framework: it combines micro-level synchronous message-passing updates with macro-level batched Monte Carlo simulation, leveraging high-dimensional tensor operations for parallel execution. To further enhance scalability, it supports distributed simulation via a novel target-node-based graph partitioning strategy that minimizes communication overhead while maintaining load balance. Theoretically, we show that under ideal assumptions, the runtime of simulations converges approximately to a constant. Extensive experiments demonstrate up to 35,000 times speedup over standard libraries such as NDlib and execution of a full Monte Carlo simulation on a Web-scale (billion-edge) graph in 11 seconds while maintaining high simulation fidelity. FS_GPlib supports 29 propagation models-including epidemic and opinion dynamics and dynamic network models-and offers a lightweight Python API compatible with mainstream data science ecosystems. By addressing the unique challenges of modeling diffusion and cascades on the Web, FS_GPlib provides a scalable, extensible, and theoretically grounded solution for large-scale propagation analysis in epidemiology, social media analysis, and online network dynamics. Code available at: https://github.com/Allen-Ciel/FS_GPlib.

Weijie Chen, Yongzhu Chang, Rongsheng Zhang et al.

Simile interpretation (SI) and simile generation (SG) are challenging tasks for NLP because models require adequate world knowledge to produce predictions. Previous works have employed many hand-crafted resources to bring knowledge-related into models, which is time-consuming and labor-intensive. In recent years, pre-trained language models (PLMs) based approaches have become the de-facto standard in NLP since they learn generic knowledge from a large corpus. The knowledge embedded in PLMs may be useful for SI and SG tasks. Nevertheless, there are few works to explore it. In this paper, we probe simile knowledge from PLMs to solve the SI and SG tasks in the unified framework of simile triple completion for the first time. The backbone of our framework is to construct masked sentences with manual patterns and then predict the candidate words in the masked position. In this framework, we adopt a secondary training process (Adjective-Noun mask Training) with the masked language model (MLM) loss to enhance the prediction diversity of candidate words in the masked position. Moreover, pattern ensemble (PE) and pattern search (PS) are applied to improve the quality of predicted words. Finally, automatic and human evaluations demonstrate the effectiveness of our framework in both SI and SG tasks.

Yuang Li, Min Zhang, Chang Su et al.

The recognition of rare named entities, such as personal names and terminologies, is challenging for automatic speech recognition (ASR) systems, especially when they are not frequently observed in the training data. In this paper, we introduce keyword spotting enhanced Whisper (KWS-Whisper), a novel ASR system that leverages the Whisper model and performs open-vocabulary keyword spotting (OV-KWS) on the hidden states of the Whisper encoder to recognize user-defined named entities. These entities serve as prompts for the Whisper decoder. To optimize the model, we propose a multitask training approach that learns OV-KWS and contextual-ASR tasks. We evaluate our approach on Chinese Aishell hot word subsets and two internal code-switching test sets and show that it significantly improves the entity recall compared to the original Whisper model. Moreover, we demonstrate that the OV-KWS can be a plug-and-play module to enhance the ASR error correction methods and frozen Whisper models.

Xinyue Hu, Lin Gu, Liangchen Liu et al.

Existing video domain adaption (DA) methods need to store all temporal combinations of video frames or pair the source and target videos, which are memory cost expensive and can't scale up to long videos. To address these limitations, we propose a memory-efficient graph-based video DA approach as follows. At first our method models each source or target video by a graph: nodes represent video frames and edges represent the temporal or visual similarity relationship between frames. We use a graph attention network to learn the weight of individual frames and simultaneously align the source and target video into a domain-invariant graph feature space. Instead of storing a large number of sub-videos, our method only constructs one graph with a graph attention mechanism for one video, reducing the memory cost substantially. The extensive experiments show that, compared with the state-of-art methods, we achieved superior performance while reducing the memory cost significantly.

Zhongkai Hao, Chang Su, Songming Liu et al. · tsinghua

Pre-training has been investigated to improve the efficiency and performance of training neural operators in data-scarce settings. However, it is largely in its infancy due to the inherent complexity and diversity, such as long trajectories, multiple scales and varying dimensions of partial differential equations (PDEs) data. In this paper, we present a new auto-regressive denoising pre-training strategy, which allows for more stable and efficient pre-training on PDE data and generalizes to various downstream tasks. Moreover, by designing a flexible and scalable model architecture based on Fourier attention, we can easily scale up the model for large-scale pre-training. We train our PDE foundation model with up to 0.5B parameters on 10+ PDE datasets with more than 100k trajectories. Extensive experiments show that we achieve SOTA on these benchmarks and validate the strong generalizability of our model to significantly enhance performance on diverse downstream PDE tasks like 3D data. Code is available at \url{https://github.com/thu-ml/DPOT}.

