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Pre-trained language models like ChatGPT have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks. Moreover, in bioinformatics, generating functional programs poses additional notable challenges due to the amount of domain knowledge, the need for complicated data operations, and intricate functional dependencies between the operations. Here, we present BioCoder, a benchmark developed to evaluate existing pre-trained models in generating bioinformatics code. In relation to function-code generation, BioCoder covers potential package dependencies, class declarations, and global variables. It incorporates 1026 functions and 1243 methods in Python and Java from GitHub and 253 examples from the Rosalind Project. BioCoder incorporates a fuzz-testing framework for evaluation, and we have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, and ChatGPT. Our detailed analysis of these models emphasizes the importance of domain knowledge, pragmatic code generation, and contextual understanding. Our dataset, benchmark, Docker images, and scripts required for testing are all available at //github.com/gersteinlab/biocoder.

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Explanation:生物信息學。 Publisher:Oxford University Press。 SIT:

Without proper safeguards, large language models will readily follow malicious instructions and generate toxic content. This risk motivates safety efforts such as red-teaming and large-scale feedback learning, which aim to make models both helpful and harmless. However, there is a tension between these two objectives, since harmlessness requires models to refuse to comply with unsafe prompts, and thus not be helpful. Recent anecdotal evidence suggests that some models may have struck a poor balance, so that even clearly safe prompts are refused if they use similar language to unsafe prompts or mention sensitive topics. In this paper, we introduce a new test suite called XSTest to identify such eXaggerated Safety behaviours in a systematic way. XSTest comprises 250 safe prompts across ten prompt types that well-calibrated models should not refuse to comply with, and 200 unsafe prompts as contrasts that models, for most applications, should refuse. We describe XSTest's creation and composition, and then use the test suite to highlight systematic failure modes in state-of-the-art language models as well as more general challenges in building safer language models.

Factual consistency evaluation is often conducted using Natural Language Inference (NLI) models, yet these models exhibit limited success in evaluating summaries. Previous work improved such models with synthetic training data. However, the data is typically based on perturbed human-written summaries, which often differ in their characteristics from real model-generated summaries and have limited coverage of possible factual errors. Alternatively, large language models (LLMs) have recently shown promising results in directly evaluating generative tasks, but are too computationally expensive for practical use. Motivated by these limitations, we introduce TrueTeacher, a method for generating synthetic data by annotating diverse model-generated summaries using a LLM. Unlike prior work, TrueTeacher does not rely on human-written summaries, and is multilingual by nature. Experiments on the TRUE benchmark show that a student model trained using our data, substantially outperforms both the state-of-the-art model with similar capacity, and the LLM teacher. In a systematic study, we compare TrueTeacher to existing synthetic data generation methods and demonstrate its superiority and robustness to domain-shift. We also show that our method generalizes to multilingual scenarios. Lastly, we release our large scale synthetic dataset (1.4M examples), generated using TrueTeacher, and a checkpoint trained on this data.

Alignment is of critical importance for training large language models (LLMs). The predominant strategy to address this is through Reinforcement Learning from Human Feedback (RLHF), where PPO serves as the de-facto algorithm. Yet, PPO is known to suffer from computational inefficiency, which is a challenge that this paper aims to address. We identify three important properties in RLHF tasks: fast simulation, deterministic transitions, and trajectory-level rewards, which are not leveraged in PPO. Based on such observations, we develop a new algorithm tailored for RLHF, called ReMax. The algorithm design of ReMax is built on a celebrated algorithm REINFORCE but is equipped with a new variance-reduction technique. Our method has three-fold advantages over PPO: first, ReMax is simple to implement and removes many hyper-parameters in PPO, which are scale-sensitive and laborious to tune. Second, ReMax saves about 50% memory usage in principle. As a result, PPO runs out-of-memory when fine-tuning a Llama2 (7B) model on 8xA100-40GB GPUs, whereas ReMax can afford training. This memory improvement is achieved by removing the value model in PPO. Third, based on our calculations, we find that even assuming PPO can afford the training of Llama2 (7B), it would still run about 2x slower than ReMax. This is due to the computational overhead of the value model, which does not exist in ReMax. Importantly, the above computational improvements do not sacrifice the performance. We hypothesize these advantages can be maintained in larger-scaled models. Our implementation of ReMax is available at //github.com/liziniu/ReMax

