Bridge-IF: Learning Inverse Protein Folding with Markov Bridges

Inverse protein folding is a fundamental task in computational protein design, which aims to design protein sequences that fold into the desired backbone structures. While the development of machine learning algorithms for this task has seen significant success, the prevailing approaches, which predominantly employ a discriminative formulation, frequently encounter the error accumulation issue and often fail to capture the extensive variety of plausible sequences. To fill these gaps, we propose Bridge-IF, a generative diffusion bridge model for inverse folding, which is designed to learn the probabilistic dependency between the distributions of backbone structures and protein sequences. Specifically, we harness an expressive structure encoder to propose a discrete, informative prior derived from structures, and establish a Markov bridge to connect this prior with native sequences. During the inference stage, Bridge-IF progressively refines the prior sequence, culminating in a more plausible design. Moreover, we introduce a reparameterization perspective on Markov bridge models, from which we derive a simplified loss function that facilitates more effective training. We also modulate protein language models (PLMs) with structural conditions to precisely approximate the Markov bridge process, thereby significantly enhancing generation performance while maintaining parameter-efficient training. Extensive experiments on well-established benchmarks demonstrate that Bridge-IF predominantly surpasses existing baselines in sequence recovery and excels in the design of plausible proteins with high foldability. The code is available at https://github.com/violet-sto/Bridge-IF.

Generalized Robot Learning Framework

Imitation based robot learning has recently gained significant attention in the robotics field due to its theoretical potential for transferability and generalizability. However, it remains notoriously costly, both in terms of hardware and data collection, and deploying it in real-world environments demands meticulous setup of robots and precise experimental conditions. In this paper, we present a low-cost robot learning framework that is both easily reproducible and transferable to various robots and environments. We demonstrate that deployable imitation learning can be successfully applied even to industrial-grade robots, not just expensive collaborative robotic arms. Furthermore, our results show that multi-task robot learning is achievable with simple network architectures and fewer demonstrations than previously thought necessary. As the current evaluating method is almost subjective when it comes to real-world manipulation tasks, we propose Voting Positive Rate (VPR) - a novel evaluation strategy that provides a more objective assessment of performance. We conduct an extensive comparison of success rates across various self-designed tasks to validate our approach. To foster collaboration and support the robot learning community, we have open-sourced all relevant datasets and model checkpoints, available at huggingface.co/ZhiChengAI.

Team up GBDTs and DNNs: Advancing Efficient and Effective Tabular Prediction with Tree-hybrid MLPs

Tabular datasets play a crucial role in various applications. Thus, developing efficient, effective, and widely compatible prediction algorithms for tabular data is important. Currently, two prominent model types, Gradient Boosted Decision Trees (GBDTs) and Deep Neural Networks (DNNs), have demonstrated performance advantages on distinct tabular prediction tasks. However, selecting an effective model for a specific tabular dataset is challenging, often demanding time-consuming hyperparameter tuning. To address this model selection dilemma, this paper proposes a new framework that amalgamates the advantages of both GBDTs and DNNs, resulting in a DNN algorithm that is as efficient as GBDTs and is competitively effective regardless of dataset preferences for GBDTs or DNNs. Our idea is rooted in an observation that deep learning (DL) offers a larger parameter space that can represent a well-performing GBDT model, yet the current back-propagation optimizer struggles to efficiently discover such optimal functionality. On the other hand, during GBDT development, hard tree pruning, entropy-driven feature gate, and model ensemble have proved to be more adaptable to tabular data. By combining these key components, we present a Tree-hybrid simple MLP (T-MLP). In our framework, a tensorized, rapidly trained GBDT feature gate, a DNN architecture pruning approach, as well as a vanilla back-propagation optimizer collaboratively train a randomly initialized MLP model. Comprehensive experiments show that T-MLP is competitive with extensively tuned DNNs and GBDTs in their dominating tabular benchmarks (88 datasets) respectively, all achieved with compact model storage and significantly reduced training duration.