Xiang Geng, Ming Zhu, Jiahuan Li et al.

The scarcity of non-English data limits the development of non-English large language models (LLMs). Transforming English-centric LLMs to non-English has been identified as an effective and resource-efficient method. Previous works start from base LLMs and perform knowledge distillation (KD) with data generated by stronger LLMs, e.g. GPT-4. Compared to base LLMs, chat LLMs are further optimized for advanced abilities, e.g. multi-turn conversation and human preference alignment, and thus more powerful in both helpfulness and safety. However, transforming a chat LLM involves two critical issues: (1) How can we effectively transfer advanced abilities without their supervised data? (2) How can we prevent the original knowledge from catastrophic forgetting during transformation? We target these issues by introducing a simple framework called TransLLM. For the first issue, TransLLM divides the transfer problem into some common sub-tasks with the translation chain-of-thought, which uses the translation as the bridge between English and non-English step-by-step. We further enhance the performance of sub-tasks with publicly available data. For the second issue, we propose a method comprising two synergistic components: low-rank adaptation for training to maintain the original LLM parameters, and recovery KD, which utilizes data generated by the chat LLM itself to recover the original knowledge from the frozen parameters. In the experiments, we transform the LLaMA-2-chat-7B to the Thai language. Our method, using only single-turn data, outperforms strong baselines and ChatGPT on multi-turn benchmark MT-bench. Furthermore, our method, without safety data, rejects more harmful queries of safety benchmark AdvBench than both ChatGPT and GPT-4. Code is available at https://github.com/hy5468/TransLLM.

Haotian Ye, Haowei Lin, Jingyi Tang et al.

Language models are increasingly used in scientific discovery to generate hypotheses, propose candidate solutions, implement systems, and iteratively refine them. At the core of these trial-and-error loops lies evaluation: the process of obtaining feedback on candidate solutions via verifiers, simulators, or task-specific scoring functions. While prior work has highlighted the importance of evaluation, it has not explicitly formulated the problem of how evaluation-driven discovery loops can be scaled up in a principled and effective manner to push the boundaries of scientific discovery, a problem this paper seeks to address. We introduce Simple Test-time Evaluation-driven Scaling (SimpleTES), a general framework that strategically combines parallel exploration, feedback-driven refinement, and local selection, revealing substantial gains unlocked by scaling evaluation-driven discovery loops along the right dimensions. Across 21 scientific problems spanning six domains, SimpleTES discovers state-of-the-art solutions using gpt-oss models, consistently outperforming both frontier-model baselines and sophisticated optimization pipelines. Particularly, we sped up the widely used LASSO algorithm by over 2x, designed quantum circuit routing policies that reduce gate overhead by 24.5%, and discovered new Erdos minimum overlap constructions that surpass the best-known results. Beyond novel discoveries, SimpleTES produces trajectory-level histories that naturally supervise feedback-driven learning. When post-trained on successful trajectories, models not only improve efficiency on seen problems but also generalize to unseen problems, discovering solutions that base models fail to uncover. Together, our results establish effective evaluation-driven loop scaling as a central axis for advancing LLM-driven scientific discovery, and provide a simple yet practical framework for realizing these gains.

Chang Su, Ming Li, Zhanglin Shangguan et al.

Coordinated operation of alkaline water electrolysis (AWE) systems with multiple electrolyzers under fluctuating renewable power input is challenging due to varying power availability and dynamic safety constraints. Moreover, the conventional separation between optimization and control may result in inconsistent decisions across timescales. To address these issues, this paper proposes a two-layer coordinated operation method integrating feedback optimization (FO) with a projection-based safety layer. The FO layer generates real-time reference inputs to improve renewable energy utilization, while the safety layer corrects these inputs to ensure compliance with operational and safety constraints. To explicitly address the safety constraints arising from the inertial dynamics of AWE systems, discrete-time control barrier function theory is incorporated into the safety layer, thereby enhancing safety assurance and online computational tractability. Theoretical analysis establishes the feasibility and effectiveness of the proposed method. Case studies based on annual wind generation data show that the proposed method achieves high energy utilization, maintains safe operation, and demonstrates online applicability, scalability, and robustness.

