Haoran Wu

Haoran Wu, Wenxuan Wang, Yuxuan Wan et al.

ChatGPT is a cutting-edge artificial intelligence language model developed by OpenAI, which has attracted a lot of attention due to its surprisingly strong ability in answering follow-up questions. In this report, we aim to evaluate ChatGPT on the Grammatical Error Correction(GEC) task, and compare it with commercial GEC product (e.g., Grammarly) and state-of-the-art models (e.g., GECToR). By testing on the CoNLL2014 benchmark dataset, we find that ChatGPT performs not as well as those baselines in terms of the automatic evaluation metrics (e.g., $F_{0.5}$ score), particularly on long sentences. We inspect the outputs and find that ChatGPT goes beyond one-by-one corrections. Specifically, it prefers to change the surface expression of certain phrases or sentence structure while maintaining grammatical correctness. Human evaluation quantitatively confirms this and suggests that ChatGPT produces less under-correction or mis-correction issues but more over-corrections. These results demonstrate that ChatGPT is severely under-estimated by the automatic evaluation metrics and could be a promising tool for GEC.

Zhenghao Xing, Tianyu Wang, Xiaowei Hu et al.

Instance shadow detection, crucial for applications such as photo editing and light direction estimation, has undergone significant advancements in predicting shadow instances, object instances, and their associations. The extension of this task to videos presents challenges in annotating diverse video data and addressing complexities arising from occlusion and temporary disappearances within associations. In response to these challenges, we introduce ViShadow, a semi-supervised video instance shadow detection framework that leverages both labeled image data and unlabeled video data for training. ViShadow features a two-stage training pipeline: the first stage, utilizing labeled image data, identifies shadow and object instances through contrastive learning for cross-frame pairing. The second stage employs unlabeled videos, incorporating an associated cycle consistency loss to enhance tracking ability. A retrieval mechanism is introduced to manage temporary disappearances, ensuring tracking continuity. The SOBA-VID dataset, comprising unlabeled training videos and labeled testing videos, along with the SOAP-VID metric, is introduced for the quantitative evaluation of VISD solutions. The effectiveness of ViShadow is further demonstrated through various video-level applications such as video inpainting, instance cloning, shadow editing, and text-instructed shadow-object manipulation.

Zefa Hu, Xiuyi Chen, Haoran Wu et al.

Medical Slot Filling (MSF) task aims to convert medical queries into structured information, playing an essential role in diagnosis dialogue systems. However, the lack of sufficient term semantics learning makes existing approaches hard to capture semantically identical but colloquial expressions of terms in medical conversations. In this work, we formalize MSF into a matching problem and propose a Term Semantics Pre-trained Matching Network (TSPMN) that takes both terms and queries as input to model their semantic interaction. To learn term semantics better, we further design two self-supervised objectives, including Contrastive Term Discrimination (CTD) and Matching-based Mask Term Modeling (MMTM). CTD determines whether it is the masked term in the dialogue for each given term, while MMTM directly predicts the masked ones. Experimental results on two Chinese benchmarks show that TSPMN outperforms strong baselines, especially in few-shot settings.

Ruochi Zhang, Haoran Wu, Yuting Xiu et al.

In recent years, the scientific community has become increasingly interested on peptides with non-canonical amino acids due to their superior stability and resistance to proteolytic degradation. These peptides present promising modifications to biological, pharmacological, and physiochemical attributes in both endogenous and engineered peptides. Notwithstanding their considerable advantages, the scientific community exhibits a conspicuous absence of an effective pre-trained model adept at distilling feature representations from such complex peptide sequences. We herein propose PepLand, a novel pre-training architecture for representation and property analysis of peptides spanning both canonical and non-canonical amino acids. In essence, PepLand leverages a comprehensive multi-view heterogeneous graph neural network tailored to unveil the subtle structural representations of peptides. Empirical validations underscore PepLand's effectiveness across an array of peptide property predictions, encompassing protein-protein interactions, permeability, solubility, and synthesizability. The rigorous evaluation confirms PepLand's unparalleled capability in capturing salient synthetic peptide features, thereby laying a robust foundation for transformative advances in peptide-centric research domains. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/pepland

Ruochi Zhang, Haoran Wu, Chang Liu et al.

