Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating 40+ protein-related datasets and 40+ popular PLMs. All implementations are open-sourced on https://github.com/ai4protein/VenusFactory. A video introduction is available at https://www.youtube.com/watch?v=MT6lPH5kgCc.

Large language models have shown their ability to become effective few-shot learners with prompting, revoluting the paradigm of learning with data scarcity. However, this approach largely depends on the quality of prompt initialization and always exhibits large variability among different runs. Such property makes prompt tuning highly unreliable and vulnerable to poorly constructed prompts, which limits its extension to more real-world applications. To tackle this issue, we propose to treat the hard prompt and soft prompt as separate inputs to mitigate noise brought by the prompt initialization. Furthermore, we optimize soft prompts with contrastive learning for utilizing class-aware information in the training process to maintain model performance. Experimental results demonstrate that StablePT outperforms state-of-the-art methods by 6.97% in accuracy and reduces the standard deviation by 1.92 on average. Furthermore, extensive experiments underscore its robustness and stability across 8 datasets covering various tasks.

Hierarchical Text Classification (HTC), which aims to predict text labels organized in hierarchical space, is a significant task lacking in investigation in natural language processing. Existing methods usually encode the entire hierarchical structure and fail to construct a robust label-dependent model, making it hard to make accurate predictions on sparse lower-level labels and achieving low Macro-F1. In this paper, we explore the level dependency and path dependency of the label hierarchy in a generative way for building the knowledge of upper-level labels of current path into lower-level ones, and thus propose a novel PAAM-HiA-T5 model for HTC: a hierarchy-aware T5 model with path-adaptive attention mechanism. Specifically, we generate a multi-level sequential label structure to exploit hierarchical dependency across different levels with Breadth-First Search (BFS) and T5 model. To further improve label dependency prediction within each path, we then propose an original path-adaptive attention mechanism (PAAM) to lead the model to adaptively focus on the path where the currently generated label is located, shielding the noise from other paths. Comprehensive experiments on three benchmark datasets show that PAAM-HiA-T5 greatly outperforms all state-of-the-art HTC approaches especially in Macro-F1.

In natural language processing (NLP), state-of-the-art (SOTA) semi-supervised learning (SSL) frameworks have shown great performance on deep pre-trained language models such as BERT, and are expected to significantly reduce the demand for manual labeling. However, our empirical studies indicate that these frameworks are not suitable for lightweight models such as TextCNN, LSTM and etc. In this work, we develop a new SSL framework called FLiText, which stands for Faster and Lighter semi-supervised Text classification. FLiText introduces an inspirer network together with the consistency regularization framework, which leverages a generalized regular constraint on the lightweight models for efficient SSL. As a result, FLiText obtains new SOTA performance for lightweight models across multiple SSL benchmarks on text classification. Compared with existing SOTA SSL methods on TextCNN, FLiText improves the accuracy of lightweight model TextCNN from 51.00% to 90.49% on IMDb, 39.8% to 58.06% on Yelp-5, and from 55.3% to 65.08% on Yahoo! Answer. In addition, compared with the fully supervised method on the full dataset, FLiText just uses less than 1% of labeled data to improve the accuracy by 6.59%, 3.94%, and 3.22% on the datasets of IMDb, Yelp-5, and Yahoo! Answer respectively.

One daunting problem for semantic parsing is the scarcity of annotation. Aiming to reduce nontrivial human labor, we propose a two-stage semantic parsing framework, where the first stage utilizes an unsupervised paraphrase model to convert an unlabeled natural language utterance into the canonical utterance. The downstream naive semantic parser accepts the intermediate output and returns the target logical form. Furthermore, the entire training process is split into two phases: pre-training and cycle learning. Three tailored self-supervised tasks are introduced throughout training to activate the unsupervised paraphrase model. Experimental results on benchmarks Overnight and GeoGranno demonstrate that our framework is effective and compatible with supervised training.

We study methods for learning sentence embeddings with syntactic structure. We focus on methods of learning syntactic sentence-embeddings by using a multilingual parallel-corpus augmented by Universal Parts-of-Speech tags. We evaluate the quality of the learned embeddings by examining sentence-level nearest neighbours and functional dissimilarity in the embedding space. We also evaluate the ability of the method to learn syntactic sentence-embeddings for low-resource languages and demonstrate strong evidence for transfer learning. Our results show that syntactic sentence-embeddings can be learned while using less training data, fewer model parameters, and resulting in better evaluation metrics than state-of-the-art language models.

Semantic parsing converts natural language queries into structured logical forms. The lack of training data is still one of the most serious problems in this area. In this work, we develop a semantic parsing framework with the dual learning algorithm, which enables a semantic parser to make full use of data (labeled and even unlabeled) through a dual-learning game. This game between a primal model (semantic parsing) and a dual model (logical form to query) forces them to regularize each other, and can achieve feedback signals from some prior-knowledge. By utilizing the prior-knowledge of logical form structures, we propose a novel reward signal at the surface and semantic levels which tends to generate complete and reasonable logical forms. Experimental results show that our approach achieves new state-of-the-art performance on ATIS dataset and gets competitive performance on OVERNIGHT dataset.

In this paper we describe an approach that both creates crosslingual acoustic monophone model sets for speech recognition tasks and objectively predicts their performance without target-language speech data or acoustic measurement techniques. This strategy is based on a series of linguistic metrics characterizing the articulatory phonetic and phonological distances of target-language phonemes from source-language phonemes. We term these algorithms the Combined Phonetic and Phonological Crosslingual Distance (CPP-CD) metric and the Combined Phonetic and Phonological Crosslingual Prediction (CPP-CP) metric. The particular motivations for this project are the current unavailability and often prohibitively high production cost of speech databases for many strategically important low- and middle-density languages. First, we describe the CPP-CD approach and compare the performance of CPP-CD-specified models to both native language models and crosslingual models selected by the Bhattacharyya acoustic-model distance metric in automatic speech recognition (ASR) experiments. Results confirm that the CPP-CD approach nearly matches those achieved by the acoustic distance metric. We then test the CPP-CP algorithm on the CPP-CD models by comparing the CPP-CP scores to the recognition phoneme error rates. Based on this comparison, we conclude that the CPP-CP algorithm is a reliable indicator of crosslingual model performance in speech recognition tasks.