Zhonghang Yuan, Zhefan Wang, Fang Hu, Zihong Chen, Jinzhe Li, Gang Li, Jie Ying, Huanjun Kong, Songyang Zhang, Nanqing Dong. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

Weed control is a critical challenge in modern agriculture, as weeds compete with crops for essential nutrient resources, significantly reducing crop yield and quality. Traditional weed control methods, including chemical and mechanical approaches, have real-life limitations such as associated environmental impact and efficiency. An emerging yet effective approach is laser weeding, which uses a laser beam as the stem cutter. Although there have been studies that use deep learning in weed recognition, its application in intelligent laser weeding still requires a comprehensive understanding. Thus, this study serves the first empirical study on weed recognition for laser weeding. To increase the efficiency of laser beam cut and avoid damaging the crops of interest, the laser beam shall be directly aimed at the weed root. Yet, weed stem detection remains an under-explored problem. We integrate the detection of crop and weed with the localization of weed stem into one end-to-end system. To train and validate the proposed system in a real-life scenario, we curate and construct a high-quality weed stem detection dataset with human annotations. The dataset consists of 7,161 high-resolution pictures collected in the field with annotations of 11,151 instances of weed. The dataset will be released upon acceptance. Experimental results show that, in contrast to seminal weed recognition systems, the proposed system can efficiently improve the weeding accuracy by 5.05% and reduce the energy cost by 32.3%.

Haoyang Su, Renqi Chen, Shixiang Tang, Zhenfei Yin, Xinzhe Zheng, Jinzhe Li, Biqing Qi, Qi Wu, Hui Li, Wanli Ouyang, Philip Torr, Bowen Zhou, Nanqing Dong. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

Jie Ying, Zihong Chen, Zhefan Wang, Wanli Jiang, Chenyang Wang, Zhonghang Yuan, Haoyang Su, Huanjun Kong, Fan Yang, Nanqing Dong. Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2025.

Peptide sequencing—the process of identifying amino acid sequences from mass spectrometry data—is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional methods. Unlike autoregressive models, which generate tokens sequentially, NATs predict all positions simultaneously, leveraging bidirectional context through unmasked self-attention. However, existing NAT approaches often rely on Connectionist Temporal Classification (CTC) loss, which presents significant optimization challenges due to CTC’s complexity and increases the risk of training failures. To address these issues, we propose an improved non-autoregressive peptide sequencing model that incorporates a structured protein sequence curriculum learning strategy. This approach adjusts protein’s learning difficulty based on the model’s estimated protein generational capabilities through a sampling process, progressively learning peptide generation from simple to complex sequences. Additionally, we introduce a self-refining inference-time module that iteratively enhances predictions using learned NAT token embeddings, improving sequence accuracy at a fine-grained level. Our curriculum learning strategy reduces NAT training failures frequency by more than 90% based on sampled training over various data distributions. Evaluations on nine benchmark species demonstrate that our approach outperforms all previous methods across multiple metrics and species. Model and source code are available at https://github.com/BEAM-Labs/denovo.

De novo peptide sequencing is a critical task in proteomics. However, the performance of current deep learning-based methods is limited by the inherent complexity of mass spectrometry data and the heterogeneous distribution of noise signals, leading to data-specific biases. We present RankNovo, the first deep reranking framework that enhances de novo peptide sequencing by leveraging the complementary strengths of multiple sequencing models. RankNovo employs a list-wise reranking approach, modeling candidate peptides as multiple sequence alignments and utilizing axial attention to extract informative features across candidates. Additionally, we introduce two new metrics, PMD (Peptide Mass Deviation) and RMD (ResidualMass Deviation), which offer delicate supervision by quantifying mass differences between peptides at both the sequence and residue levels. Extensive experiments demonstrate that RankNovo not only surpasses its base models used to generate training candidates for reranking pre-training, but also sets a new state-of-the-art benchmark. Moreover, RankNovo exhibits strong zero-shot generalization to unseen models—those whose generations were not exposed during training, highlighting its robustness and potential as a universal reranking framework for peptide sequencing. Our work presents a novel reranking strategy that fundamentally challenges existing single-model paradigms and advances the frontier of accurate de novo sequencing. Our source code is provided on GitHub.

