Physical formula enhanced multi-task learning for pharmacokinetics prediction

Artificial intelligence (AI) technology has demonstrated remarkable potential in drug dis-covery, where pharmacokinetics plays a crucial role in determining the dosage, safety, and efficacy of new drugs. A major challenge for AI-driven drug discovery (AIDD) is the scarcity of high-quality data, which often requires extensive wet-lab work. A typical example of this is pharmacokinetic experiments. In this work, we develop a physical formula enhanced mul-ti-task learning (PEMAL) method that predicts four key parameters of pharmacokinetics simultaneously. By incorporating physical formulas into the multi-task framework, PEMAL facilitates effective knowledge sharing and target alignment among the pharmacokinetic parameters, thereby enhancing the accuracy of prediction. Our experiments reveal that PEMAL significantly lowers the data demand, compared to typical Graph Neural Networks. Moreover, we demonstrate that PEMAL enhances the robustness to noise, an advantage that conventional Neural Networks do not possess. Another advantage of PEMAL is its high flexibility, which can be potentially applied to other multi-task machine learning scenarios. Overall, our work illustrates the benefits and potential of using PEMAL in AIDD and other scenarios with data scarcity and noise.

ChemLLM: A Chemical Large Language Model

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Towards Simple and Accurate Human Pose Estimation with Stair Network

In this paper, we focus on tackling the precise keypoint coordinates regression task. Most existing approaches adopt complicated networks with a large number of parameters, leading to a heavy model with poor cost-effectiveness in practice. To overcome this limitation, we develop a small yet discrimicative model called STair Network, which can be simply stacked towards an accurate multi-stage pose estimation system. Specifically, to reduce computational cost, STair Network is composed of novel basic feature extraction blocks which focus on promoting feature diversity and obtaining rich local representations with fewer parameters, enabling a satisfactory balance on efficiency and performance. To further improve the performance, we introduce two mechanisms with negligible computational cost, focusing on feature fusion and replenish. We demonstrate the effectiveness of the STair Network on two standard datasets, e.g., 1-stage STair Network achieves a higher accuracy than HRNet by 5.5% on COCO test dataset with 80\% fewer parameters and 68% fewer GFLOPs.

Improving Model Robustness with Latent Distribution Locally and Globally

In this work, we consider model robustness of deep neural networks against adversarial attacks from a global manifold perspective. Leveraging both the local and global latent information, we propose a novel adversarial training method through robust optimization, and a tractable way to generate Latent Manifold Adversarial Examples (LMAEs) via an adversarial game between a discriminator and a classifier. The proposed adversarial training with latent distribution (ATLD) method defends against adversarial attacks by crafting LMAEs with the latent manifold in an unsupervised manner. ATLD preserves the local and global information of latent manifold and promises improved robustness against adversarial attacks. To verify the effectiveness of our proposed method, we conduct extensive experiments over different datasets (e.g., CIFAR-10, CIFAR-100, SVHN) with different adversarial attacks (e.g., PGD, CW), and show that our method substantially outperforms the state-of-the-art (e.g., Feature Scattering) in adversarial robustness by a large accuracy margin. The source codes are available at https://github.com/LitterQ/ATLD-pytorch.

Robust Generative Adversarial Network

Generative adversarial networks (GANs) are powerful generative models, but usually suffer from instability and generalization problem which may lead to poor generations. Most existing works focus on stabilizing the training of the discriminator while ignoring the generalization properties. In this work, we aim to improve the generalization capability of GANs by promoting the local robustness within the small neighborhood of the training samples. We also prove that the robustness in small neighborhood of training sets can lead to better generalization. Particularly, we design a robust optimization framework where the generator and discriminator compete with each other in a \textit{worst-case} setting within a small Wasserstein ball. The generator tries to map \textit{the worst input distribution} (rather than a Gaussian distribution used in most GANs) to the real data distribution, while the discriminator attempts to distinguish the real and fake distribution \textit{with the worst perturbation}. We have proved that our robust method can obtain a tighter generalization upper bound than traditional GANs under mild assumptions, ensuring a theoretical superiority of RGAN over GANs. A series of experiments on CIFAR-10, STL-10 and CelebA datasets indicate that our proposed robust framework can improve on five baseline GAN models substantially and consistently.

On Model Robustness Against Adversarial Examples

We study the model robustness against adversarial examples, referred to as small perturbed input data that may however fool many state-of-the-art deep learning models. Unlike previous research, we establish a novel theory addressing the robustness issue from the perspective of stability of the loss function in the small neighborhood of natural examples. We propose to exploit an energy function to describe the stability and prove that reducing such energy guarantees the robustness against adversarial examples. We also show that the traditional training methods including adversarial training with the $l_2$ norm constraint (AT) and Virtual Adversarial Training (VAT) tend to minimize the lower bound of our proposed energy function. We make an analysis showing that minimization of such lower bound can however lead to insufficient robustness within the neighborhood around the input sample. Furthermore, we design a more rational method with the energy regularization which proves to achieve better robustness than previous methods. Through a series of experiments, we demonstrate the superiority of our model on both supervised tasks and semi-supervised tasks. In particular, our proposed adversarial framework achieves the best performance compared with previous adversarial training methods on benchmark datasets MNIST, CIFAR-10, and SVHN. Importantly, they demonstrate much better robustness against adversarial examples than all the other comparison methods.

Manifold Adversarial Learning

The recently proposed adversarial training methods show the robustness to both adversarial and original examples and achieve state-of-the-art results in supervised and semi-supervised learning. All the existing adversarial training methods con- sider only how the worst perturbed examples (i.e., adversarial examples) could affect the model output. Despite their success, we argue that such setting may be in lack of generalization, since the output space (or label space) is apparently less informative. In this paper, we propose a novel method, called Manifold Adver- sarial Training (MAT). MAT manages to build an adversarial framework based on how the worst perturbation could affect the distributional manifold rather than the output space. Particularly, a latent data space with the Gaussian Mixture Model (GMM) will be first derived. On one hand, MAT tries to perturb the input samples in the way that would rough the distributional manifold the worst. On the other hand, the deep learning model is trained trying to promote in the latent space the manifold smoothness, measured by the variation of Gaussian mixtures (given the local perturbation around the data point). Importantly, since the latent space is more informative than the output space, the proposed MAT can learn better a ro- bust and compact data representation, leading to further performance improvemen- t. The proposed MAT is important in that it can be considered as a superset of one recently-proposed discriminative feature learning approach called center loss. We conducted a series of experiments in both supervised and semi-supervised learn- ing on three benchmark data sets, showing that the proposed MAT can achieve remarkable performance, much better than those of the state-of-the-art adversarial approaches.