Alignment is of critical importance for training large language models (LLMs). The predominant strategy to address this is through Reinforcement Learning from Human Feedback (RLHF), where PPO serves as the de-facto algorithm. Yet, PPO is known to suffer from computational inefficiency, a challenge that this paper aims to address. We identify three important properties in RLHF tasks: fast simulation, deterministic transitions, and trajectory-level rewards, which are not leveraged in PPO. Based on such observations, we develop a new algorithm tailored for RLHF, called ReMax. The algorithm design of ReMax is built on a celebrated algorithm REINFORCE but is equipped with a new variance-reduction technique. Our method has three-fold advantages over PPO: first, it saves about 50% memory usage in principle. As a result, PPO runs out-of-memory when fine-tuning a Llama2 (7B) model on 8xA100-40GB GPUs, whereas ReMax can afford training. This memory improvement is achieved by removing the value model in PPO. Second, ReMax is simple to implement and removes many hyper-parameters in PPO, which are scale-sensitive and laborious to tune. Third, on GPT2 (137M), we observe 2.2x speed-up in terms of wall-clock time. Importantly, the above computational improvements do not sacrifice the performance. We hypothesize these advantages can be maintained in larger-scaled models. Our implementation of ReMax is available at //github.com/liziniu/ReMax

Joint speech-language training is challenging due to the large demand for training data and GPU consumption, as well as the modality gap between speech and language. We present ComSL, a speech-language model built atop a composite architecture of public pretrained speech-only and language-only models and optimized data-efficiently for spoken language tasks. Particularly, we propose to incorporate cross-modality learning into transfer learning and conduct them simultaneously for downstream tasks in a multi-task learning manner. Our approach has demonstrated effectiveness in end-to-end speech-to-text translation tasks, achieving a new state-of-the-art average BLEU score of 31.5 on the multilingual speech to English text translation task for 21 languages, as measured on the public CoVoST2 evaluation set.

Security has always been a critical issue in machine learning (ML) applications. Due to the high cost of model training -- such as collecting relevant samples, labeling data, and consuming computing power -- model-stealing attack is one of the most fundamental but vitally important issues. When it comes to quantum computing, such a quantum machine learning (QML) model-stealing attack also exists and is even more severe because the traditional encryption method, such as homomorphic encryption can hardly be directly applied to quantum computation. On the other hand, due to the limited quantum computing resources, the monetary cost of training QML model can be even higher than classical ones in the near term. Therefore, a well-tuned QML model developed by a third-party company can be delegated to a quantum cloud provider as a service to be used by ordinary users. In this case, the QML model will likely be leaked if the cloud provider is under attack. To address such a problem, we propose a novel framework, namely QuMoS, to preserve model security. We propose to divide the complete QML model into multiple parts and distribute them to multiple physically isolated quantum cloud providers for execution. As such, even if the adversary in a single provider can obtain a partial model, it does not have sufficient information to retrieve the complete model. Although promising, we observed that an arbitrary model design under distributed settings cannot provide model security. We further developed a reinforcement learning-based security engine, which can automatically optimize the model design under the distributed setting, such that a good trade-off between model performance and security can be made. Experimental results on four datasets show that the model design proposed by QuMoS can achieve competitive performance while providing the highest security than the baselines.