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks like de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding 9-species benchmark of de novo peptide sequencing task show our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Our code is available on GitHub: https://github.com/BEAM-Labs/denovo

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates PRotein-protein INteraction prediction from a Graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

Protein sequence not only determines its structure but also provides important clues of its subcellular localization. Although a series of artificial intelligence models have been reported to predict protein subcellular localization, most of them provide only textual outputs. Here, we present deepGPS, a deep generative model for protein subcellular localization prediction. After training with protein primary sequences and fluorescence images, deepGPS shows the ability to predict cytoplasmic and nuclear localizations by reporting both textual labels and generative images as outputs. In addition, cell-type-specific deepGPS models can be developed by using distinct image datasets from different cell lines for comparative analyses. Moreover, deepGPS shows potential to be further extended for other specific organelles, such as vesicles and endoplasmic reticulum, even with limited volumes of training data. Finally, the openGPS website (https://bits.fudan.edu.cn/opengps) is constructed to provide a publicly accessible and user-friendly platform for studying protein subcellular localization and function.

Federated learning (FL) is a machine learning paradigm, which enables multiple and decentralized clients to collaboratively train a model under the orchestration of a central aggregator. FL can be a scalable machine learning solution inbig datascenarios. Traditional FL relies on the trust assumption of the central aggregator, which forms cohorts of clients honestly. However, a malicious aggregator, in reality, could abandon and replace the client's training models, or insert fake clients, to manipulate the final training results. In this work, we introducezkFL, which leverages zero-knowledge proofs to tackle the issue of a malicious aggregator during the training model aggregation process. To guarantee the correct aggregation results, the aggregator provides a proof per round, demonstrating to the clients that the aggregator executes the intended behavior faithfully. To further reduce the verification cost of clients, we use blockchain to handle the proof in a zero-knowledge way, where miners (i.e., the participants validating and maintaining the blockchain data) can verify the proof without knowing the clients' local and aggregated models. The theoretical analysis and empirical results show thatzkFLachieves better security and privacy than traditional FL, without modifying the underlying FL network structure or heavily compromising the training speed.

De novo peptide sequencing from mass spectrometry (MS) data is a critical task in proteomics research. Traditional de novo algorithms have encountered a bottleneck in accuracy due to the inherent complexity of proteomics data. While deep learning-based methods have shown progress, they reduce the problem to a translation task, potentially overlooking critical nuances between spectra and peptides. In our research, we present ContraNovo, a pioneering algorithm that leverages contrastive learning to extract the relationship between spectra and peptides and incorporates the mass information into peptide decoding, aiming to address these intricacies more efficiently. Through rigorous evaluations on two benchmark datasets, ContraNovo consistently outshines contemporary state-of-the-art solutions, underscoring its promising potential in enhancing de novo peptide sequencing.

Foundation models have made significant strides in understanding the genomic language of DNA sequences. However, previous models typically adopt the tokenization methods designed for natural language, which are unsuitable for DNA sequences due to their unique characteristics. In addition, the optimal approach to tokenize DNA remains largely under-explored, and may not be intuitively understood by humans even if discovered. To address these challenges, we introduce MxDNA, a novel framework where the model autonomously learns an effective DNA tokenization strategy through gradient decent. MxDNA employs a sparse Mixture of Convolution Experts coupled with a deformable convolution to model the tokenization process, with the discontinuous, overlapping, and ambiguous nature of meaningful genomic segments explicitly considered. On Nucleotide Transformer Benchmarks and Genomic Benchmarks, MxDNA demonstrates superior performance to existing methods with less pretraining data and time, highlighting its effectiveness. Finally, we show that MxDNA learns unique tokenization strategy distinct to those of previous methods and captures genomic functionalities at a token level during self-supervised pretraining. Our MxDNA aims to provide a new perspective on DNA tokenization, potentially offering broad applications in various domains and yielding profound insights. Code is available at https://github.com/qiaoqiaoLF/MxDNA.