Personalized Heart Disease Detection via ECG Digital Twin Generation

Heart diseases rank among the leading causes of global mortality, demonstrating a crucial need for early diagnosis and intervention. Most traditional electrocardiogram (ECG) based automated diagnosis methods are trained at population level, neglecting the customization of personalized ECGs to enhance individual healthcare management. A potential solution to address this limitation is to employ digital twins to simulate symptoms of diseases in real patients. In this paper, we present an innovative prospective learning approach for personalized heart disease detection, which generates digital twins of healthy individuals' anomalous ECGs and enhances the model sensitivity to the personalized symptoms. In our approach, a vector quantized feature separator is proposed to locate and isolate the disease symptom and normal segments in ECG signals with ECG report guidance. Thus, the ECG digital twins can simulate specific heart diseases used to train a personalized heart disease detection model. Experiments demonstrate that our approach not only excels in generating high-fidelity ECG signals but also improves personalized heart disease detection. Moreover, our approach ensures robust privacy protection, safeguarding patient data in model development.

Making Pre-trained Language Models Great on Tabular Prediction

The transferability of deep neural networks (DNNs) has made significant progress in image and language processing. However, due to the heterogeneity among tables, such DNN bonus is still far from being well exploited on tabular data prediction (e.g., regression or classification tasks). Condensing knowledge from diverse domains, language models (LMs) possess the capability to comprehend feature names from various tables, potentially serving as versatile learners in transferring knowledge across distinct tables and diverse prediction tasks, but their discrete text representation space is inherently incompatible with numerical feature values in tables. In this paper, we present TP-BERTa, a specifically pre-trained LM for tabular data prediction. Concretely, a novel relative magnitude tokenization converts scalar numerical feature values to finely discrete, high-dimensional tokens, and an intra-feature attention approach integrates feature values with the corresponding feature names. Comprehensive experiments demonstrate that our pre-trained TP-BERTa leads the performance among tabular DNNs and is competitive with Gradient Boosted Decision Tree models in typical tabular data regime.

SERVAL: Synergy Learning between Vertical Models and LLMs towards Oracle-Level Zero-shot Medical Prediction

Recent development of large language models (LLMs) has exhibited impressive zero-shot proficiency on generic and common sense questions. However, LLMs' application on domain-specific vertical questions still lags behind, primarily due to the humiliation problems and deficiencies in vertical knowledge. Furthermore, the vertical data annotation process often requires labor-intensive expert involvement, thereby presenting an additional challenge in enhancing the model's vertical capabilities. In this paper, we propose SERVAL, a synergy learning pipeline designed for unsupervised development of vertical capabilities in both LLMs and small models by mutual enhancement. Specifically, SERVAL utilizes the LLM's zero-shot outputs as annotations, leveraging its confidence to teach a robust vertical model from scratch. Reversely, the trained vertical model guides the LLM fine-tuning to enhance its zero-shot capability, progressively improving both models through an iterative process. In medical domain, known for complex vertical knowledge and costly annotations, comprehensive experiments show that, without access to any gold labels, SERVAL with the synergy learning of OpenAI GPT-3.5 and a simple model attains fully-supervised competitive performance across ten widely used medical datasets. These datasets represent vertically specialized medical diagnostic scenarios (e.g., diabetes, heart diseases, COVID-19), highlighting the potential of SERVAL in refining the vertical capabilities of LLMs and training vertical models from scratch, all achieved without the need for annotations.

