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.

Fine-tuning is the primary methodology for tailoring pre-trained large language models to specific tasks. As the model's scale and the diversity of tasks expand, parameter-efficient fine-tuning methods are of paramount importance. One of the most widely used family of methods is low-rank adaptation (LoRA) and its variants. LoRA encodes weight update as the product of two low-rank matrices. Despite its advantages, LoRA falls short of full-parameter fine-tuning in terms of generalization error for certain tasks. We introduce Chain of LoRA (COLA), an iterative optimization framework inspired by the Frank-Wolfe algorithm, to bridge the gap between LoRA and full parameter fine-tuning, without incurring additional computational costs or memory overheads. COLA employs a residual learning procedure where it merges learned LoRA modules into the pre-trained language model parameters and re-initilize optimization for new born LoRA modules. We provide theoretical convergence guarantees as well as empirical results to validate the effectiveness of our algorithm. Across various models (OPT and llama-2) and seven benchmarking tasks, we demonstrate that COLA can consistently outperform LoRA without additional computational or memory costs.

We introduce Mixtral 8x7B, a Sparse Mixture of Experts (SMoE) language model. Mixtral has the same architecture as Mistral 7B, with the difference that each layer is composed of 8 feedforward blocks (i.e. experts). For every token, at each layer, a router network selects two experts to process the current state and combine their outputs. Even though each token only sees two experts, the selected experts can be different at each timestep. As a result, each token has access to 47B parameters, but only uses 13B active parameters during inference. Mixtral was trained with a context size of 32k tokens and it outperforms or matches Llama 2 70B and GPT-3.5 across all evaluated benchmarks. In particular, Mixtral vastly outperforms Llama 2 70B on mathematics, code generation, and multilingual benchmarks. We also provide a model fine-tuned to follow instructions, Mixtral 8x7B - Instruct, that surpasses GPT-3.5 Turbo, Claude-2.1, Gemini Pro, and Llama 2 70B - chat model on human benchmarks. Both the base and instruct models are released under the Apache 2.0 license.

State Space Models (SSMs) have become serious contenders in the field of sequential modeling, challenging the dominance of Transformers. At the same time, Mixture of Experts (MoE) has significantly improved Transformer-based LLMs, including recent state-of-the-art open-source models. We propose that to unlock the potential of SSMs for scaling, they should be combined with MoE. We showcase this on Mamba, a recent SSM-based model that achieves remarkable, Transformer-like performance. Our model, MoE-Mamba, outperforms both Mamba and Transformer-MoE. In particular, MoE-Mamba reaches the same performance as Mamba in 2.2x less training steps while preserving the inference performance gains of Mamba against the Transformer.

The rise of generative artificial intelligence, particularly Large Language Models (LLMs), has intensified the imperative to scrutinize fairness alongside accuracy. Recent studies have begun to investigate fairness evaluations for LLMs within domains such as recommendations. Given that personalization is an intrinsic aspect of recommendation systems, its incorporation into fairness assessments is paramount. Yet, the degree to which current fairness evaluation frameworks account for personalization remains unclear. Our comprehensive literature review aims to fill this gap by examining how existing frameworks handle fairness evaluations of LLMs, with a focus on the integration of personalization factors. Despite an exhaustive collection and analysis of relevant works, we discovered that most evaluations overlook personalization, a critical facet of recommendation systems, thereby inadvertently perpetuating unfair practices. Our findings shed light on this oversight and underscore the urgent need for more nuanced fairness evaluations that acknowledge personalization. Such improvements are vital for fostering equitable development within the AI community.

