HelixFold-Multimer: Elevating Protein Complex Structure Prediction to New Heights

While monomer protein structure prediction tools boast impressive accuracy, the prediction of protein complex structures remains a daunting challenge in the field. This challenge is particularly pronounced in scenarios involving complexes with protein chains from different species, such as antigen-antibody interactions, where accuracy often falls short. Limited by the accuracy of complex prediction, tasks based on precise protein-protein interaction analysis also face obstacles. In this report, we highlight the ongoing advancements of our protein complex structure prediction model, HelixFold-Multimer, underscoring its enhanced performance. HelixFold-Multimer provides precise predictions for diverse protein complex structures, especially in therapeutic protein interactions. Notably, HelixFold-Multimer achieves remarkable success in antigen-antibody and peptide-protein structure prediction, surpassing AlphaFold-Multimer by several folds. HelixFold-Multimer is now available for public use on the PaddleHelix platform, offering both a general version and an antigen-antibody version. Researchers can conveniently access and utilize this service for their development needs.

Efficient Image Super-Resolution via Symmetric Visual Attention Network

An important development direction in the Single-Image Super-Resolution (SISR) algorithms is to improve the efficiency of the algorithms. Recently, efficient Super-Resolution (SR) research focuses on reducing model complexity and improving efficiency through improved deep small kernel convolution, leading to a small receptive field. The large receptive field obtained by large kernel convolution can significantly improve image quality, but the computational cost is too high. To improve the reconstruction details of efficient super-resolution reconstruction, we propose a Symmetric Visual Attention Network (SVAN) by applying large receptive fields. The SVAN decomposes a large kernel convolution into three different combinations of convolution operations and combines them with an attention mechanism to form a Symmetric Large Kernel Attention Block (SLKAB), which forms a symmetric attention block with a bottleneck structure by the size of the receptive field in the convolution combination to extract depth features effectively as the basic component of the SVAN. Our network gets a large receptive field while minimizing the number of parameters and improving the perceptual ability of the model. The experimental results show that the proposed SVAN can obtain high-quality super-resolution reconstruction results using only about 30% of the parameters of existing SOTA methods.

UMedNeRF: Uncertainty-aware Single View Volumetric Rendering for Medical Neural Radiance Fields

In the field of clinical medicine, computed tomography (CT) is an effective medical imaging modality for the diagnosis of various pathologies. Compared with X-ray images, CT images can provide more information, including multi-planar slices and three-dimensional structures for clinical diagnosis. However, CT imaging requires patients to be exposed to large doses of ionizing radiation for a long time, which may cause irreversible physical harm. In this paper, we propose an Uncertainty-aware MedNeRF (UMedNeRF) network based on generated radiation fields. The network can learn a continuous representation of CT projections from 2D X-ray images by obtaining the internal structure and depth information and using adaptive loss weights to ensure the quality of the generated images. Our model is trained on publicly available knee and chest datasets, and we show the results of CT projection rendering with a single X-ray and compare our method with other methods based on generated radiation fields.

Uncertainty-aware Single View Volumetric Rendering for Medical Neural Radiance Fields

In the field of clinical medicine, computed tomography (CT) is an effective medical imaging modality for the diagnosis of various pathologies. Compared with X-ray images, CT images can provide more information, including multi-planar slices and three-dimensional structures for clinical diagnosis. However, CT imaging requires patients to be exposed to large doses of ionizing radiation for a long time, which may cause irreversible physical harm. In this paper, we propose an Uncertainty-aware MedNeRF (UMedNeRF) network based on generated radiation fields. The network can learn a continuous representation of CT projections from 2D X-ray images by obtaining the internal structure and depth information and using adaptive loss weights to ensure the quality of the generated images. Our model is trained on publicly available knee and chest datasets, and we show the results of CT projection rendering with a single X-ray and compare our method with other methods based on generated radiation fields.

Controlling Neural Style Transfer with Deep Reinforcement Learning

Controlling the degree of stylization in the Neural Style Transfer (NST) is a little tricky since it usually needs hand-engineering on hyper-parameters. In this paper, we propose the first deep Reinforcement Learning (RL) based architecture that splits one-step style transfer into a step-wise process for the NST task. Our RL-based method tends to preserve more details and structures of the content image in early steps, and synthesize more style patterns in later steps. It is a user-easily-controlled style-transfer method. Additionally, as our RL-based model performs the stylization progressively, it is lightweight and has lower computational complexity than existing one-step Deep Learning (DL) based models. Experimental results demonstrate the effectiveness and robustness of our method.

