Pre-trained large language models have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks and to be appropriately specialized to particular domains. Here, we target bioinformatics due to the amount of specialized domain knowledge, algorithms, and data operations this discipline requires. We present BioCoder, a benchmark developed to evaluate large language models (LLMs) in generating bioinformatics-specific code. BioCoder spans a broad spectrum of the field and covers cross-file dependencies, class declarations, and global variables. It incorporates 1026 Python functions and 1243 Java methods extracted from GitHub, along with 253 examples from the Rosalind Project, all pertaining to bioinformatics. Using topic modeling we show that overall coverage of the included code is representative of the full spectrum of bioinformatics calculations. BioCoder incorporates a fuzz-testing framework for evaluation. We have applied it to evaluate many models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, GPT-3.5, and GPT-4. Furthermore, we finetuned StarCoder, demonstrating how our dataset can effectively enhance the performance of LLMs on our benchmark (by >15% in terms of Pass@K in certain prompt configurations and always >3%). The results highlight two key aspects of successful models: (1) Successful models accommodate a long prompt (> ~2600 tokens) with full context, for functional dependencies. (2) They contain specific domain knowledge of bioinformatics, beyond just general coding knowledge. This is evident from the performance gain of GPT-3.5/4 compared to the smaller models on the benchmark (50% vs up to ~25%). Our dataset, benchmark, Docker images, and scripts required for testing are all available at //github.com/gersteinlab/biocoder.
Neural language models are probabilistic models of human text. They are predominantly trained using maximum likelihood estimation (MLE), which is equivalent to minimizing the forward cross-entropy between the empirical data distribution and the model distribution. However, various degeneration phenomena are still widely observed when decoding from the distributions learned by such models. We establish that the forward cross-entropy is suboptimal as a distance metric for aligning human and model distribution due to its (1) recall-prioritization (2) negative diversity ignorance and (3) train-test mismatch. In this paper, we propose Earth Mover Distance Optimization (EMO) for auto-regressive language modeling. EMO capitalizes on the inherent properties of earth mover distance to address the aforementioned challenges. Due to the high complexity of direct computation, we further introduce a feasible upper bound for EMO to ease end-to-end training. Upon extensive evaluation of language models trained using EMO and MLE. We find that EMO demonstrates a consistently better language modeling performance than MLE across domains. Moreover, EMO demonstrates noteworthy enhancements in downstream performance with minimal fine-tuning on merely 25,000 sentences. This highlights the tremendous potential of EMO as a lightweight calibration method for enhancing large-scale pre-trained language models.
Recent advances in large language models elicit reasoning in a chain-of-thought that allows models to decompose problems in a human-like fashion. Though this paradigm improves multi-step reasoning ability in language models, it is limited by being unimodal and applied mainly to question-answering tasks. We claim that incorporating visual augmentation into reasoning is essential, especially for complex, imaginative tasks. Consequently, we introduce VCoT, a novel method that leverages chain-of-thought prompting with vision-language grounding to recursively bridge the logical gaps within sequential data. Our method uses visual guidance to generate synthetic multimodal infillings that add consistent and novel information to reduce the logical gaps for downstream tasks that can benefit from temporal reasoning, as well as provide interpretability into models' multi-step reasoning. We apply VCoT to the Visual Storytelling and WikiHow summarization datasets and demonstrate through human evaluation that VCoT offers novel and consistent synthetic data augmentation beating chain-of-thought baselines, which can be used to enhance downstream performance.
Current speech large language models build upon discrete speech representations, which can be categorized into semantic tokens and acoustic tokens. However, existing speech tokens are not specifically designed for speech language modeling. To assess the suitability of speech tokens for building speech language models, we established the first benchmark, SLMTokBench. Our results indicate that neither semantic nor acoustic tokens are ideal for this purpose. Therefore, we propose SpeechTokenizer, a unified speech tokenizer for speech large language models. SpeechTokenizer adopts the Encoder-Decoder architecture with residual vector quantization (RVQ). Unifying semantic and acoustic tokens, SpeechTokenizer disentangles different aspects of speech information hierarchically across different RVQ layers. Furthermore, We construct a Unified Speech Language Model (USLM) leveraging SpeechTokenizer. Experiments show that SpeechTokenizer performs comparably to EnCodec in speech reconstruction and demonstrates strong performance on the SLMTokBench benchmark. Also, USLM outperforms VALL-E in zero-shot Text-to-Speech tasks. Code and models are available at //github.com/ZhangXInFD/SpeechTokenizer/.