Minggui He, Yilun Liu, Shimin Tao et al.

Despite recent breakthroughs in reasoning-enhanced large language models (LLMs) like DeepSeek-R1, incorporating inference-time reasoning into machine translation (MT), where human translators naturally employ structured, multi-layered reasoning chain-of-thoughts (CoTs), is yet underexplored. Existing methods either design a fixed CoT tailored for a specific MT sub-task (e.g., literature translation), or rely on synthesizing CoTs unaligned with humans and supervised fine-tuning (SFT) prone to overfitting, limiting their adaptability to diverse translation scenarios. This paper introduces R1-Translator (R1-T1), a novel framework to achieve inference-time reasoning for general MT via reinforcement learning (RL) with human-aligned CoTs comprising six common patterns. Our approach pioneers three innovations: (1) extending reasoning-based translation to broader MT scenarios (e.g., multilingual MT, domain MT) unseen in the training phase; (2) formalizing six expert-curated CoT templates that mirror hybrid human strategies like context-aware paraphrasing and back translation; and (3) enabling self-evolving CoT discovery through RL. Both human and automatic evaluation results indicate a steady translation performance improvement in a total of 10+ languages and 40+ translation directions on Flores-101 test set and four domain-specific MT tasks, especially on the languages unseen from training.

Haofei Zhao, Yilun Liu, Shimin Tao et al.

Machine Translation Quality Estimation (MTQE) is the task of estimating the quality of machine-translated text in real time without the need for reference translations, which is of great importance for the development of MT. After two decades of evolution, QE has yielded a wealth of results. This article provides a comprehensive overview of QE datasets, annotation methods, shared tasks, methodologies, challenges, and future research directions. It begins with an introduction to the background and significance of QE, followed by an explanation of the concepts and evaluation metrics for word-level QE, sentence-level QE, document-level QE, and explainable QE. The paper categorizes the methods developed throughout the history of QE into those based on handcrafted features, deep learning, and Large Language Models (LLMs), with a further division of deep learning-based methods into classic deep learning and those incorporating pre-trained language models (LMs). Additionally, the article details the advantages and limitations of each method and offers a straightforward comparison of different approaches. Finally, the paper discusses the current challenges in QE research and provides an outlook on future research directions.

Songming Liu, Chang Su, Jiachen Yao et al.

Physics-informed neural networks (PINNs) have shown promise in solving various partial differential equations (PDEs). However, training pathologies have negatively affected the convergence and prediction accuracy of PINNs, which further limits their practical applications. In this paper, we propose to use condition number as a metric to diagnose and mitigate the pathologies in PINNs. Inspired by classical numerical analysis, where the condition number measures sensitivity and stability, we highlight its pivotal role in the training dynamics of PINNs. We prove theorems to reveal how condition number is related to both the error control and convergence of PINNs. Subsequently, we present an algorithm that leverages preconditioning to improve the condition number. Evaluations of 18 PDE problems showcase the superior performance of our method. Significantly, in 7 of these problems, our method reduces errors by an order of magnitude. These empirical findings verify the critical role of the condition number in PINNs' training.

Jiaxin Guo, Minghan Wang, Xiaosong Qiao et al.

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). Previous works usually adopt end-to-end models and has strong dependency on Pseudo Paired Data and Original Paired Data. But when only pre-training on Pseudo Paired Data, previous models have negative effect on correction. While fine-tuning on Original Paired Data, the source side data must be transcribed by a well-trained ASR model, which takes a lot of time and not universal. In this paper, we propose UCorrect, an unsupervised Detector-Generator-Selector framework for ASR Error Correction. UCorrect has no dependency on the training data mentioned before. The whole procedure is first to detect whether the character is erroneous, then to generate some candidate characters and finally to select the most confident one to replace the error character. Experiments on the public AISHELL-1 dataset and WenetSpeech dataset show the effectiveness of UCorrect for ASR error correction: 1) it achieves significant WER reduction, achieves 6.83\% even without fine-tuning and 14.29\% after fine-tuning; 2) it outperforms the popular NAR correction models by a large margin with a competitive low latency; and 3) it is an universal method, as it reduces all WERs of the ASR model with different decoding strategies and reduces all WERs of ASR models trained on different scale datasets.