Decoder-only Transformer models such as GPT have demonstrated superior performance in text generation, by autoregressively predicting the next token. However, the performance of GPT is bounded by low compute-to-memory-ratio and high memory access. Throughput-oriented architectures such as GPUs target parallel processing rather than sequential token generation, and are not efficient for GPT acceleration, particularly on-device inference applications. Process-in-memory (PIM) architectures can significantly reduce data movement and provide high computation parallelism, and are promising candidates to accelerate GPT inference. In this work, we propose PIM-GPT that aims to achieve high throughput, high energy efficiency and end-to-end acceleration of GPT inference. PIM-GPT leverages DRAM-based PIM solutions to perform multiply-accumulate (MAC) operations on the DRAM chips, greatly reducing data movement. A compact application-specific integrated chip (ASIC) is designed and synthesized to initiate instructions to PIM chips and support data communication along with necessary arithmetic computations. At the software level, the mapping scheme is designed to maximize data locality and computation parallelism by partitioning a matrix among DRAM channels and banks to utilize all in-bank computation resources concurrently. We develop an event-driven clock-cycle accurate simulator to validate the efficacy of the proposed PIM-GPT architecture. Overall, PIM-GPT achieves 41$-$137$\times$, 631$-$1074$\times$ speedup and 339$-$1085$\times$, 890$-$1632$\times$ energy efficiency over GPU and CPU baseline, respectively, on 8 GPT models with up to 1.4 billion parameters.

Large language models (LLMs) have demonstrated powerful text generation capabilities, bringing unprecedented innovation to the healthcare field. While LLMs hold immense promise for applications in healthcare, applying them to real clinical scenarios presents significant challenges, as these models may generate content that deviates from established medical facts and even exhibit potential biases. In our research, we develop an augmented LLM framework based on the Unified Medical Language System (UMLS), aiming to better serve the healthcare community. We employ LLaMa2-13b-chat and ChatGPT-3.5 as our benchmark models, and conduct automatic evaluations using the ROUGE Score and BERTScore on 104 questions from the LiveQA test set. Additionally, we establish criteria for physician-evaluation based on four dimensions: Factuality, Completeness, Readability and Relevancy. ChatGPT-3.5 is used for physician evaluation with 20 questions on the LiveQA test set. Multiple resident physicians conducted blind reviews to evaluate the generated content, and the results indicate that this framework effectively enhances the factuality, completeness, and relevance of generated content. Our research demonstrates the effectiveness of using UMLS-augmented LLMs and highlights the potential application value of LLMs in in medical question-answering.

Knowledge enhanced pre-trained language models (K-PLMs) are shown to be effective for many public tasks in the literature but few of them have been successfully applied in practice. To address this problem, we propose K-AID, a systematic approach that includes a low-cost knowledge acquisition process for acquiring domain knowledge, an effective knowledge infusion module for improving model performance, and a knowledge distillation component for reducing the model size and deploying K-PLMs on resource-restricted devices (e.g., CPU) for real-world application. Importantly, instead of capturing entity knowledge like the majority of existing K-PLMs, our approach captures relational knowledge, which contributes to better-improving sentence-level text classification and text matching tasks that play a key role in question answering (QA). We conducted a set of experiments on five text classification tasks and three text matching tasks from three domains, namely E-commerce, Government, and Film&TV, and performed online A/B tests in E-commerce. Experimental results show that our approach is able to achieve substantial improvement on sentence-level question answering tasks and bring beneficial business value in industrial settings.

Recently pre-trained language representation models such as BERT have shown great success when fine-tuned on downstream tasks including information retrieval (IR). However, pre-training objectives tailored for ad-hoc retrieval have not been well explored. In this paper, we propose Pre-training with Representative wOrds Prediction (PROP) for ad-hoc retrieval. PROP is inspired by the classical statistical language model for IR, specifically the query likelihood model, which assumes that the query is generated as the piece of text representative of the "ideal" document. Based on this idea, we construct the representative words prediction (ROP) task for pre-training. Given an input document, we sample a pair of word sets according to the document language model, where the set with higher likelihood is deemed as more representative of the document. We then pre-train the Transformer model to predict the pairwise preference between the two word sets, jointly with the Masked Language Model (MLM) objective. By further fine-tuning on a variety of representative downstream ad-hoc retrieval tasks, PROP achieves significant improvements over baselines without pre-training or with other pre-training methods. We also show that PROP can achieve exciting performance under both the zero- and low-resource IR settings. The code and pre-trained models are available at //github.com/Albert-Ma/PROP.

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