Comparison of deep learning and conventional methods for disease onset prediction

Background: Conventional prediction methods such as logistic regression and gradient boosting have been widely utilized for disease onset prediction for their reliability and interpretability. Deep learning methods promise enhanced prediction performance by extracting complex patterns from clinical data, but face challenges like data sparsity and high dimensionality. Methods: This study compares conventional and deep learning approaches to predict lung cancer, dementia, and bipolar disorder using observational data from eleven databases from North America, Europe, and Asia. Models were developed using logistic regression, gradient boosting, ResNet, and Transformer, and validated both internally and externally across the data sources. Discrimination performance was assessed using AUROC, and calibration was evaluated using Eavg. Findings: Across 11 datasets, conventional methods generally outperformed deep learning methods in terms of discrimination performance, particularly during external validation, highlighting their better transportability. Learning curves suggest that deep learning models require substantially larger datasets to reach the same performance levels as conventional methods. Calibration performance was also better for conventional methods, with ResNet showing the poorest calibration. Interpretation: Despite the potential of deep learning models to capture complex patterns in structured observational healthcare data, conventional models remain highly competitive for disease onset prediction, especially in scenarios involving smaller datasets and if lengthy training times need to be avoided. The study underscores the need for future research focused on optimizing deep learning models to handle the sparsity, high dimensionality, and heterogeneity inherent in healthcare datasets, and find new strategies to exploit the full capabilities of deep learning methods.

H2RSVLM: Towards Helpful and Honest Remote Sensing Large Vision Language Model

The generic large Vision-Language Models (VLMs) is rapidly developing, but still perform poorly in Remote Sensing (RS) domain, which is due to the unique and specialized nature of RS imagery and the comparatively limited spatial perception of current VLMs. Existing Remote Sensing specific Vision Language Models (RSVLMs) still have considerable potential for improvement, primarily owing to the lack of large-scale, high-quality RS vision-language datasets. We constructed HqDC-1.4M, the large scale High quality and Detailed Captions for RS images, containing 1.4 million image-caption pairs, which not only enhance the RSVLM's understanding of RS images but also significantly improve the model's spatial perception abilities, such as localization and counting, thereby increasing the helpfulness of the RSVLM. Moreover, to address the inevitable "hallucination" problem in RSVLM, we developed RSSA, the first dataset aimed at enhancing the Self-Awareness capability of RSVLMs. By incorporating a variety of unanswerable questions into typical RS visual question-answering tasks, RSSA effectively improves the truthfulness and reduces the hallucinations of the model's outputs, thereby enhancing the honesty of the RSVLM. Based on these datasets, we proposed the H2RSVLM, the Helpful and Honest Remote Sensing Vision Language Model. H2RSVLM has achieved outstanding performance on multiple RS public datasets and is capable of recognizing and refusing to answer the unanswerable questions, effectively mitigating the incorrect generations. We will release the code, data and model weights at https://github.com/opendatalab/H2RSVLM .

CEHR-GPT: Generating Electronic Health Records with Chronological Patient Timelines

Synthetic Electronic Health Records (EHR) have emerged as a pivotal tool in advancing healthcare applications and machine learning models, particularly for researchers without direct access to healthcare data. Although existing methods, like rule-based approaches and generative adversarial networks (GANs), generate synthetic data that resembles real-world EHR data, these methods often use a tabular format, disregarding temporal dependencies in patient histories and limiting data replication. Recently, there has been a growing interest in leveraging Generative Pre-trained Transformers (GPT) for EHR data. This enables applications like disease progression analysis, population estimation, counterfactual reasoning, and synthetic data generation. In this work, we focus on synthetic data generation and demonstrate the capability of training a GPT model using a particular patient representation derived from CEHR-BERT, enabling us to generate patient sequences that can be seamlessly converted to the Observational Medical Outcomes Partnership (OMOP) data format.

HiCD: Change Detection in Quality-Varied Images via Hierarchical Correlation Distillation

Advanced change detection techniques primarily target image pairs of equal and high quality. However, variations in imaging conditions and platforms frequently lead to image pairs with distinct qualities: one image being high-quality, while the other being low-quality. These disparities in image quality present significant challenges for understanding image pairs semantically and extracting change features, ultimately resulting in a notable decline in performance. To tackle this challenge, we introduce an innovative training strategy grounded in knowledge distillation. The core idea revolves around leveraging task knowledge acquired from high-quality image pairs to guide the model's learning process when dealing with image pairs that exhibit differences in quality. Additionally, we develop a hierarchical correlation distillation approach (involving self-correlation, cross-correlation, and global correlation). This approach compels the student model to replicate the correlations inherent in the teacher model, rather than focusing solely on individual features. This ensures effective knowledge transfer while maintaining the student model's training flexibility.

ERNIE-Music: Text-to-Waveform Music Generation with Diffusion Models

In recent years, there has been an increased popularity in image and speech generation using diffusion models. However, directly generating music waveforms from free-form text prompts is still under-explored. In this paper, we propose the first text-to-waveform music generation model that can receive arbitrary texts using diffusion models. We incorporate the free-form textual prompt as the condition to guide the waveform generation process of diffusion models. To solve the problem of lacking such text-music parallel data, we collect a dataset of text-music pairs from the Internet with weak supervision. Besides, we compare the effect of two prompt formats of conditioning texts (music tags and free-form texts) and prove the superior performance of our method in terms of text-music relevance. We further demonstrate that our generated music in the waveform domain outperforms previous works by a large margin in terms of diversity, quality, and text-music relevance.