Large language models (LLMs) have demonstrated remarkable efficacy across knowledge-intensive tasks. Nevertheless, their untapped potential in crop science presents an opportunity for advancement. To narrow this gap, we introduce CROP, which includes a novel instruction tuning dataset specifically designed to enhance LLMs’ professional capabilities in the crop science sector, along with a benchmark that serves as a comprehensive evaluation of LLMs’ understanding of the domain knowledge. The CROP dataset is curated through a task-oriented and LLM-human integrated pipeline, comprising 210,038 single-turn and 1,871 multi-turn dialogues related to crop science scenarios. The CROP benchmark includes 5,045 multiple-choice questions covering three difficulty levels. Our experiments based on the CROP benchmark demonstrate notable enhancements in crop science-related tasks when LLMs are fine-tuned with the CROP dataset. To the best of our knowledge, CROP dataset is the first-ever instruction tuning dataset in the crop science domain. We anticipate that CROP will accelerate the adoption of LLMs in the domain of crop science, ultimately contributing to global food production.

Self-supervised pre-training, based on the pretext task of instance discrimination, has fueled the recent advance in label-efficient object detection. However, existing studies focus on pre-training only a feature extractor network to learn transferable representations for downstream detection tasks. This leads to the necessity of training multiple detection-specific modules from scratch in the fine-tuning phase. We argue that the region proposal network (RPN), a common detection-specific module, can additionally be pre-trained towards reducing the localization error of multi-stage detectors. In this work, we propose a simple pretext task that provides an effective pre-training for the RPN, towards efficiently improving downstream object detection performance. We evaluate the efficacy of our approach on benchmark object detection tasks and additional downstream tasks, including instance segmentation and few-shot detection. In comparison with multi-stage detectors without RPN pre-training, our approach is able to consistently improve downstream task performance, with largest gains found in label-scarce settings.

Data government has played an instrumental role in securing the privacy-critical infrastructure in the medical domain and has led to an increased need of federated learning (FL). While decentralization can limit the effectiveness of standard supervised learning, the impact of decentralization on partially supervised learning remains unclear. Besides, due to data scarcity, each client may have access to only limited partially labeled data. As a remedy, this work formulates and discusses a new learning problem federated partially supervised learning (FPSL) for limited decentralized medical images with partial labels. We study the impact of decentralized partially labeled data on deep learning-based models via an exemplar of FPSL, namely, federated partially supervised learning multi-label classification. By dissecting FedAVG, a seminal FL framework, we formulate and analyze two major challenges of FPSL and propose a simple yet robust FPSL framework, FedPSL, which addresses these challenges. In particular, FedPSL contains two modules, task-dependent model aggregation and task-agnostic decoupling learning, where the first module addresses the weight assignment and the second module improves the generalization ability of the feature extractor. We provide a comprehensive empirical understanding of FSPL under data scarcity with simulated experiments. The empirical results not only indicate that FPSL is an under-explored problem with practical value but also show that the proposed FedPSL can achieve robust performance against baseline methods on data challenges such as data scarcity and domain shifts. The findings of this study also pose a new research direction towards label-efficient learning on medical images.

Ubiquitous accumulation of large volumes of data, and increased availability of annotated medical data in particular, has made it possible to show the many and varied benefits of deep learning to the semantic segmentation of medical images. Nevertheless, data access and annotation come at a high cost in clinician time. The power of Vision Transformer (ViT) is well-documented for generic computer vision tasks involving millions of images of every day objects, of which only relatively few have been annotated. Its translation to relatively more modest (i.e. thousands of images of) medical data is not immediately straightforward. This paper presents practical avenues for training a Computationally-Efficient Semi-Supervised Vision Transformer (CESS-ViT) for medical image segmentation task.We propose a self-attention-based image segmentation network which requires only limited computational resources. Additionally, we develop a dual pseudo-label supervision scheme for use with semi-supervision in a simple pure ViT.Our method has been evaluated on a publicly available cardiac MRI dataset with direct comparison against other semi-supervised methods. Our results illustrate the proposed ViT-based semi-supervised method outperforms the existing methods in the semantic segmentation of cardiac ventricles.

