Tian Han

Deqian Kong, Bo Pang, Tian Han et al.

Generation of molecules with desired chemical and biological properties such as high drug-likeness, high binding affinity to target proteins, is critical for drug discovery. In this paper, we propose a probabilistic generative model to capture the joint distribution of molecules and their properties. Our model assumes an energy-based model (EBM) in the latent space. Conditional on the latent vector, the molecule and its properties are modeled by a molecule generation model and a property regression model respectively. To search for molecules with desired properties, we propose a sampling with gradual distribution shifting (SGDS) algorithm, so that after learning the model initially on the training data of existing molecules and their properties, the proposed algorithm gradually shifts the model distribution towards the region supported by molecules with desired values of properties. Our experiments show that our method achieves very strong performances on various molecule design tasks.

Bo Pang, Erik Nijkamp, Jiali Cui et al.

This paper proposes a latent space energy-based prior model for semi-supervised learning. The model stands on a generator network that maps a latent vector to the observed example. The energy term of the prior model couples the latent vector and a symbolic one-hot vector, so that classification can be based on the latent vector inferred from the observed example. In our learning method, the symbol-vector coupling, the generator network and the inference network are learned jointly. Our method is applicable to semi-supervised learning in various data domains such as image, text, and tabular data. Our experiments demonstrate that our method performs well on semi-supervised learning tasks.

Bo Pang, Tian Han, Ying Nian Wu

Deep generative models have recently been applied to molecule design. If the molecules are encoded in linear SMILES strings, modeling becomes convenient. However, models relying on string representations tend to generate invalid samples and duplicates. Prior work addressed these issues by building models on chemically-valid fragments or explicitly enforcing chemical rules in the generation process. We argue that an expressive model is sufficient to implicitly and automatically learn the complicated chemical rules from the data, even if molecules are encoded in simple character-level SMILES strings. We propose to learn latent space energy-based prior model with SMILES representation for molecule modeling. Our experiments show that our method is able to generate molecules with validity and uniqueness competitive with state-of-the-art models. Interestingly, generated molecules have structural and chemical features whose distributions almost perfectly match those of the real molecules.

Tian Han, Erik Nijkamp, Xiaolin Fang et al.

This paper proposes the divergence triangle as a framework for joint training of generator model, energy-based model and inference model. The divergence triangle is a compact and symmetric (anti-symmetric) objective function that seamlessly integrates variational learning, adversarial learning, wake-sleep algorithm, and contrastive divergence in a unified probabilistic formulation. This unification makes the processes of sampling, inference, energy evaluation readily available without the need for costly Markov chain Monte Carlo methods. Our experiments demonstrate that the divergence triangle is capable of learning (1) an energy-based model with well-formed energy landscape, (2) direct sampling in the form of a generator network, and (3) feed-forward inference that faithfully reconstructs observed as well as synthesized data. The divergence triangle is a robust training method that can learn from incomplete data.

Xianglei Xing, Ruiqi Gao, Tian Han et al.

We present a deformable generator model to disentangle the appearance and geometric information for both image and video data in a purely unsupervised manner. The appearance generator network models the information related to appearance, including color, illumination, identity or category, while the geometric generator performs geometric warping, such as rotation and stretching, through generating deformation field which is used to warp the generated appearance to obtain the final image or video sequences. Two generators take independent latent vectors as input to disentangle the appearance and geometric information from image or video sequences. For video data, a nonlinear transition model is introduced to both the appearance and geometric generators to capture the dynamics over time. The proposed scheme is general and can be easily integrated into different generative models. An extensive set of qualitative and quantitative experiments shows that the appearance and geometric information can be well disentangled, and the learned geometric generator can be conveniently transferred to other image datasets to facilitate knowledge transfer tasks.

Tian Han, Jiawen Wu, Ying Nian Wu

A recent Cell paper [Chang and Tsao, 2017] reports an interesting discovery. For the face stimuli generated by a pre-trained active appearance model (AAM), the responses of neurons in the areas of the primate brain that are responsible for face recognition exhibit strong linear relationship with the shape variables and appearance variables of the AAM that generates the face stimuli. In this paper, we show that this behavior can be replicated by a deep generative model called the generator network, which assumes that the observed signals are generated by latent random variables via a top-down convolutional neural network. Specifically, we learn the generator network from the face images generated by a pre-trained AAM model using variational auto-encoder, and we show that the inferred latent variables of the learned generator network have strong linear relationship with the shape and appearance variables of the AAM model that generates the face images. Unlike the AAM model that has an explicit shape model where the shape variables generate the control points or landmarks, the generator network has no such shape model and shape variables. Yet the generator network can learn the shape knowledge in the sense that some of the latent variables of the learned generator network capture the shape variations in the face images generated by AAM.