Chang Su, Zhongkai Hao, Zhizhou Zhang et al.

Large language models (LLMs) with reasoning abilities have demonstrated growing promise for tackling complex scientific problems. Yet such tasks are inherently domain-specific, unbounded and open-ended, demanding exploration across vast and flexible solution spaces. Existing approaches, whether purely learning-based or reliant on carefully designed workflows, often suffer from limited exploration efficiency and poor generalization. To overcome these challenges, we present HELIX -- a Hierarchical Evolutionary reinforcement Learning framework with In-context eXperiences. HELIX introduces two key novelties: (i) a diverse yet high-quality pool of candidate solutions that broadens exploration through in-context learning, and (ii) reinforcement learning for iterative policy refinement that progressively elevates solution quality. This synergy enables the discovery of more advanced solutions. On the circle packing task, HELIX achieves state-of-the-art result with a sum of radii of 2.63598308 using only a 14B model. Across standard machine learning benchmarks, HELIX further surpasses GPT-4o with a carefully engineered pipeline, delivering an average F1 improvement of 5.95 points on the Adult and Bank Marketing datasets.

Yigang Chen, Xiang Ji, Ziyue Zhang et al.

Deep learning-based drug-target interaction (DTI) prediction methods have demonstrated strong performance; however, real-world applicability remains constrained by limited data diversity and modeling complexity. To address these challenges, we propose SCOPE-DTI, a unified framework combining a large-scale, balanced semi-inductive human DTI dataset with advanced deep learning modeling. Constructed from 13 public repositories, the SCOPE dataset expands data volume by up to 100-fold compared to common benchmarks such as the Human dataset. The SCOPE model integrates three-dimensional protein and compound representations, graph neural networks, and bilinear attention mechanisms to effectively capture cross domain interaction patterns, significantly outperforming state-of-the-art methods across various DTI prediction tasks. Additionally, SCOPE-DTI provides a user-friendly interface and database. We further validate its effectiveness by experimentally identifying anticancer targets of Ginsenoside Rh1. By offering comprehensive data, advanced modeling, and accessible tools, SCOPE-DTI accelerates drug discovery research.

Chang Su, Dengliang Shi, Siyuan Huang et al.

Large language models (LLMs) have increasingly been explored as powerful text embedders. Existing LLM-based text embedding approaches often leverage the embedding of the final token, typically a reserved special token such as [EOS]. However, these tokens have not been intentionally trained to capture the semantics of the whole context, limiting their capacity as text embeddings, especially for retrieval and re-ranking tasks. We propose to add a new training stage before contrastive learning to enrich the semantics of the final token embedding. This stage employs bidirectional generative reconstruction tasks, namely EBQ2D (Embedding-Based Query-to-Document) and EBD2Q (Embedding-Based Document-to-Query), which interleave to anchor the [EOS] embedding and reconstruct either side of Query-Document pairs. Experimental results demonstrate that our additional training stage significantly improves LLM performance on the Massive Text Embedding Benchmark (MTEB), achieving new state-of-the-art results across different LLM base models and scales.

Zhijun Zeng, Youjia Zheng, Chang Su et al.

Tissue mechanics--stiffness, density and impedance contrast--are broadly informative biomarkers across diseases, yet routine CT, MRI, and B-mode ultrasound rarely quantify them directly. While ultrasound tomography (UT) is intrinsically suited to in-vivo biomechanical assessment by capturing transmitted and reflected wavefields, efficient and accurate full-wave scattering models remain a bottleneck. Here, we introduce a generative neural physics framework that fuses generative models with physics-informed partial differential equation (PDE) solvers to produce rapid, high-fidelity 3D quantitative imaging of tissue mechanics. A compact neural surrogate for full-wave propagation is trained on limited cross-modality data, preserving physical accuracy while enabling efficient inversion. This enables, for the first time, accurate and efficient quantitative volumetric imaging of in vivo human breast and musculoskeletal tissues in under ten minutes, providing spatial maps of tissue mechanical properties not available from conventional reflection-mode or standard UT reconstructions. The resulting images reveal biomechanical features in bone, muscle, fat, and glandular tissues, maintaining structural resolution comparable to 3T MRI while providing substantially greater sensitivity to disease-related tissue mechanics.