Recent advances in protein language models have catalyzed significant progress in peptide sequence representation. Despite extensive exploration in this field, pre-trained models tailored for peptide-specific needs remain largely unaddressed due to the difficulty in capturing the complex and sometimes unstable structures of peptides. This study introduces a novel multi-view contrastive learning framework PepHarmony for the sequence-based peptide encoding task. PepHarmony innovatively combines both sequence- and structure-level information into a sequence-level encoding module through contrastive learning. We carefully select datasets from the Protein Data Bank (PDB) and AlphaFold database to encompass a broad spectrum of peptide sequences and structures. The experimental data highlights PepHarmony's exceptional capability in capturing the intricate relationship between peptide sequences and structures compared with the baseline and fine-tuned models. The robustness of our model is confirmed through extensive ablation studies, which emphasize the crucial roles of contrastive loss and strategic data sorting in enhancing predictive performance. The proposed PepHarmony framework serves as a notable contribution to peptide representations, and offers valuable insights for future applications in peptide drug discovery and peptide engineering. We have made all the source code utilized in this study publicly accessible via GitHub at https://github.com/zhangruochi/PepHarmony or http://www.healthinformaticslab.org/supp/.

Xu Cai, Yang Wu, Qianli Chen et al.

We present an ultra-efficient post-training method for shortcutting large-scale pre-trained flow matching diffusion models into efficient few-step samplers, enabled by novel velocity field self-distillation. While shortcutting in flow matching, originally introduced by shortcut models, offers flexible trajectory-skipping capabilities, it requires a specialized step-size embedding incompatible with existing models unless retraining from scratch$\unicode{x2013}$a process nearly as costly as pretraining itself. Our key contribution is thus imparting a more aggressive shortcut mechanism to standard flow matching models (e.g., Flux), leveraging a unique distillation principle that obviates the need for step-size embedding. Working on the velocity field rather than sample space and learning rapidly from self-guided distillation in an online manner, our approach trains efficiently, e.g., producing a 3-step Flux less than one A100 day. Beyond distillation, our method can be incorporated into the pretraining stage itself, yielding models that inherently learn efficient, few-step flows without compromising quality. This capability also enables, to our knowledge, the first few-shot distillation method (e.g., 10 text-image pairs) for dozen-billion-parameter diffusion models, delivering state-of-the-art performance at almost free cost.

Haoran Wu, Axel Marmoret, Jérémy E. Cohen

Automatic Music Transcription, which consists in transforming an audio recording of a musical performance into symbolic format, remains a difficult Music Information Retrieval task. In this work, which focuses on piano transcription, we propose a semi-supervised approach using low-rank matrix factorization techniques, in particular Convolutive Nonnegative Matrix Factorization. In the semi-supervised setting, only a single recording of each individual notes is required. We show on the MAPS dataset that the proposed semi-supervised CNMF method performs better than state-of-the-art low-rank factorization techniques and a little worse than supervised deep learning state-of-the-art methods, while however suffering from generalization issues.

Laetitia Chapel, Rémi Flamary, Haoran Wu et al.

This paper addresses the problem of Unbalanced Optimal Transport (UOT) in which the marginal conditions are relaxed (using weighted penalties in lieu of equality) and no additional regularization is enforced on the OT plan. In this context, we show that the corresponding optimization problem can be reformulated as a non-negative penalized linear regression problem. This reformulation allows us to propose novel algorithms inspired from inverse problems and nonnegative matrix factorization. In particular, we consider majorization-minimization which leads in our setting to efficient multiplicative updates for a variety of penalties. Furthermore, we derive for the first time an efficient algorithm to compute the regularization path of UOT with quadratic penalties. The proposed algorithm provides a continuity of piece-wise linear OT plans converging to the solution of balanced OT (corresponding to infinite penalty weights). We perform several numerical experiments on simulated and real data illustrating the new algorithms, and provide a detailed discussion about more sophisticated optimization tools that can further be used to solve OT problems thanks to our reformulation.