Recent code large language models (LLMs) have shown promising performance in generating standalone functions but face limitations in repository-level code generation due to their lack of awareness of repository-level dependencies (e.g., user-defined attributes), resulting in dependency errors such as undefined-variable and no-member errors. In this work, we introduce ToolGen, an approach that integrates autocompletion tools into the code LLM generation process to address these dependencies. ToolGen comprises two main phases: Trigger Insertion and Model Fine-tuning (Offline), and Tool-integrated Code Generation (Online). During the offline phase, ToolGen augments functions within a given code corpus with a special mark token, indicating positions to trigger autocompletion tools. These augmented functions, along with their corresponding docstrings, are then used to fine-tune a selected code LLM. In the online phase, ToolGen iteratively generates functions by predicting tokens step-by-step using the fine-tuned LLM. Whenever a mark token is encountered, ToolGen invokes the autocompletion tool to suggest code completions and selects the most appropriate one. We conduct comprehensive experiments to evaluate ToolGen's effectiveness in repository-level code generation. To facilitate this evaluation, we create a benchmark comprising 680 real-world code repositories and introduce two new repository-level metrics: Dependency Coverage and Static Validity Rate. The results demonstrate that ToolGen significantly improves Dependency Coverage by 15.2% to 45.8% and Static Validity Rate by 10.9% to 42.2% across three distinct code LLMs, while maintaining competitive performance in widely-recognized similarity metrics. Furthermore, our generalizability evaluation confirms ToolGen's consistent performance when applied to diverse code LLMs, including various model architectures and scales.
Large language models (LLMs) are shown to benefit from chain-of-thought (COT) prompting, particularly when tackling tasks that require systematic reasoning processes. On the other hand, COT prompting also poses new vulnerabilities in the form of backdoor attacks, wherein the model will output unintended malicious content under specific backdoor-triggered conditions during inference. Traditional methods for launching backdoor attacks involve either contaminating the training dataset with backdoored instances or directly manipulating the model parameters during deployment. However, these approaches are not practical for commercial LLMs that typically operate via API access. In this paper, we propose BadChain, the first backdoor attack against LLMs employing COT prompting, which does not require access to the training dataset or model parameters and imposes low computational overhead. BadChain leverages the inherent reasoning capabilities of LLMs by inserting a backdoor reasoning step into the sequence of reasoning steps of the model output, thereby altering the final response when a backdoor trigger exists in the query prompt. Empirically, we show the effectiveness of BadChain for two COT strategies across four LLMs (Llama2, GPT-3.5, PaLM2, and GPT-4) and six complex benchmark tasks encompassing arithmetic, commonsense, and symbolic reasoning. Moreover, we show that LLMs endowed with stronger reasoning capabilities exhibit higher susceptibility to BadChain, exemplified by a high average attack success rate of 97.0% across the six benchmark tasks on GPT-4. Finally, we propose two defenses based on shuffling and demonstrate their overall ineffectiveness against BadChain. Therefore, BadChain remains a severe threat to LLMs, underscoring the urgency for the development of robust and effective future defenses.
Large Language models (LLMs) usually rely on extensive training datasets. In the financial domain, creating numerical reasoning datasets that include a mix of tables and long text often involves substantial manual annotation expenses. To address the limited data resources and reduce the annotation cost, we introduce FinLLMs, a method for generating financial question-answering data based on common financial formulas using Large Language Models. First, we compile a list of common financial formulas and construct a graph based on the variables these formulas employ. We then augment the formula set by combining those that share identical variables as new elements. Specifically, we explore formulas obtained by manual annotation and merge those formulas with shared variables by traversing the constructed graph. Finally, utilizing GPT-3.5, we generate financial question-answering data that encompasses both tabular information and long textual content, building on the collected formula set. Our experiments demonstrate that synthetic data generated by FinLLMs effectively enhances the performance of several large-scale numerical reasoning models in the financial domain, outperforming two established benchmark financial question-answering datasets.
