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. Bioinformatics provides an important domain. In this field generating functional programs poses additional notable challenges due to the amount of specialized 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+, GPT-3.5, and GPT-4. The results highlight two key aspects of successful models: 1) that they contain specific domain knowledge of bioinformatics (beyond just coding knowledge); 2) that they accommodate a long prompt with full context (i.e. functional dependencies). Our dataset, benchmark, Docker images, and scripts required for testing are all available at //github.com/gersteinlab/biocoder.
In recent times, large language models (LLMs) have shown impressive performance on various document-level tasks such as document classification, summarization, and question-answering. However, research on understanding their capabilities on the task of self-contradictions in long documents has been very limited. In this work, we introduce ContraDoc, the first human-annotated dataset to study self-contradictions in long documents across multiple domains, varying document lengths, self-contradictions types, and scope. We then analyze the current capabilities of four state-of-the-art open-source and commercially available LLMs: GPT3.5, GPT4, PaLM2, and LLaMAv2 on this dataset. While GPT4 performs the best and can outperform humans on this task, we find that it is still unreliable and struggles with self-contradictions that require more nuance and context. We release the dataset and all the code associated with the experiments.
Powerful large language models have facilitated the development of writing assistants that promise to significantly improve the quality and efficiency of composition and communication. However, a barrier to effective assistance is the lack of personalization in LLM outputs to the author's communication style and specialized knowledge. In this paper, we address this challenge by proposing PEARL, a retrieval-augmented LLM writing assistant personalized with a generation-calibrated retriever. Our retriever is trained to select historic user-authored documents for prompt augmentation, such that they are likely to best personalize LLM generations for a user request. We propose two key novelties for training our retriever: 1) A training data selection method that identifies user requests likely to benefit from personalization and documents that provide that benefit; and 2) A scale-calibrating KL-divergence objective that ensures that our retriever closely tracks the benefit of a document for personalized generation. We demonstrate the effectiveness of PEARL in generating personalized workplace social media posts and Reddit comments. Finally, we showcase the potential of a generation-calibrated retriever to double as a performance predictor and further improve low-quality generations via LLM chaining.
Although image captioning has a vast array of applications, it has not reached its full potential in languages other than English. Arabic, for instance, although the native language of more than 400 million people, remains largely underrepresented in this area. This is due to the lack of labeled data and powerful Arabic generative models. We alleviate this issue by presenting a novel vision-language model dedicated to Arabic, dubbed \textit{Violet}. Our model is based on a vision encoder and a Gemini text decoder that maintains generation fluency while allowing fusion between the vision and language components. To train our model, we introduce a new method for automatically acquiring data from available English datasets. We also manually prepare a new dataset for evaluation. \textit{Violet} performs sizeably better than our baselines on all of our evaluation datasets. For example, it reaches a CIDEr score of $61.2$ on our manually annotated dataset and achieves an improvement of $13$ points on Flickr8k.
Adversarial testing of large language models (LLMs) is crucial for their safe and responsible deployment. We introduce a novel approach for automated generation of adversarial evaluation datasets to test the safety of LLM generations on new downstream applications. We call it AI-assisted Red-Teaming (AART) - an automated alternative to current manual red-teaming efforts. AART offers a data generation and augmentation pipeline of reusable and customizable recipes that reduce human effort significantly and enable integration of adversarial testing earlier in new product development. AART generates evaluation datasets with high diversity of content characteristics critical for effective adversarial testing (e.g. sensitive and harmful concepts, specific to a wide range of cultural and geographic regions and application scenarios). The data generation is steered by AI-assisted recipes to define, scope and prioritize diversity within the application context. This feeds into a structured LLM-generation process that scales up evaluation priorities. Compared to some state-of-the-art tools, AART shows promising results in terms of concept coverage and data quality.
