PhaGO: Protein function annotation for bacteriophages by integrating the genomic context

Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, PhaGO surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. PhaGO can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of PhaGO by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of PhaGO to extend our understanding of newly discovered phages.

Why Not Transform Chat Large Language Models to Non-English?

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.

Enforcing Paraphrase Generation via Controllable Latent Diffusion

Paraphrase generation aims to produce high-quality and diverse utterances of a given text. Though state-of-the-art generation via the diffusion model reconciles generation quality and diversity, textual diffusion suffers from a truncation issue that hinders efficiency and quality control. In this work, we propose \textit{L}atent \textit{D}iffusion \textit{P}araphraser~(LDP), a novel paraphrase generation by modeling a controllable diffusion process given a learned latent space. LDP achieves superior generation efficiency compared to its diffusion counterparts. It facilitates only input segments to enforce paraphrase semantics, which further improves the results without external features. Experiments show that LDP achieves improved and diverse paraphrase generation compared to baselines. Further analysis shows that our method is also helpful to other similar text generations and domain adaptations. Our code and data are available at https://github.com/NIL-zhuang/ld4pg.

MMCert: Provable Defense against Adversarial Attacks to Multi-modal Models

Different from a unimodal model whose input is from a single modality, the input (called multi-modal input) of a multi-modal model is from multiple modalities such as image, 3D points, audio, text, etc. Similar to unimodal models, many existing studies show that a multi-modal model is also vulnerable to adversarial perturbation, where an attacker could add small perturbation to all modalities of a multi-modal input such that the multi-modal model makes incorrect predictions for it. Existing certified defenses are mostly designed for unimodal models, which achieve sub-optimal certified robustness guarantees when extended to multi-modal models as shown in our experimental results. In our work, we propose MMCert, the first certified defense against adversarial attacks to a multi-modal model. We derive a lower bound on the performance of our MMCert under arbitrary adversarial attacks with bounded perturbations to both modalities (e.g., in the context of auto-driving, we bound the number of changed pixels in both RGB image and depth image). We evaluate our MMCert using two benchmark datasets: one for the multi-modal road segmentation task and the other for the multi-modal emotion recognition task. Moreover, we compare our MMCert with a state-of-the-art certified defense extended from unimodal models. Our experimental results show that our MMCert outperforms the baseline.

Cross Pseudo-Labeling for Semi-Supervised Audio-Visual Source Localization

Audio-Visual Source Localization (AVSL) is the task of identifying specific sounding objects in the scene given audio cues. In our work, we focus on semi-supervised AVSL with pseudo-labeling. To address the issues with vanilla hard pseudo-labels including bias accumulation, noise sensitivity, and instability, we propose a novel method named Cross Pseudo-Labeling (XPL), wherein two models learn from each other with the cross-refine mechanism to avoid bias accumulation. We equip XPL with two effective components. Firstly, the soft pseudo-labels with sharpening and pseudo-label exponential moving average mechanisms enable models to achieve gradual self-improvement and ensure stable training. Secondly, the curriculum data selection module adaptively selects pseudo-labels with high quality during training to mitigate potential bias. Experimental results demonstrate that XPL significantly outperforms existing methods, achieving state-of-the-art performance while effectively mitigating confirmation bias and ensuring training stability.

Dual Mean-Teacher: An Unbiased Semi-Supervised Framework for Audio-Visual Source Localization

Audio-Visual Source Localization (AVSL) aims to locate sounding objects within video frames given the paired audio clips. Existing methods predominantly rely on self-supervised contrastive learning of audio-visual correspondence. Without any bounding-box annotations, they struggle to achieve precise localization, especially for small objects, and suffer from blurry boundaries and false positives. Moreover, the naive semi-supervised method is poor in fully leveraging the information of abundant unlabeled data. In this paper, we propose a novel semi-supervised learning framework for AVSL, namely Dual Mean-Teacher (DMT), comprising two teacher-student structures to circumvent the confirmation bias issue. Specifically, two teachers, pre-trained on limited labeled data, are employed to filter out noisy samples via the consensus between their predictions, and then generate high-quality pseudo-labels by intersecting their confidence maps. The sufficient utilization of both labeled and unlabeled data and the proposed unbiased framework enable DMT to outperform current state-of-the-art methods by a large margin, with CIoU of 90.4% and 48.8% on Flickr-SoundNet and VGG-Sound Source, obtaining 8.9%, 9.6% and 4.6%, 6.4% improvements over self- and semi-supervised methods respectively, given only 3% positional-annotations. We also extend our framework to some existing AVSL methods and consistently boost their performance.

