Jie Chen

Sirui Liu, Jun Zhang, Haotian Chu et al.

Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of new models is restricted by the lack of dataset and benchmark training procedure. To the best of our knowledge, the existing open source datasets are far less to satisfy the needs of modern protein sequence-structure related research. To solve this problem, we present the first million-level protein structure prediction dataset with high coverage and diversity, named as PSP. This dataset consists of 570k true structure sequences (10TB) and 745k complementary distillation sequences (15TB). We provide in addition the benchmark training procedure for SOTA protein structure prediction model on this dataset. We validate the utility of this dataset for training by participating CAMEO contest in which our model won the first place. We hope our PSP dataset together with the training benchmark can enable a broader community of AI/biology researchers for AI-driven protein related research.

Min Zhao, Nicolas Dobigeon, Jie Chen

When adopting a model-based formulation, solving inverse problems encountered in multiband imaging requires to define spatial and spectral regularizations. In most of the works of the literature, spectral information is extracted from the observations directly to derive data-driven spectral priors. Conversely, the choice of the spatial regularization often boils down to the use of conventional penalizations (e.g., total variation) promoting expected features of the reconstructed image (e.g., piecewise constant). In this work, we propose a generic framework able to capitalize on an auxiliary acquisition of high spatial resolution to derive tailored data-driven spatial regularizations. This approach leverages on the ability of deep learning to extract high level features. More precisely, the regularization is conceived as a deep generative network able to encode spatial semantic features contained in this auxiliary image of high spatial resolution. To illustrate the versatility of this approach, it is instantiated to conduct two particular tasks, namely multiband image fusion and multiband image inpainting. Experimental results obtained on these two tasks demonstrate the benefit of this class of informed regularizations when compared to more conventional ones.

Bin Chen, Zhenyu Zhang, Weiqi Li et al.

While deep neural networks (NN) significantly advance image compressed sensing (CS) by improving reconstruction quality, the necessity of training current CS NNs from scratch constrains their effectiveness and hampers rapid deployment. Although recent methods utilize pre-trained diffusion models for image reconstruction, they struggle with slow inference and restricted adaptability to CS. To tackle these challenges, this paper proposes Invertible Diffusion Models (IDM), a novel efficient, end-to-end diffusion-based CS method. IDM repurposes a large-scale diffusion sampling process as a reconstruction model, and fine-tunes it end-to-end to recover original images directly from CS measurements, moving beyond the traditional paradigm of one-step noise estimation learning. To enable such memory-intensive end-to-end fine-tuning, we propose a novel two-level invertible design to transform both (1) multi-step sampling process and (2) noise estimation U-Net in each step into invertible networks. As a result, most intermediate features are cleared during training to reduce up to 93.8% GPU memory. In addition, we develop a set of lightweight modules to inject measurements into noise estimator to further facilitate reconstruction. Experiments demonstrate that IDM outperforms existing state-of-the-art CS networks by up to 2.64dB in PSNR. Compared to the recent diffusion-based approach DDNM, our IDM achieves up to 10.09dB PSNR gain and 14.54 times faster inference. Code is available at https://github.com/Guaishou74851/IDM.

Kaining Mao, Wei Zhang, Deborah Baofeng Wang et al.

Depression is increasingly impacting individuals both physically and psychologically worldwide. It has become a global major public health problem and attracts attention from various research fields. Traditionally, the diagnosis of depression is formulated through semi-structured interviews and supplementary questionnaires, which makes the diagnosis heavily relying on physicians experience and is subject to bias. Mental health monitoring and cloud-based remote diagnosis can be implemented through an automated depression diagnosis system. In this article, we propose an attention-based multimodality speech and text representation for depression prediction. Our model is trained to estimate the depression severity of participants using the Distress Analysis Interview Corpus-Wizard of Oz (DAIC-WOZ) dataset. For the audio modality, we use the collaborative voice analysis repository (COVAREP) features provided by the dataset and employ a Bidirectional Long Short-Term Memory Network (Bi-LSTM) followed by a Time-distributed Convolutional Neural Network (T-CNN). For the text modality, we use global vectors for word representation (GloVe) to perform word embeddings and the embeddings are fed into the Bi-LSTM network. Results show that both audio and text models perform well on the depression severity estimation task, with best sequence level F1 score of 0.9870 and patient-level F1 score of 0.9074 for the audio model over five classes (healthy, mild, moderate, moderately severe, and severe), as well as sequence level F1 score of 0.9709 and patient-level F1 score of 0.9245 for the text model over five classes. Results are similar for the multimodality fused model, with the highest F1 score of 0.9580 on the patient-level depression detection task over five classes. Experiments show statistically significant improvements over previous works.

Tengfei Ma, Jie Chen, Cao Xiao

Deep generative models have achieved remarkable success in various data domains, including images, time series, and natural languages. There remain, however, substantial challenges for combinatorial structures, including graphs. One of the key challenges lies in the difficulty of ensuring semantic validity in context. For examples, in molecular graphs, the number of bonding-electron pairs must not exceed the valence of an atom; whereas in protein interaction networks, two proteins may be connected only when they belong to the same or correlated gene ontology terms. These constraints are not easy to be incorporated into a generative model. In this work, we propose a regularization framework for variational autoencoders as a step toward semantic validity. We focus on the matrix representation of graphs and formulate penalty terms that regularize the output distribution of the decoder to encourage the satisfaction of validity constraints. Experimental results confirm a much higher likelihood of sampling valid graphs in our approach, compared with others reported in the literature.