Xuan Wang, Kai Ruan, Liyang Qian et al.

Text-driven motion generation has attracted increasing attention due to its broad applications in virtual reality, animation, and robotics. While existing methods typically model human and animal motion separately, a joint cross-species approach offers key advantages, such as a unified representation and improved generalization. However, morphological differences across species remain a key challenge, often compromising motion plausibility. To address this, we propose X-MoGen, the first unified framework for cross-species text-driven motion generation covering both humans and animals. X-MoGen adopts a two-stage architecture. First, a conditional graph variational autoencoder learns canonical T-pose priors, while an autoencoder encodes motion into a shared latent space regularized by morphological loss. In the second stage, we perform masked motion modeling to generate motion embeddings conditioned on textual descriptions. During training, a morphological consistency module is employed to promote skeletal plausibility across species. To support unified modeling, we construct UniMo4D, a large-scale dataset of 115 species and 119k motion sequences, which integrates human and animal motions under a shared skeletal topology for joint training. Extensive experiments on UniMo4D demonstrate that X-MoGen outperforms state-of-the-art methods on both seen and unseen species.

Feifan Wang, Tengfei Song, Minggui He et al.

Facial emotion perception in the vision large language model (VLLM) is crucial for achieving natural human-machine interaction. However, creating high-quality annotations for both coarse- and fine-grained facial emotion analysis demands costly expertise. The lack of such high-quality instruction data limits the performance of VLLMs in facial emotion perception. To address this, we propose a self-verification approach with emotion knowledge enhancement (SEKE), which generates high-quality instruction data for multi-grained emotion analysis cost-effectively using closed-source VLLM. This approach integrates prior human knowledge to VLLM inference, guided by the inherent correlations between three grained levels of emotion descriptions, i.e., discrete expression, valence-arousal, and action unit, to reliably generate comprehensive annotations. A self-verification strategy with Uncertainty-Aware Monte Carlo sampling (SV-UAMC) is further embedded to efficiently extract more accurate VLLM predictions, further improving annotation reliability. Consequently, we construct a facial emotion instruction dataset (FEID) containing three comprehensive descriptions, which provides coarse- and fine-grained emotional information for effective model training. Additionally, we introduce a facial emotion analysis benchmark (FEAB) to measure the VLLM's corresponding ability. Our method significantly outperforms state-of-the-art methods on three downstream facial emotion analysis tasks.

Jie Yang, Chang Su, Yuhan Zhang et al.

The advancement of sensing technology has driven the widespread application of high-dimensional data. However, issues such as missing entries during acquisition and transmission negatively impact the accuracy of subsequent tasks. Tensor reconstruction aims to recover the underlying complete data from under-sampled observed data by exploring prior information in high-dimensional data. However, due to insufficient exploration, reconstruction methods still face challenges when sampling rate is extremely low. This work proposes a tensor reconstruction method integrating multiple priors to comprehensively exploit the inherent structure of the data. Specifically, the method combines learnable tensor decomposition to enforce low-rank constraints of the reconstructed data, a pre-trained convolutional neural network for smoothing and denoising, and block-matching and 3D filtering regularization to enhance the non-local similarity in the reconstructed data. An alternating direction method of the multipliers algorithm is designed to decompose the resulting optimization problem into three subproblems for efficient resolution. Extensive experiments on color images, hyperspectral images, and grayscale videos datasets demonstrate the superiority of our method in extreme cases as compared with state-of-the-art methods.

Marianne Arriola, Weishen Pan, Manqi Zhou et al.

Joint analysis of multi-omic single-cell data across cohorts has significantly enhanced the comprehensive analysis of cellular processes. However, most of the existing approaches for this purpose require access to samples with complete modality availability, which is impractical in many real-world scenarios. In this paper, we propose (Single-Cell Cross-Cohort Cross-Category) integration, a novel framework that learns unified cell representations under domain shift without requiring full-modality reference samples. Our generative approach learns rich cross-modal and cross-domain relationships that enable imputation of these missing modalities. Through experiments on real-world multi-omic datasets, we demonstrate that offers a robust solution to single-cell tasks such as cell type clustering, cell type classification, and feature imputation.

Zhengzhe Yu, Jiaxin Guo, Minghan Wang et al.