PoisonedRAG: Knowledge Poisoning Attacks to Retrieval-Augmented Generation of Large Language Models

Large language models (LLMs) have achieved remarkable success due to their exceptional generative capabilities. Despite their success, they also have inherent limitations such as a lack of up-to-date knowledge and hallucination. Retrieval-Augmented Generation (RAG) is a state-of-the-art technique to mitigate those limitations. In particular, given a question, RAG retrieves relevant knowledge from a knowledge database to augment the input of the LLM. For instance, the retrieved knowledge could be a set of top-k texts that are most semantically similar to the given question when the knowledge database contains millions of texts collected from Wikipedia. As a result, the LLM could utilize the retrieved knowledge as the context to generate an answer for the given question. Existing studies mainly focus on improving the accuracy or efficiency of RAG, leaving its security largely unexplored. We aim to bridge the gap in this work. Particularly, we propose PoisonedRAG , a set of knowledge poisoning attacks to RAG, where an attacker could inject a few poisoned texts into the knowledge database such that the LLM generates an attacker-chosen target answer for an attacker-chosen target question. We formulate knowledge poisoning attacks as an optimization problem, whose solution is a set of poisoned texts. Depending on the background knowledge (e.g., black-box and white-box settings) of an attacker on the RAG, we propose two solutions to solve the optimization problem, respectively. Our results on multiple benchmark datasets and LLMs show our attacks could achieve 90% attack success rates when injecting 5 poisoned texts for each target question into a database with millions of texts. We also evaluate recent defenses and our results show they are insufficient to defend against our attacks, highlighting the need for new defenses.

MAPO: Advancing Multilingual Reasoning through Multilingual Alignment-as-Preference Optimization

Though reasoning abilities are considered language-agnostic, existing LLMs exhibit inconsistent reasoning abilities across different languages, e.g., reasoning in a pivot language is superior to other languages due to the imbalance of multilingual training data.To enhance reasoning abilities in non-pivot languages, we propose an alignment-as-preference optimization framework. Specifically, we adopt an open-source translation model to estimate the consistency between answers in non-pivot and pivot languages. We further adopt the answer consistency as the preference for DPO or PPO thus optimizing the lesser reasoning. Experiments show that our method significantly improves the model's multilingual reasoning, with better reasoning consistency across languages. Our framework achieved a 13.7% accuracy improvement on out-of-domain datasets MSVAMP while preserving the competitive performance on MGSM. Moreover, we find that iterative DPO is helpful for further alignment and improvement of the model's multilingual mathematical reasoning ability, further pushing the improvement to 16.7%

From LLM to Conversational Agent: A Memory Enhanced Architecture with Fine-Tuning of Large Language Models

This paper introduces RAISE (Reasoning and Acting through Scratchpad and Examples), an advanced architecture enhancing the integration of Large Language Models (LLMs) like GPT-4 into conversational agents. RAISE, an enhancement of the ReAct framework, incorporates a dual-component memory system, mirroring human short-term and long-term memory, to maintain context and continuity in conversations. It entails a comprehensive agent construction scenario, including phases like Conversation Selection, Scene Extraction, CoT Completion, and Scene Augmentation, leading to the LLMs Training phase. This approach appears to enhance agent controllability and adaptability in complex, multi-turn dialogues. Our preliminary evaluations in a real estate sales context suggest that RAISE has some advantages over traditional agents, indicating its potential for broader applications. This work contributes to the AI field by providing a robust framework for developing more context-aware and versatile conversational agents.

DUMA: a Dual-Mind Conversational Agent with Fast and Slow Thinking

Inspired by the dual-process theory of human cognition, we introduce DUMA, a novel conversational agent framework that embodies a dual-mind mechanism through the utilization of two generative Large Language Models (LLMs) dedicated to fast and slow thinking respectively. The fast thinking model serves as the primary interface for external interactions and initial response generation, evaluating the necessity for engaging the slow thinking model based on the complexity of the complete response. When invoked, the slow thinking model takes over the conversation, engaging in meticulous planning, reasoning, and tool utilization to provide a well-analyzed response. This dual-mind configuration allows for a seamless transition between intuitive responses and deliberate problem-solving processes based on the situation. We have constructed a conversational agent to handle online inquiries in the real estate industry. The experiment proves that our method balances effectiveness and efficiency, and has a significant improvement compared to the baseline.