In recent years, DNNs have shown promising results This paper describes methods for training autonomous in the field of behavioural cloning (BC) [5, 18]. BC is a agents to play the game "Doom 2" through Imitation form of Imitation Learning (IL), where we train an artificial Learning (IL) using only pixel data as input. We also explore "agent" to mimic actions from an observable state of how Reinforcement Learning (RL) compares to IL expert data [34]. Agents are trained using a number of historical for humanness by comparing camera movement and trajectory states, be they image frames or other data, and their data. Through behavioural cloning, we examine the corresponding actions. The learning is performed by using ability of individual models to learn varying behavioural the final frame's associated action as the "target", this target traits. We attempt to mimic the behaviour of real players being passed to some loss function. The loss function will with different play styles, and find we can train agents that reinforce the observed frame's predicted action, doing this behave aggressively, passively, or simply more human-like over an extremely large dataset will achieve an agent that than traditional AIs. We propose these methods of introducing can predict the best action to take at any one given set of more depth and human-like behaviour to agents in video input image frames [17].

Recent advancements in Large Language Models (LLMs) have led to high-quality Machine-Generated Text (MGT), giving rise to countless new use cases and applications. However, easy access to LLMs is posing new challenges due to misuse. To address malicious usage, researchers have released datasets to effectively train models on MGT-related tasks. Similar strategies are used to compile these datasets, but no tool currently unifies them. In this scenario, we introduce TextMachina, a modular and extensible Python framework, designed to aid in the creation of high-quality, unbiased datasets to build robust models for MGT-related tasks such as detection, attribution, or boundary detection. It provides a user-friendly pipeline that abstracts away the inherent intricacies of building MGT datasets, such as LLM integrations, prompt templating, and bias mitigation. The quality of the datasets generated by TextMachina has been assessed in previous works, including shared tasks where more than one hundred teams trained robust MGT detectors.

Large language models like GPT-4 have achieved remarkable proficiency in a broad spectrum of language-based tasks, some of which are traditionally associated with hallmarks of human intelligence. This has prompted ongoing disagreements about the extent to which we can meaningfully ascribe any kind of linguistic or cognitive competence to language models. Such questions have deep philosophical roots, echoing longstanding debates about the status of artificial neural networks as cognitive models. This article -- the first part of two companion papers -- serves both as a primer on language models for philosophers, and as an opinionated survey of their significance in relation to classic debates in the philosophy cognitive science, artificial intelligence, and linguistics. We cover topics such as compositionality, language acquisition, semantic competence, grounding, world models, and the transmission of cultural knowledge. We argue that the success of language models challenges several long-held assumptions about artificial neural networks. However, we also highlight the need for further empirical investigation to better understand their internal mechanisms. This sets the stage for the companion paper (Part II), which turns to novel empirical methods for probing the inner workings of language models, and new philosophical questions prompted by their latest developments.

Motivated by the increasing popularity of code generation from human descriptions using large language models (LLMs), several benchmarks have been proposed to assess the capabilities of existing and emerging models. This study presents a large-scale human evaluation of HumanEval and MBPP, two widely used benchmarks for Python code generation, focusing on their diversity and difficulty. Our findings reveal a significant bias towards a limited number of programming concepts, with negligible or no representation of most concepts. Additionally, we identify a concerningly high proportion of easy programming questions, potentially leading to an overestimation of model performance on code generation tasks.

In this technical report, we present TeleChat, a collection of large language models (LLMs) with parameters of 3 billion, 7 billion and 12 billion. It includes pretrained language models as well as fine-tuned chat models that is aligned with human preferences. TeleChat is initially pretrained on an extensive corpus containing a diverse collection of texts from both English and Chinese languages, including trillions of tokens. Subsequently, the model undergoes fine-tuning to align with human preferences, following a detailed methodology that we describe. We evaluate the performance of TeleChat on various tasks, including language understanding, mathematics, reasoning, code generation, and knowledge-based question answering. Our findings indicate that TeleChat achieves comparable performance to other open-source models of similar size across a wide range of public benchmarks. To support future research and applications utilizing LLMs, we release the fine-tuned model checkpoints of TeleChat's 7B and 12B variant, along with code and a portion of our pretraining data, to the public community.