This paper is concerned with contrastive learning (CL) for low-level image restoration and enhancement tasks. We propose a new label-efficient learning paradigm based on residuals, residual contrastive learning (RCL), and derive an unsupervised visual representation learning framework, suitable for low-level vision tasks with noisy inputs. While supervised image reconstruction aims to minimize residual terms directly, RCL alternatively builds a connection between residuals and CL by defining a novel instance discrimination pretext task, using residuals as the discriminative feature. Our formulation mitigates the severe task misalignment between instance discrimination pretext tasks and downstream image reconstruction tasks, present in existing CL frameworks. Experimentally, we find that RCL can learn robust and transferable representations that improve the performance of various downstream tasks, such as denoising and super resolution, in comparison with recent self-supervised methods designed specifically for noisy inputs. Additionally, our unsupervised pre-training can significantly reduce annotation costs whilst maintaining performance competitive with fully-supervised image reconstruction.

Although quantum neural networks (QNNs) have shown promising results in solving simple machine learning tasks recently, the behavior of QNNs in binary pattern classification is still underexplored. In this work, we find that QNNs have an Achilles’ heel in binary pattern classification. To illustrate this point, we provide a theoretical insight into the properties of QNNs by presenting and analyzing a new form of symmetry embedded in a family of QNNs with full entanglement , which we term negational symmetry . Due to negational symmetry, QNNs can not differentiate between a quantum binary signal and its negational counterpart. We empirically evaluate the negational symmetry of QNNs in binary pattern classification tasks using Google’s quantum computing framework. Both theoretical and experimental results suggest that negational symmetry is a fundamental property of QNNs, which is not shared by classical models. Our findings also imply that negational symmetry is a double-edged sword in practical quantum applications.

Adversarial training is a useful approach to promote the learning of transferable representations across the source and target domains, which has been widely applied for domain adaptation (DA) tasks based on deep neural networks. Until very recently, existing adversarial domain adaptation (ADA) methods ignore the useful information from the label space, which is an important factor accountable for the complicated data distributions associated with different semantic classes. Especially, the inter-class semantic relationships have been rarely considered and discussed in the current work of transfer learning. In this paper, we propose a novel relationship-aware adversarial domain adaptation (RADA) algorithm, which first utilizes a single multi-class domain discriminator to enforce the learning of inter-class dependency structure during domain-adversarial training and then aligns this structure with the inter-class dependencies that are characterized from training the label predictor on source domain. Specifically, we impose a regularization term to penalize the structure discrepancy between the inter-class dependencies respectively estimated from domain discriminator and label predictor. Through this alignment, our proposed method makes the adversarial domain adaptation aware of the class relationships. Empirical studies show that the incorporation of class relationships significantly improves the performance on benchmark datasets.

Salient segmentation aims to segment out attentiongrabbing regions, a critical yet challenging task and the foundation of many high-level computer vision applications. It requires semantic-aware grouping of pixels into salient regions and benefits from the utilization of global multi-scale contexts to achieve good local reasoning. Previous works often address it as two-class segmentation problems utilizing complicated multi-step procedures including refinement networks and complex graphical models. We argue that semantic salient segmentation can instead be effectively resolved by reformulating it as a simple yet intuitive pixel-pair based connectivity prediction task. Following the intuition that salient objects can be naturally grouped via semanticaware connectivity between neighboring pixels, we propose a pure Connectivity Net (ConnNet). ConnNet predicts connectivity probabilities of each pixel with its neighboring pixels by leveraging multi-level cascade contexts embedded in the image and long-range pixel relations. We investigate our approach on two tasks, namely salient object segmentation and salient instancelevel segmentation, and illustrate that consistent improvements can be obtained by modeling these tasks as connectivity instead of binary segmentation tasks for a variety of network architectures. We achieve state-of-the-art performance, outperforming or being comparable to existing approaches while reducing inference time due to our less complex approach.