Deep encoders have been proven to be effective in improving neural machine translation (NMT) systems, but it reaches the upper bound of translation quality when the number of encoder layers exceeds 18. Worse still, deeper networks consume a lot of memory, making it impossible to train efficiently. In this paper, we present Symbiosis Networks, which include a full network as the Symbiosis Main Network (M-Net) and another shared sub-network with the same structure but less layers as the Symbiotic Sub Network (S-Net). We adopt Symbiosis Networks on Transformer-deep (m-n) architecture and define a particular regularization loss $\mathcal{L}_τ$ between the M-Net and S-Net in NMT. We apply joint-training on the Symbiosis Networks and aim to improve the M-Net performance. Our proposed training strategy improves Transformer-deep (12-6) by 0.61, 0.49 and 0.69 BLEU over the baselines under classic training on WMT'14 EN->DE, DE->EN and EN->FR tasks. Furthermore, our Transformer-deep (12-6) even outperforms classic Transformer-deep (18-6).

Jiaxin Guo, Minghan Wang, Daimeng Wei et al.

Recently, non-autoregressive (NAT) models predict outputs in parallel, achieving substantial improvements in generation speed compared to autoregressive (AT) models. While performing worse on raw data, most NAT models are trained as student models on distilled data generated by AT teacher models, which is known as sequence-level Knowledge Distillation. An effective training strategy to improve the performance of AT models is Self-Distillation Mixup (SDM) Training, which pre-trains a model on raw data, generates distilled data by the pre-trained model itself and finally re-trains a model on the combination of raw data and distilled data. In this work, we aim to view SDM for NAT models, but find directly adopting SDM to NAT models gains no improvements in terms of translation quality. Through careful analysis, we observe the invalidation is correlated to Modeling Diversity and Confirmation Bias between the AT teacher model and the NAT student models. Based on these findings, we propose an enhanced strategy named SDMRT by adding two stages to classic SDM: one is Pre-Rerank on self-distilled data, the other is Fine-Tune on Filtered teacher-distilled data. Our results outperform baselines by 0.6 to 1.2 BLEU on multiple NAT models. As another bonus, for Iterative Refinement NAT models, our methods can outperform baselines within half iteration number, which means 2X acceleration.

Minghan Wang, Jiaxin Guo, Yuxia Wang et al.

Autoregressive (AR) and Non-autoregressive (NAR) models have their own superiority on the performance and latency, combining them into one model may take advantage of both. Current combination frameworks focus more on the integration of multiple decoding paradigms with a unified generative model, e.g. Masked Language Model. However, the generalization can be harmful to the performance due to the gap between training objective and inference. In this paper, we aim to close the gap by preserving the original objective of AR and NAR under a unified framework. Specifically, we propose the Directional Transformer (Diformer) by jointly modelling AR and NAR into three generation directions (left-to-right, right-to-left and straight) with a newly introduced direction variable, which works by controlling the prediction of each token to have specific dependencies under that direction. The unification achieved by direction successfully preserves the original dependency assumption used in AR and NAR, retaining both generalization and performance. Experiments on 4 WMT benchmarks demonstrate that Diformer outperforms current united-modelling works with more than 1.5 BLEU points for both AR and NAR decoding, and is also competitive to the state-of-the-art independent AR and NAR models.

Minghan Wang, Yuxia Wang, Chang Su et al.

This paper describes our work in participation of the IWSLT-2021 offline speech translation task. Our system was built in a cascade form, including a speaker diarization module, an Automatic Speech Recognition (ASR) module and a Machine Translation (MT) module. We directly use the LIUM SpkDiarization tool as the diarization module. The ASR module is trained with three ASR datasets from different sources, by multi-source training, using a modified Transformer encoder. The MT module is pretrained on the large-scale WMT news translation dataset and fine-tuned on the TED corpus. Our method achieves 24.6 BLEU score on the 2021 test set.

Jianlan Luo, Oleg Sushkov, Rugile Pevceviciute et al.

