Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Generalist foundation models such as GPT-4 have displayed surprising capabilities in a wide variety of domains and tasks. Yet, there is a prevalent assumption that they cannot match specialist capabilities of fine-tuned models. For example, most explorations to date on medical competency benchmarks have leveraged domain-specific training, as exemplified by efforts on BioGPT and Med-PaLM. We build on a prior study of GPT-4's capabilities on medical challenge benchmarks in the absence of special training. Rather than using simple prompting to highlight the model's out-of-the-box capabilities, we perform a systematic exploration of prompt engineering. We find that prompting innovation can unlock deeper specialist capabilities and show that GPT-4 easily tops prior leading results for medical benchmarks. The prompting methods we explore are general purpose, and make no specific use of domain expertise, removing the need for expert-curated content. Our experimental design carefully controls for overfitting during the prompt engineering process. We introduce Medprompt, based on a composition of several prompting strategies. With Medprompt, GPT-4 achieves state-of-the-art results on all nine of the benchmark datasets in the MultiMedQA suite. The method outperforms leading specialist models such as Med-PaLM 2 by a significant margin with an order of magnitude fewer calls to the model. Steering GPT-4 with Medprompt achieves a 27% reduction in error rate on the MedQA dataset over the best methods to date achieved with specialist models and surpasses a score of 90% for the first time. Beyond medical problems, we show the power of Medprompt to generalize to other domains and provide evidence for the broad applicability of the approach via studies of the strategy on exams in electrical engineering, machine learning, philosophy, accounting, law, nursing, and clinical psychology.

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e., BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large scale biomedical literature. We evaluate BioGPT on six biomedical NLP tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms. Code is available at https://github.com/microsoft/BioGPT.

Error correction techniques have been used to refine the output sentences from automatic speech recognition (ASR) models and achieve a lower word error rate (WER) than original ASR outputs. Previous works usually use a sequence-to-sequence model to correct an ASR output sentence autoregressively, which causes large latency and cannot be deployed in online ASR services. A straightforward solution to reduce latency, inspired by non-autoregressive (NAR) neural machine translation, is to use an NAR sequence generation model for ASR error correction, which, however, comes at the cost of significantly increased ASR error rate. In this paper, observing distinctive error patterns and correction operations (i.e., insertion, deletion, and substitution) in ASR, we propose FastCorrect, a novel NAR error correction model based on edit alignment. In training, FastCorrect aligns each source token from an ASR output sentence to the target tokens from the corresponding ground-truth sentence based on the edit distance between the source and target sentences, and extracts the number of target tokens corresponding to each source token during edition/correction, which is then used to train a length predictor and to adjust the source tokens to match the length of the target sentence for parallel generation. In inference, the token number predicted by the length predictor is used to adjust the source tokens for target sequence generation. Experiments on the public AISHELL-1 dataset and an internal industrial-scale ASR dataset show the effectiveness of FastCorrect for ASR error correction: 1) it speeds up the inference by 6-9 times and maintains the accuracy (8-14% WER reduction) compared with the autoregressive correction model; and 2) it outperforms the popular NAR models adopted in neural machine translation and text edition by a large margin.

While pre-trained language models (e.g., BERT) have achieved impressive results on different natural language processing tasks, they have large numbers of parameters and suffer from big computational and memory costs, which make them difficult for real-world deployment. Therefore, model compression is necessary to reduce the computation and memory cost of pre-trained models. In this work, we aim to compress BERT and address the following two challenging practical issues: (1) The compression algorithm should be able to output multiple compressed models with different sizes and latencies, in order to support devices with different memory and latency limitations; (2) The algorithm should be downstream task agnostic, so that the compressed models are generally applicable for different downstream tasks. We leverage techniques in neural architecture search (NAS) and propose NAS-BERT, an efficient method for BERT compression. NAS-BERT trains a big supernet on a search space containing a variety of architectures and outputs multiple compressed models with adaptive sizes and latency. Furthermore, the training of NAS-BERT is conducted on standard self-supervised pre-training tasks (e.g., masked language model) and does not depend on specific downstream tasks. Thus, the compressed models can be used across various downstream tasks. The technical challenge of NAS-BERT is that training a big supernet on the pre-training task is extremely costly. We employ several techniques including block-wise search, search space pruning, and performance approximation to improve search efficiency and accuracy. Extensive experiments on GLUE and SQuAD benchmark datasets demonstrate that NAS-BERT can find lightweight models with better accuracy than previous approaches, and can be directly applied to different downstream tasks with adaptive model sizes for different requirements of memory or latency.

Text to speech (TTS) has been broadly used to synthesize natural and intelligible speech in different scenarios. Deploying TTS in various end devices such as mobile phones or embedded devices requires extremely small memory usage and inference latency. While non-autoregressive TTS models such as FastSpeech have achieved significantly faster inference speed than autoregressive models, their model size and inference latency are still large for the deployment in resource constrained devices. In this paper, we propose LightSpeech, which leverages neural architecture search~(NAS) to automatically design more lightweight and efficient models based on FastSpeech. We first profile the components of current FastSpeech model and carefully design a novel search space containing various lightweight and potentially effective architectures. Then NAS is utilized to automatically discover well performing architectures within the search space. Experiments show that the model discovered by our method achieves 15x model compression ratio and 6.5x inference speedup on CPU with on par voice quality. Audio demos are provided at https://speechresearch.github.io/lightspeech.

Neural architecture search (NAS) with an accuracy predictor that predicts the accuracy of candidate architectures has drawn increasing interests due to its simplicity and effectiveness. Previous works employ neural network based predictors which unfortunately cannot well exploit the tabular data representations of network architectures. As decision tree-based models can better handle tabular data, in this paper, we propose to leverage gradient boosting decision tree (GBDT) as the predictor for NAS and demonstrate that it can improve the prediction accuracy and help to find better architectures than neural network based predictors. Moreover, considering that a better and compact search space can ease the search process, we propose to prune the search space gradually according to important features derived from GBDT using an interpreting tool named SHAP. In this way, NAS can be performed by first pruning the search space (using GBDT as a pruner) and then searching a neural architecture (using GBDT as a predictor), which is more efficient and effective. Experiments on NASBench-101 and ImageNet demonstrate the effectiveness of GBDT for NAS: (1) NAS with GBDT predictor finds top-10 architecture (among all the architectures in the search space) with $0.18\%$ test regret on NASBench-101, and achieves $24.2\%$ top-1 error rate on ImageNet; and (2) GBDT based search space pruning and neural architecture search further achieves $23.5\%$ top-1 error rate on ImageNet.

Automatic neural architecture design has shown its potential in discovering powerful neural network architectures. Existing methods, no matter based on reinforcement learning or evolutionary algorithms (EA), conduct architecture search in a discrete space, which is highly inefficient. In this paper, we propose a simple and efficient method to automatic neural architecture design based on continuous optimization. We call this new approach neural architecture optimization (NAO). There are three key components in our proposed approach: (1) An encoder embeds/maps neural network architectures into a continuous space.