VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning

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/tyang816/VenusFactory.

TVNet: A Novel Time Series Analysis Method Based on Dynamic Convolution and 3D-Variation

With the recent development and advancement of Transformer and MLP architectures, significant strides have been made in time series analysis. Conversely, the performance of Convolutional Neural Networks (CNNs) in time series analysis has fallen short of expectations, diminishing their potential for future applications. Our research aims to enhance the representational capacity of Convolutional Neural Networks (CNNs) in time series analysis by introducing novel perspectives and design innovations. To be specific, We introduce a novel time series reshaping technique that considers the inter-patch, intra-patch, and cross-variable dimensions. Consequently, we propose TVNet, a dynamic convolutional network leveraging a 3D perspective to employ time series analysis. TVNet retains the computational efficiency of CNNs and achieves state-of-the-art results in five key time series analysis tasks, offering a superior balance of efficiency and performance over the state-of-the-art Transformer-based and MLP-based models. Additionally, our findings suggest that TVNet exhibits enhanced transferability and robustness. Therefore, it provides a new perspective for applying CNN in advanced time series analysis tasks.

DP-GTR: Differentially Private Prompt Protection via Group Text Rewriting

Prompt privacy is crucial, especially when using online large language models (LLMs), due to the sensitive information often contained within prompts. While LLMs can enhance prompt privacy through text rewriting, existing methods primarily focus on document-level rewriting, neglecting the rich, multi-granular representations of text. This limitation restricts LLM utilization to specific tasks, overlooking their generalization and in-context learning capabilities, thus hindering practical application. To address this gap, we introduce DP-GTR, a novel three-stage framework that leverages local differential privacy (DP) and the composition theorem via group text rewriting. DP-GTR is the first framework to integrate both document-level and word-level information while exploiting in-context learning to simultaneously improve privacy and utility, effectively bridging local and global DP mechanisms at the individual data point level. Experiments on CommonSense QA and DocVQA demonstrate that DP-GTR outperforms existing approaches, achieving a superior privacy-utility trade-off. Furthermore, our framework is compatible with existing rewriting techniques, serving as a plug-in to enhance privacy protection. Our code is publicly available at https://github.com/FatShion-FTD/DP-GTR for reproducibility.

Automatic Pruning via Structured Lasso with Class-wise Information

Most pruning methods concentrate on unimportant filters of neural networks. However, they face the loss of statistical information due to a lack of consideration for class-wise data. In this paper, from the perspective of leveraging precise class-wise information for model pruning, we utilize structured lasso with guidance from Information Bottleneck theory. Our approach ensures that statistical information is retained during the pruning process. With these techniques, we introduce two innovative adaptive network pruning schemes: sparse graph-structured lasso pruning with Information Bottleneck (\textbf{sGLP-IB}) and sparse tree-guided lasso pruning with Information Bottleneck (\textbf{sTLP-IB}). The key aspect is pruning model filters using sGLP-IB and sTLP-IB to better capture class-wise relatedness. Compared to multiple state-of-the-art methods, our approaches demonstrate superior performance across three datasets and six model architectures in extensive experiments. For instance, using the VGG16 model on the CIFAR-10 dataset, we achieve a parameter reduction of 85%, a decrease in FLOPs by 61%, and maintain an accuracy of 94.10% (0.14% higher than the original model); we reduce the parameters by 55% with the accuracy at 76.12% using the ResNet architecture on ImageNet (only drops 0.03%). In summary, we successfully reduce model size and computational resource usage while maintaining accuracy. Our codes are at https://anonymous.4open.science/r/IJCAI-8104.

The Rising Threat to Emerging AI-Powered Search Engines

Recent advancements in Large Language Models (LLMs) have significantly enhanced the capabilities of AI-Powered Search Engines (AIPSEs), offering precise and efficient responses by integrating external databases with pre-existing knowledge. However, we observe that these AIPSEs raise risks such as quoting malicious content or citing malicious websites, leading to harmful or unverified information dissemination. In this study, we conduct the first safety risk quantification on seven production AIPSEs by systematically defining the threat model, risk level, and evaluating responses to various query types. With data collected from PhishTank, ThreatBook, and LevelBlue, our findings reveal that AIPSEs frequently generate harmful content that contains malicious URLs even with benign queries (e.g., with benign keywords). We also observe that directly query URL will increase the risk level while query with natural language will mitigate such risk. We further perform two case studies on online document spoofing and phishing to show the ease of deceiving AIPSEs in the real-world setting. To mitigate these risks, we develop an agent-based defense with a GPT-4o-based content refinement tool and an XGBoost-based URL detector. Our evaluation shows that our defense can effectively reduce the risk but with the cost of reducing available information. Our research highlights the urgent need for robust safety measures in AIPSEs.