Over the past several years there has been a considerable research investment into learning-based approaches to industrial assembly, but despite significant progress these techniques have yet to be adopted by industry. We argue that it is the prohibitively large design space for Deep Reinforcement Learning (DRL), rather than algorithmic limitations per se, that are truly responsible for this lack of adoption. Pushing these techniques into the industrial mainstream requires an industry-oriented paradigm which differs significantly from the academic mindset. In this paper we define criteria for industry-oriented DRL, and perform a thorough comparison according to these criteria of one family of learning approaches, DRL from demonstration, against a professional industrial integrator on the recently established NIST assembly benchmark. We explain the design choices, representing several years of investigation, which enabled our DRL system to consistently outperform the integrator baseline in terms of both speed and reliability. Finally, we conclude with a competition between our DRL system and a human on a challenge task of insertion into a randomly moving target. This study suggests that DRL is capable of outperforming not only established engineered approaches, but the human motor system as well, and that there remains significant room for improvement. Videos can be found on our project website: https://sites.google.com/view/shield-nist.

Xinyi Zhong, Chang Su, Zhou Fan

When the dimension of data is comparable to or larger than the number of data samples, Principal Components Analysis (PCA) may exhibit problematic high-dimensional noise. In this work, we propose an Empirical Bayes PCA method that reduces this noise by estimating a joint prior distribution for the principal components. EB-PCA is based on the classical Kiefer-Wolfowitz nonparametric MLE for empirical Bayes estimation, distributional results derived from random matrix theory for the sample PCs, and iterative refinement using an Approximate Message Passing (AMP) algorithm. In theoretical "spiked" models, EB-PCA achieves Bayes-optimal estimation accuracy in the same settings as an oracle Bayes AMP procedure that knows the true priors. Empirically, EB-PCA significantly improves over PCA when there is strong prior structure, both in simulation and on quantitative benchmarks constructed from the 1000 Genomes Project and the International HapMap Project. An illustration is presented for analysis of gene expression data obtained by single-cell RNA-seq.

Jie Xu, Benjamin S. Glicksberg, Chang Su et al.

With the rapid development of computer software and hardware technologies, more and more healthcare data are becoming readily available from clinical institutions, patients, insurance companies and pharmaceutical industries, among others. This access provides an unprecedented opportunity for data science technologies to derive data-driven insights and improve the quality of care delivery. Healthcare data, however, are usually fragmented and private making it difficult to generate robust results across populations. For example, different hospitals own the electronic health records (EHR) of different patient populations and these records are difficult to share across hospitals because of their sensitive nature. This creates a big barrier for developing effective analytical approaches that are generalizable, which need diverse, "big data". Federated learning, a mechanism of training a shared global model with a central server while keeping all the sensitive data in local institutions where the data belong, provides great promise to connect the fragmented healthcare data sources with privacy-preservation. The goal of this survey is to provide a review for federated learning technologies, particularly within the biomedical space. In particular, we summarize the general solutions to the statistical challenges, system challenges and privacy issues in federated learning, and point out the implications and potentials in healthcare.

Sendong Zhao, Chang Su, Andrea Sboner et al.

Effective biomedical literature retrieval (BLR) plays a central role in precision medicine informatics. In this paper, we propose GRAPHENE, which is a deep learning based framework for precise BLR. GRAPHENE consists of three main different modules 1) graph-augmented document representation learning; 2) query expansion and representation learning and 3) learning to rank biomedical articles. The graph-augmented document representation learning module constructs a document-concept graph containing biomedical concept nodes and document nodes so that global biomedical related concept from external knowledge source can be captured, which is further connected to a BiLSTM so both local and global topics can be explored. Query expansion and representation learning module expands the query with abbreviations and different names, and then builds a CNN-based model to convolve the expanded query and obtain a vector representation for each query. Learning to rank minimizes a ranking loss between biomedical articles with the query to learn the retrieval function. Experimental results on applying our system to TREC Precision Medicine track data are provided to demonstrate its effectiveness.

Xi Sheryl Zhang, Dandi Chen, Yongjun Zhu et al.

This paper presents details of our winning solutions to the task IV of NIPS 2017 Competition Track entitled Classifying Clinically Actionable Genetic Mutations. The machine learning task aims to classify genetic mutations based on text evidence from clinical literature with promising performance. We develop a novel multi-view machine learning framework with ensemble classification models to solve the problem. During the Challenge, feature combinations derived from three views including document view, entity text view, and entity name view, which complements each other, are comprehensively explored. As the final solution, we submitted an ensemble of nine basic gradient boosting models which shows the best performance in the evaluation. The approach scores 0.5506 and 0.6694 in terms of logarithmic loss on a fixed split in stage-1 testing phase and 5-fold cross validation respectively, which also makes us ranked as a top-1 team out of more than 1,300 solutions in NIPS 2017 Competition Track IV.