Recent achievements in language models have showcased their extraordinary capabilities in bridging visual information with semantic language understanding. This leads us to a novel question: can language models connect textual semantics with IoT sensory signals to perform recognition tasks, e.g., Human Activity Recognition (HAR)? If so, an intelligent HAR system with human-like cognition can be built, capable of adapting to new environments and unseen categories. This paper explores its feasibility with an innovative approach, IoT-sEnsors-language alignmEnt pre-Training (TENT), which jointly aligns textual embeddings with IoT sensor signals, including camera video, LiDAR, and mmWave. Through the IoT-language contrastive learning, we derive a unified semantic feature space that aligns multi-modal features with language embeddings, so that the IoT data corresponds to specific words that describe the IoT data. To enhance the connection between textual categories and their IoT data, we propose supplementary descriptions and learnable prompts that bring more semantic information into the joint feature space. TENT can not only recognize actions that have been seen but also ``guess'' the unseen action by the closest textual words from the feature space. We demonstrate TENT achieves state-of-the-art performance on zero-shot HAR tasks using different modalities, improving the best vision-language models by over 12%.
Inspired by the recent success of large language models (LLMs) like ChatGPT, researchers start to explore the adoption of LLMs for agile hardware design, such as generating design RTL based on natural-language instructions. However, in existing works, their target designs are all relatively simple and in a small scale, and proposed by the authors themselves, making a fair comparison among different LLM solutions challenging. In addition, many prior works only focus on the design correctness, without evaluating the design qualities of generated design RTL. In this work, we propose an open-source benchmark named RTLLM, for generating design RTL with natural language instructions. To systematically evaluate the auto-generated design RTL, we summarized three progressive goals, named syntax goal, functionality goal, and design quality goal. This benchmark can automatically provide a quantitative evaluation of any given LLM-based solution. Furthermore, we propose an easy-to-use yet surprisingly effective prompt engineering technique named self-planning, which proves to significantly boost the performance of GPT-3.5 in our proposed benchmark.
Convolution models with long filters have demonstrated state-of-the-art reasoning abilities in many long-sequence tasks but lag behind the most optimized Transformers in wall-clock time. A major bottleneck is the Fast Fourier Transform (FFT)--which allows long convolutions to run in $O(N logN)$ time in sequence length $N$ but has poor hardware utilization. In this paper, we study how to optimize the FFT convolution. We find two key bottlenecks: the FFT does not effectively use specialized matrix multiply units, and it incurs expensive I/O between layers of the memory hierarchy. In response, we propose FlashFFTConv. FlashFFTConv uses a matrix decomposition that computes the FFT using matrix multiply units and enables kernel fusion for long sequences, reducing I/O. We also present two sparse convolution algorithms--1) partial convolutions and 2) frequency-sparse convolutions--which can be implemented simply by skipping blocks in the matrix decomposition, enabling further opportunities for memory and compute savings. FlashFFTConv speeds up exact FFT convolutions by up to 7.93$\times$ over PyTorch and achieves up to 4.4$\times$ speedup end-to-end. Given the same compute budget, FlashFFTConv allows Hyena-GPT-s to achieve 2.3 points better perplexity on the PILE and M2-BERT-base to achieve 3.3 points higher GLUE score--matching models with twice the parameter count. FlashFFTConv also achieves 96.1% accuracy on Path-512, a high-resolution vision task where no model had previously achieved better than 50%. Furthermore, partial convolutions enable longer-sequence models--yielding the first DNA model that can process the longest human genes (2.3M base pairs)--and frequency-sparse convolutions speed up pretrained models while maintaining or improving model quality.
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.
The success of language models has inspired the NLP community to attend to tasks that require implicit and complex reasoning, relying on human-like commonsense mechanisms. While such vertical thinking tasks have been relatively popular, lateral thinking puzzles have received little attention. To bridge this gap, we devise BRAINTEASER: a multiple-choice Question Answering task designed to test the model's ability to exhibit lateral thinking and defy default commonsense associations. We design a three-step procedure for creating the first lateral thinking benchmark, consisting of data collection, distractor generation, and generation of adversarial examples, leading to 1,100 puzzles with high-quality annotations. To assess the consistency of lateral reasoning by models, we enrich BRAINTEASER based on a semantic and contextual reconstruction of its questions. Our experiments with state-of-the-art instruction- and commonsense language models reveal a significant gap between human and model performance, which is further widened when consistency across adversarial formats is considered. We make all of our code and data available to stimulate work on developing and evaluating lateral thinking models.
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 .