Recent advancements in large language models have facilitated the execution of complex language tasks, not only in English but also in non-English languages. However, the tokenizers of most language models, such as Llama, trained on English-centric corpora, tend to excessively fragment tokens in non-English languages. This issue is especially pronounced in non-roman alphabetic languages, which are often divided at a character or even Unicode level, leading to slower text generation. To address this, our study introduces a novel framework designed to expedite text generation in these languages. This framework predicts larger linguistic units than those of conventional multilingual tokenizers and is specifically tailored to the target language, thereby reducing the number of decoding steps required. Our empirical results demonstrate that the proposed framework increases the generation speed by a factor of 1.9 compared to standard decoding while maintaining the performance of a pre-trained multilingual model on monolingual tasks.
Large language models (LLMs) have demonstrated remarkable generalizability, such as understanding arbitrary entities and relations. Instruction tuning has proven effective for distilling LLMs into more cost-efficient models such as Alpaca and Vicuna. Yet such student models still trail the original LLMs by large margins in downstream applications. In this paper, we explore targeted distillation with mission-focused instruction tuning to train student models that can excel in a broad application class such as open information extraction. Using named entity recognition (NER) for case study, we show how ChatGPT can be distilled into much smaller UniversalNER models for open NER. For evaluation, we assemble the largest NER benchmark to date, comprising 43 datasets across 9 diverse domains such as biomedicine, programming, social media, law, finance. Without using any direct supervision, UniversalNER attains remarkable NER accuracy across tens of thousands of entity types, outperforming general instruction-tuned models such as Alpaca and Vicuna by over 30 absolute F1 points in average. With a tiny fraction of parameters, UniversalNER not only acquires ChatGPT's capability in recognizing arbitrary entity types, but also outperforms its NER accuracy by 7-9 absolute F1 points in average. Remarkably, UniversalNER even outperforms by a large margin state-of-the-art multi-task instruction-tuned systems such as InstructUIE, which uses supervised NER examples. We also conduct thorough ablation studies to assess the impact of various components in our distillation approach. We release the distillation recipe, data, and UniversalNER models to facilitate future research on targeted distillation.
Recent vision-language models have shown impressive multi-modal generation capabilities. However, typically they require training huge models on massive datasets. As a more scalable alternative, we introduce Prismer, a data- and parameter-efficient vision-language model that leverages an ensemble of task-specific experts. Prismer only requires training of a small number of components, with the majority of network weights inherited from multiple readily-available, pre-trained experts, and kept frozen during training. By leveraging experts from a wide range of domains, we show Prismer can efficiently pool this expert knowledge and adapt it to various vision-language reasoning tasks. In our experiments, we show that Prismer achieves fine-tuned and few-shot learning performance which is competitive with current state-of-the-arts, whilst requiring up to two orders of magnitude less training data. Code is available at //github.com/NVlabs/prismer.
Diffusion models have emerged as a prominent class of generative models, surpassing previous methods regarding sample quality and training stability. Recent works have shown the advantages of diffusion models in improving reinforcement learning (RL) solutions, including as trajectory planners, expressive policy classes, data synthesizers, etc. This survey aims to provide an overview of the advancements in this emerging field and hopes to inspire new avenues of research. First, we examine several challenges encountered by current RL algorithms. Then, we present a taxonomy of existing methods based on the roles played by diffusion models in RL and explore how the existing challenges are addressed. We further outline successful applications of diffusion models in various RL-related tasks while discussing the limitations of current approaches. Finally, we conclude the survey and offer insights into future research directions, focusing on enhancing model performance and applying diffusion models to broader tasks. We are actively maintaining a GitHub repository for papers and other related resources in applying diffusion models in RL: //github.com/apexrl/Diff4RLSurvey .