Detecting Building Changes with Off-Nadir Aerial Images

The tilted viewing nature of the off-nadir aerial images brings severe challenges to the building change detection (BCD) problem: the mismatch of the nearby buildings and the semantic ambiguity of the building facades. To tackle these challenges, we present a multi-task guided change detection network model, named as MTGCD-Net. The proposed model approaches the specific BCD problem by designing three auxiliary tasks, including: (1) a pixel-wise classification task to predict the roofs and facades of buildings; (2) an auxiliary task for learning the roof-to-footprint offsets of each building to account for the misalignment between building roof instances; and (3) an auxiliary task for learning the identical roof matching flow between bi-temporal aerial images to tackle the building roof mismatch problem. These auxiliary tasks provide indispensable and complementary building parsing and matching information. The predictions of the auxiliary tasks are finally fused to the main building change detection branch with a multi-modal distillation module. To train and test models for the BCD problem with off-nadir aerial images, we create a new benchmark dataset, named BANDON. Extensive experiments demonstrate that our model achieves superior performance over the previous state-of-the-art competitors.

ERNIE-Code: Beyond English-Centric Cross-lingual Pretraining for Programming Languages

Software engineers working with the same programming language (PL) may speak different natural languages (NLs) and vice versa, erecting huge barriers to communication and working efficiency. Recent studies have demonstrated the effectiveness of generative pre-training in computer programs, yet they are always English-centric. In this work, we step towards bridging the gap between multilingual NLs and multilingual PLs for large language models (LLMs). We release ERNIE-Code, a unified pre-trained language model for 116 NLs and 6 PLs. We employ two methods for universal cross-lingual pre-training: span-corruption language modeling that learns patterns from monolingual NL or PL; and pivot-based translation language modeling that relies on parallel data of many NLs and PLs. Extensive results show that ERNIE-Code outperforms previous multilingual LLMs for PL or NL across a wide range of end tasks of code intelligence, including multilingual code-to-text, text-to-code, code-to-code, and text-to-text generation. We further show its advantage of zero-shot prompting on multilingual code summarization and text-to-text translation. We will make our code and pre-trained models publicly available.

Multi-view deep learning based molecule design and structural optimization accelerates the SARS-CoV-2 inhibitor discovery

In this work, we propose MEDICO, a Multi-viEw Deep generative model for molecule generation, structural optimization, and the SARS-CoV-2 Inhibitor disCOvery. To the best of our knowledge, MEDICO is the first-of-this-kind graph generative model that can generate molecular graphs similar to the structure of targeted molecules, with a multi-view representation learning framework to sufficiently and adaptively learn comprehensive structural semantics from targeted molecular topology and geometry. We show that our MEDICO significantly outperforms the state-of-the-art methods in generating valid, unique, and novel molecules under benchmarking comparisons. In particular, we showcase the multi-view deep learning model enables us to generate not only the molecules structurally similar to the targeted molecules but also the molecules with desired chemical properties, demonstrating the strong capability of our model in exploring the chemical space deeply. Moreover, case study results on targeted molecule generation for the SARS-CoV-2 main protease (Mpro) show that by integrating molecule docking into our model as chemical priori, we successfully generate new small molecules with desired drug-like properties for the Mpro, potentially accelerating the de novo design of Covid-19 drugs. Further, we apply MEDICO to the structural optimization of three well-known Mpro inhibitors (N3, 11a, and GC376) and achieve ~88% improvement in their binding affinity to Mpro, demonstrating the application value of our model for the development of therapeutics for SARS-CoV-2 infection.

ERNIE-SAT: Speech and Text Joint Pretraining for Cross-Lingual Multi-Speaker Text-to-Speech

Speech representation learning has improved both speech understanding and speech synthesis tasks for single language. However, its ability in cross-lingual scenarios has not been explored. In this paper, we extend the pretraining method for cross-lingual multi-speaker speech synthesis tasks, including cross-lingual multi-speaker voice cloning and cross-lingual multi-speaker speech editing. We propose a speech-text joint pretraining framework, where we randomly mask the spectrogram and the phonemes given a speech example and its transcription. By learning to reconstruct the masked parts of the input in different languages, our model shows great improvements over speaker-embedding-based multi-speaker TTS methods. Moreover, our framework is end-to-end for both the training and the inference without any finetuning effort. In cross-lingual multi-speaker voice cloning and cross-lingual multi-speaker speech editing tasks, our experiments show that our model outperforms speaker-embedding-based multi-speaker TTS methods. The code and model are publicly available at PaddleSpeech.

MechRetro is a chemical-mechanism-driven graph learning framework for interpretable retrosynthesis prediction and pathway planning

Leveraging artificial intelligence for automatic retrosynthesis speeds up organic pathway planning in digital laboratories. However, existing deep learning approaches are unexplainable, like "black box" with few insights, notably limiting their applications in real retrosynthesis scenarios. Here, we propose MechRetro, a chemical-mechanism-driven graph learning framework for interpretable retrosynthetic prediction and pathway planning, which learns several retrosynthetic actions to simulate a reverse reaction via elaborate self-adaptive joint learning. By integrating chemical knowledge as prior information, we design a novel Graph Transformer architecture to adaptively learn discriminative and chemically meaningful molecule representations, highlighting the strong capacity in molecule feature representation learning. We demonstrate that MechRetro outperforms the state-of-the-art approaches for retrosynthetic prediction with a large margin on large-scale benchmark datasets. Extending MechRetro to the multi-step retrosynthesis analysis, we identify efficient synthetic routes via an interpretable reasoning mechanism, leading to a better understanding in the realm of knowledgeable synthetic chemists. We also showcase that MechRetro discovers a novel pathway for protokylol, along with energy scores for uncertainty assessment, broadening the applicability for practical scenarios. Overall, we expect MechRetro to provide meaningful insights for high-throughput automated organic synthesis in drug discovery.