RAMIE: Retrieval-Augmented Multi-task Information Extraction with Large Language Models on Dietary Supplements

\textbf{Objective:} We aimed to develop an advanced multi-task large language model (LLM) framework to extract multiple types of information about dietary supplements (DS) from clinical records. \textbf{Methods:} We used four core DS information extraction tasks - namely, named entity recognition (NER: 2,949 clinical sentences), relation extraction (RE: 4,892 sentences), triple extraction (TE: 2,949 sentences), and usage classification (UC: 2,460 sentences) as our multitasks. We introduced a novel Retrieval-Augmented Multi-task Information Extraction (RAMIE) Framework, including: 1) employed instruction fine-tuning techniques with task-specific prompts, 2) trained LLMs for multiple tasks with improved storage efficiency and lower training costs, and 3) incorporated retrieval augmentation generation (RAG) techniques by retrieving similar examples from the training set. We compared RAMIE's performance to LLMs with instruction fine-tuning alone and conducted an ablation study to assess the contributions of multi-task learning and RAG to improved multitasking performance. \textbf{Results:} With the aid of the RAMIE framework, Llama2-13B achieved an F1 score of 87.39 (3.51\% improvement) on the NER task and demonstrated outstanding performance on the RE task with an F1 score of 93.74 (1.15\% improvement). For the TE task, Llama2-7B scored 79.45 (14.26\% improvement), and MedAlpaca-7B achieved the highest F1 score of 93.45 (0.94\% improvement) on the UC task. The ablation study revealed that while MTL increased efficiency with a slight trade-off in performance, RAG significantly boosted overall accuracy. \textbf{Conclusion:} This study presents a novel RAMIE framework that demonstrates substantial improvements in multi-task information extraction for DS-related data from clinical records. Our framework can potentially be applied to other domains.

Selective Attention: Enhancing Transformer through Principled Context Control

The attention mechanism within the transformer architecture enables the model to weigh and combine tokens based on their relevance to the query. While self-attention has enjoyed major success, it notably treats all queries $q$ in the same way by applying the mapping $V^\top\text{softmax}(Kq)$, where $V,K$ are the value and key embeddings respectively. In this work, we argue that this uniform treatment hinders the ability to control contextual sparsity and relevance. As a solution, we introduce the $\textit{Selective Self-Attention}$ (SSA) layer that augments the softmax nonlinearity with a principled temperature scaling strategy. By controlling temperature, SSA adapts the contextual sparsity of the attention map to the query embedding and its position in the context window. Through theory and experiments, we demonstrate that this alleviates attention dilution, aids the optimization process, and enhances the model's ability to control softmax spikiness of individual queries. We also incorporate temperature scaling for value embeddings and show that it boosts the model's ability to suppress irrelevant/noisy tokens. Notably, SSA is a lightweight method which introduces less than 0.5% new parameters through a weight-sharing strategy and can be fine-tuned on existing LLMs. Extensive empirical evaluations demonstrate that SSA-equipped models achieve a noticeable and consistent accuracy improvement on language modeling benchmarks.

CPE-Pro: A Structure-Sensitive Deep Learning Model for Protein Representation and Origin Evaluation

Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Discriminating the origin of structures is crucial for distinguishing between experimentally resolved and computationally predicted structures, evaluating the reliability of prediction methods, and guiding downstream biological studies. Building on works in structure prediction, We developed a structure-sensitive supervised deep learning model, Crystal vs Predicted Evaluator for Protein Structure (CPE-Pro), to represent and discriminate the origin of protein structures. CPE-Pro learns the structural information of proteins and captures inter-structural differences to achieve accurate traceability on four data classes, and is expected to be extended to more. Simultaneously, we utilized Foldseek to encode protein structures into "structure-sequence" and trained a protein Structural Sequence Language Model, SSLM. Preliminary experiments demonstrated that, compared to large-scale protein language models pre-trained on vast amounts of amino acid sequences, the "structure-sequences" enable the language model to learn more informative protein features, enhancing and optimizing structural representations. We have provided the code, model weights, and all related materials on https://github.com/GouWenrui/CPE-Pro-main.git.

RiTeK: A Dataset for Large Language Models Complex Reasoning over Textual Knowledge Graphs

Answering complex real-world questions often requires accurate retrieval from textual knowledge graphs (TKGs). The scarcity of annotated data, along with intricate topological structures, makes this task particularly challenging. As the nature of relational path information could enhance the inference ability of Large Language Models (LLMs), efficiently retrieving more complex relational path information from TKGs presents another key challenge. To tackle these challenges, we first develop a Dataset for LLMs Complex Reasoning over Textual Knowledge Graphs (RiTeK) with a broad topological structure coverage.We synthesize realistic user queries that integrate diverse topological structures, relational information, and complex textual descriptions. We conduct rigorous expert evaluation to validate the quality of our synthesized queries. And then, we introduce an enhanced Monte Carlo Tree Search (MCTS) method, Relational MCTS, to automatically extract relational path information from textual graphs for specific queries. Our dataset mainly covers the medical domain as the relation types and entity are complex and publicly available. Experimental results indicate that RiTeK poses significant challenges for current retrieval and LLM systems, while the proposed Relational MCTS method enhances LLM inference ability and achieves state-of-the-art performance on RiTeK.

On the Power of Convolution Augmented Transformer

The transformer architecture has catalyzed revolutionary advances in language modeling. However, recent architectural recipes, such as state-space models, have bridged the performance gap. Motivated by this, we examine the benefits of Convolution-Augmented Transformer (CAT) for recall, copying, and length generalization tasks. CAT incorporates convolutional filters in the K/Q/V embeddings of an attention layer. Through CAT, we show that the locality of the convolution synergizes with the global view of the attention. Unlike comparable architectures, such as Mamba or transformer, CAT can provably solve the associative recall (AR) and copying tasks using a single layer while also enjoying guaranteed length generalization. We also establish computational tradeoffs between convolution and attention by characterizing how convolution can mitigate the need for full attention by summarizing the context window and creating salient summary tokens to attend. Evaluations on real datasets corroborate our findings and demonstrate that CAT and its variations indeed enhance the language modeling performance.