Large language models in bioinformatics: applications and perspectives

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of artificial neural networks with numerous parameters, trained on large amounts of unlabeled input using self-supervised or semi-supervised learning. However, their potential for solving bioinformatics problems may even exceed their proficiency in modeling human language. In this review, we will present a summary of the prominent large language models used in natural language processing, such as BERT and GPT, and focus on exploring the applications of large language models at different omics levels in bioinformatics, mainly including applications of large language models in genomics, transcriptomics, proteomics, drug discovery and single cell analysis. Finally, this review summarizes the potential and prospects of large language models in solving bioinformatic problems.

Large Multimodal Model Compression via Efficient Pruning and Distillation at AntGroup

The deployment of Large Multimodal Models (LMMs) within AntGroup has significantly advanced multimodal tasks in payment, security, and advertising, notably enhancing advertisement audition tasks in Alipay. However, the deployment of such sizable models introduces challenges, particularly in increased latency and carbon emissions, which are antithetical to the ideals of Green AI. This paper introduces a novel multi-stage compression strategy for our proprietary LLM, AntGMM. Our methodology pivots on three main aspects: employing small training sample sizes, addressing multi-level redundancy through multi-stage pruning, and introducing an advanced distillation loss design. In our research, we constructed a dataset, the Multimodal Advertisement Audition Dataset (MAAD), from real-world scenarios within Alipay, and conducted experiments to validate the reliability of our proposed strategy. Furthermore, the effectiveness of our strategy is evident in its operational success in Alipay's real-world multimodal advertisement audition for three months from September 2023. Notably, our approach achieved a substantial reduction in latency, decreasing it from 700ms to 90ms, while maintaining online performance with only a slight performance decrease. Moreover, our compressed model is estimated to reduce electricity consumption by approximately 75 million kWh annually compared to the direct deployment of AntGMM, demonstrating our commitment to green AI initiatives. We will publicly release our code and the MAAD dataset after some reviews\footnote{https://github.com/MorinW/AntGMM$\_$Pruning}.

Learning Implicit Entity-object Relations by Bidirectional Generative Alignment for Multimodal NER

The challenge posed by multimodal named entity recognition (MNER) is mainly two-fold: (1) bridging the semantic gap between text and image and (2) matching the entity with its associated object in image. Existing methods fail to capture the implicit entity-object relations, due to the lack of corresponding annotation. In this paper, we propose a bidirectional generative alignment method named BGA-MNER to tackle these issues. Our BGA-MNER consists of \texttt{image2text} and \texttt{text2image} generation with respect to entity-salient content in two modalities. It jointly optimizes the bidirectional reconstruction objectives, leading to aligning the implicit entity-object relations under such direct and powerful constraints. Furthermore, image-text pairs usually contain unmatched components which are noisy for generation. A stage-refined context sampler is proposed to extract the matched cross-modal content for generation. Extensive experiments on two benchmarks demonstrate that our method achieves state-of-the-art performance without image input during inference.

Don't Watch Me: A Spatio-Temporal Trojan Attack on Deep-Reinforcement-Learning-Augment Autonomous Driving

Deep reinforcement learning (DRL) is one of the most popular algorithms to realize an autonomous driving (AD) system. The key success factor of DRL is that it embraces the perception capability of deep neural networks which, however, have been proven vulnerable to Trojan attacks. Trojan attacks have been widely explored in supervised learning (SL) tasks (e.g., image classification), but rarely in sequential decision-making tasks solved by DRL. Hence, in this paper, we explore Trojan attacks on DRL for AD tasks. First, we propose a spatio-temporal DRL algorithm based on the recurrent neural network and attention mechanism to prove that capturing spatio-temporal traffic features is the key factor to the effectiveness and safety of a DRL-augment AD system. We then design a spatial-temporal Trojan attack on DRL policies, where the trigger is hidden in a sequence of spatial and temporal traffic features, rather than a single instant state used in existing Trojan on SL and DRL tasks. With our Trojan, the adversary acts as a surrounding normal vehicle and can trigger attacks via specific spatial-temporal driving behaviors, rather than physical or wireless access. Through extensive experiments, we show that while capturing spatio-temporal traffic features can improve the performance of DRL for different AD tasks, they suffer from Trojan attacks since our designed Trojan shows high stealthy (various spatio-temporal trigger patterns), effective (less than 3.1\% performance variance rate and more than 98.5\% attack success rate), and sustainable to existing advanced defenses.

A Temporal-Pattern Backdoor Attack to Deep Reinforcement Learning

Deep reinforcement learning (DRL) has made significant achievements in many real-world applications. But these real-world applications typically can only provide partial observations for making decisions due to occlusions and noisy sensors. However, partial state observability can be used to hide malicious behaviors for backdoors. In this paper, we explore the sequential nature of DRL and propose a novel temporal-pattern backdoor attack to DRL, whose trigger is a set of temporal constraints on a sequence of observations rather than a single observation, and effect can be kept in a controllable duration rather than in the instant. We validate our proposed backdoor attack to a typical job scheduling task in cloud computing. Numerous experimental results show that our backdoor can achieve excellent effectiveness, stealthiness, and sustainability. Our backdoor's average clean data accuracy and attack success rate can reach 97.8% and 97.5%, respectively.