Deep Reinforcement Learning for Image-to-Image Translation

Most existing Image-to-Image Translation (I2IT) methods generate images in a single run of a deep learning (DL) model. However, designing such a single-step model is always challenging, requiring a huge number of parameters and easily falling into bad global minimums and overfitting. In this work, we reformulate I2IT as a step-wise decision-making problem via deep reinforcement learning (DRL) and propose a novel framework that performs RL-based I2IT (RL-I2IT). The key feature in the RL-I2IT framework is to decompose a monolithic learning process into small steps with a lightweight model to progressively transform a source image successively to a target image. Considering that it is challenging to handle high dimensional continuous state and action spaces in the conventional RL framework, we introduce meta policy with a new concept Plan to the standard Actor-Critic model, which is of a lower dimension than the original image and can facilitate the actor to generate a tractable high dimensional action. In the RL-I2IT framework, we also employ a task-specific auxiliary learning strategy to stabilize the training process and improve the performance of the corresponding task. Experiments on several I2IT tasks demonstrate the effectiveness and robustness of the proposed method when facing high-dimensional continuous action space problems.

In-context Autoencoder for Context Compression in a Large Language Model

We propose the In-context Autoencoder (ICAE) for context compression in a large language model (LLM). The ICAE has two modules: a learnable encoder adapted with LoRA from an LLM for compressing a long context into a limited number of memory slots, and a fixed decoder which is the target LLM that can condition on the memory slots for various purposes. We first pretrain the ICAE using both autoencoding and language modeling objectives on massive text data, enabling it to generate memory slots that accurately and comprehensively represent the original context. Then, we fine-tune the pretrained ICAE on a small amount of instruct data to enhance its interaction with various prompts for producing desirable responses. Our experimental results demonstrate that the ICAE learned with our proposed pretraining and fine-tuning paradigm can effectively produce memory slots with $4\times$ context compression, which can be well conditioned on by the target LLM to respond to various prompts. The promising results demonstrate significant implications of the ICAE for its novel approach to the long context problem and its potential to reduce computation and memory overheads for LLM inference in practice, suggesting further research effort in context management for an LLM. Our code and data will be released shortly.

DeepOHeat: Operator Learning-based Ultra-fast Thermal Simulation in 3D-IC Design

Thermal issue is a major concern in 3D integrated circuit (IC) design. Thermal optimization of 3D IC often requires massive expensive PDE simulations. Neural network-based thermal prediction models can perform real-time prediction for many unseen new designs. However, existing works either solve 2D temperature fields only or do not generalize well to new designs with unseen design configurations (e.g., heat sources and boundary conditions). In this paper, for the first time, we propose DeepOHeat, a physics-aware operator learning framework to predict the temperature field of a family of heat equations with multiple parametric or non-parametric design configurations. This framework learns a functional map from the function space of multiple key PDE configurations (e.g., boundary conditions, power maps, heat transfer coefficients) to the function space of the corresponding solution (i.e., temperature fields), enabling fast thermal analysis and optimization by changing key design configurations (rather than just some parameters). We test DeepOHeat on some industrial design cases and compare it against Celsius 3D from Cadence Design Systems. Our results show that, for the unseen testing cases, a well-trained DeepOHeat can produce accurate results with $1000\times$ to $300000\times$ speedup.

Extensible Prompts for Language Models

We propose eXtensible Prompt (X-Prompt) for prompting a large language model (LLM) beyond natural language (NL). X-Prompt instructs an LLM with not only NL but also an extensible vocabulary of imaginary words that are introduced to help represent what NL words hardly describe, allowing a prompt to be more descriptive. Like NL prompts, X-Prompt is out-of-distribution (OOD) robust, for which we propose context-guided learning with prompt augmentation to learn its imaginary words for general usability, enabling them to use in different prompt contexts for fine-grain specifications. The promising results of X-Prompt demonstrate its potential of approaching advanced interaction between humans and LLMs to bridge their communication gap.

TCR: A Transformer Based Deep Network for Predicting Cancer Drugs Response

Predicting clinical outcomes to anti-cancer drugs on a personalized basis is challenging in cancer treatment due to the heterogeneity of tumors. Traditional computational efforts have been made to model the effect of drug response on individual samples depicted by their molecular profile, yet overfitting occurs because of the high dimension for omics data, hindering models from clinical application. Recent research shows that deep learning is a promising approach to build drug response models by learning alignment patterns between drugs and samples. However, existing studies employed the simple feature fusion strategy and only considered the drug features as a whole representation while ignoring the substructure information that may play a vital role when aligning drugs and genes. Hereby in this paper, we propose TCR (Transformer based network for Cancer drug Response) to predict anti-cancer drug response. By utilizing an attention mechanism, TCR is able to learn the interactions between drug atom/sub-structure and molecular signatures efficiently in our study. Furthermore, a dual loss function and cross sampling strategy were designed to improve the prediction power of TCR. We show that TCR outperformed all other methods under various data splitting strategies on all evaluation matrices (some with significant improvement). Extensive experiments demonstrate that TCR shows significantly improved generalization ability on independent in-vitro experiments and in-vivo real patient data. Our study highlights the prediction power of TCR and its potential value for cancer drug repurpose and precision oncology treatment.