Text2Tree: Aligning Text Representation to the Label Tree Hierarchy for Imbalanced Medical Classification

Deep learning approaches exhibit promising performances on various text tasks. However, they are still struggling on medical text classification since samples are often extremely imbalanced and scarce. Different from existing mainstream approaches that focus on supplementary semantics with external medical information, this paper aims to rethink the data challenges in medical texts and present a novel framework-agnostic algorithm called Text2Tree that only utilizes internal label hierarchy in training deep learning models. We embed the ICD code tree structure of labels into cascade attention modules for learning hierarchy-aware label representations. Two new learning schemes, Similarity Surrogate Learning (SSL) and Dissimilarity Mixup Learning (DML), are devised to boost text classification by reusing and distinguishing samples of other labels following the label representation hierarchy, respectively. Experiments on authoritative public datasets and real-world medical records show that our approach stably achieves superior performances over classical and advanced imbalanced classification methods.

Battle of the Large Language Models: Dolly vs LLaMA vs Vicuna vs Guanaco vs Bard vs ChatGPT -- A Text-to-SQL Parsing Comparison

The success of ChatGPT has ignited an AI race, with researchers striving to develop new large language models (LLMs) that can match or surpass the language understanding and generation abilities of commercial ones. In recent times, a number of models have emerged, claiming performance near that of GPT-3.5 or GPT-4 through various instruction-tuning methods. As practitioners of Text-to-SQL parsing, we are grateful for their valuable contributions to open-source research. However, it is important to approach these claims with a sense of scrutiny and ascertain the actual effectiveness of these models. Therefore, we pit six popular large language models against each other, systematically evaluating their Text-to-SQL parsing capability on nine benchmark datasets with five different prompting strategies, covering both zero-shot and few-shot scenarios. Regrettably, the open-sourced models fell significantly short of the performance achieved by closed-source models like GPT-3.5, highlighting the need for further work to bridge the performance gap between these models.

GCL: Gradient-Guided Contrastive Learning for Medical Image Segmentation with Multi-Perspective Meta Labels

Since annotating medical images for segmentation tasks commonly incurs expensive costs, it is highly desirable to design an annotation-efficient method to alleviate the annotation burden. Recently, contrastive learning has exhibited a great potential in learning robust representations to boost downstream tasks with limited labels. In medical imaging scenarios, ready-made meta labels (i.e., specific attribute information of medical images) inherently reveal semantic relationships among images, which have been used to define positive pairs in previous work. However, the multi-perspective semantics revealed by various meta labels are usually incompatible and can incur intractable "semantic contradiction" when combining different meta labels. In this paper, we tackle the issue of "semantic contradiction" in a gradient-guided manner using our proposed Gradient Mitigator method, which systematically unifies multi-perspective meta labels to enable a pre-trained model to attain a better high-level semantic recognition ability. Moreover, we emphasize that the fine-grained discrimination ability is vital for segmentation-oriented pre-training, and develop a novel method called Gradient Filter to dynamically screen pixel pairs with the most discriminating power based on the magnitude of gradients. Comprehensive experiments on four medical image segmentation datasets verify that our new method GCL: (1) learns informative image representations and considerably boosts segmentation performance with limited labels, and (2) shows promising generalizability on out-of-distribution datasets.

Sample-efficient Multi-objective Molecular Optimization with GFlowNets

Many crucial scientific problems involve designing novel molecules with desired properties, which can be formulated as an expensive black-box optimization problem over the discrete chemical space. Computational methods have achieved initial success but still struggle with simultaneously optimizing multiple competing properties in a sample-efficient manner. In this work, we propose a multi-objective Bayesian optimization (MOBO) algorithm leveraging the hypernetwork-based GFlowNets (HN-GFN) as an acquisition function optimizer, with the purpose of sampling a diverse batch of candidate molecular graphs from an approximate Pareto front. Using a single preference-conditioned hypernetwork, HN-GFN learns to explore various trade-offs between objectives. Inspired by reinforcement learning, we further propose a hindsight-like off-policy strategy to share high-performing molecules among different preferences in order to speed up learning for HN-GFN. Through synthetic experiments, we illustrate that HN-GFN has adequate capacity to generalize over preferences. Extensive experiments show that our framework outperforms the best baselines by a large margin in terms of hypervolume in various real-world MOBO settings.