Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

Automatic image colorization is a particularly challenging problem. Due to the high illness of the problem and multi-modal uncertainty, directly training a deep neural network usually leads to incorrect semantic colors and low color richness. Existing transformer-based methods can deliver better results but highly depend on hand-crafted dataset-level empirical distribution priors. In this work, we propose DDColor, a new end-to-end method with dual decoders, for image colorization. More specifically, we design a multi-scale image decoder and a transformer-based color decoder. The former manages to restore the spatial resolution of the image, while the latter establishes the correlation between semantic representations and color queries via cross-attention. The two decoders incorporate to learn semantic-aware color embedding by leveraging the multi-scale visual features. With the help of these two decoders, our method succeeds in producing semantically consistent and visually plausible colorization results without any additional priors. In addition, a simple but effective colorfulness loss is introduced to further improve the color richness of generated results. Our extensive experiments demonstrate that the proposed DDColor achieves significantly superior performance to existing state-of-the-art works both quantitatively and qualitatively. Codes will be made publicly available.

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Recently, the success of pre-training in text domain has been fully extended to vision, audio, and cross-modal scenarios. The proposed pre-training models of different modalities are showing a rising trend of homogeneity in their model structures, which brings the opportunity to implement different pre-training models within a uniform framework. In this paper, we present TencentPretrain, a toolkit supporting pre-training models of different modalities. The core feature of TencentPretrain is the modular design. The toolkit uniformly divides pre-training models into 5 components: embedding, encoder, target embedding, decoder, and target. As almost all of common modules are provided in each component, users can choose the desired modules from different components to build a complete pre-training model. The modular design enables users to efficiently reproduce existing pre-training models or build brand-new one. We test the toolkit on text, vision, and audio benchmarks and show that it can match the performance of the original implementations.

Considerable progress has recently been made in leveraging CLIP (Contrastive Language-Image Pre-Training) models for text-guided image manipulation. However, all existing works rely on additional generative models to ensure the quality of results, because CLIP alone cannot provide enough guidance information for fine-scale pixel-level changes. In this paper, we introduce CLIPVG, a text-guided image manipulation framework using differentiable vector graphics, which is also the first CLIP-based general image manipulation framework that does not require any additional generative models. We demonstrate that CLIPVG can not only achieve state-of-art performance in both semantic correctness and synthesis quality, but also is flexible enough to support various applications far beyond the capability of all existing methods.

As an effective method to deliver external materials into biological cells, microinjection has been widely applied in the biomedical field. However, the cognition of cell mechanical property is still inadequate, which greatly limits the efficiency and success rate of injection. Thus, a new rate-dependent mechanical model based on membrane theory is proposed for the first time. In this model, an analytical equilibrium equation between the injection force and cell deformation is established by considering the speed effect of microinjection. Different from the traditional membrane-theory-based model, the elastic coefficient of the constitutive material in the proposed model is modified as a function of the injection velocity and acceleration, effectively simulating the influence of speeds on the mechanical responses and providing a more generalized and practical model. Using this model, other mechanical responses at different speeds can be also accurately predicted, including the distribution of membrane tension and stress and the deformed shape. To verify the validity of the model, numerical simulations and experiments are carried out. The results show that the proposed model can match the real mechanical responses well at different injection speeds.

Large language models (LLMs) have been shown to be able to perform new tasks based on a few demonstrations or natural language instructions. While these capabilities have led to widespread adoption, most LLMs are developed by resource-rich organizations and are frequently kept from the public. As a step towards democratizing this powerful technology, we present BLOOM, a 176B-parameter open-access language model designed and built thanks to a collaboration of hundreds of researchers. BLOOM is a decoder-only Transformer language model that was trained on the ROOTS corpus, a dataset comprising hundreds of sources in 46 natural and 13 programming languages (59 in total). We find that BLOOM achieves competitive performance on a wide variety of benchmarks, with stronger results after undergoing multitask prompted finetuning. To facilitate future research and applications using LLMs, we publicly release our models and code under the Responsible AI License.

Contemporary methods have shown promising results on cardiac image segmentation, but merely in static learning, i.e., optimizing the network once for all, ignoring potential needs for model updating. In real-world scenarios, new data continues to be gathered from multiple institutions over time and new demands keep growing to pursue more satisfying performance. The desired model should incrementally learn from each incoming dataset and progressively update with improved functionality as time goes by. As the datasets sequentially delivered from multiple sites are normally heterogenous with domain discrepancy, each updated model should not catastrophically forget previously learned domains while well generalizing to currently arrived domains or even unseen domains. In medical scenarios, this is particularly challenging as accessing or storing past data is commonly not allowed due to data privacy. To this end, we propose a novel domain-incremental learning framework to recover past domain inputs first and then regularly replay them during model optimization. Particularly, we first present a style-oriented replay module to enable structure-realistic and memory-efficient reproduction of past data, and then incorporate the replayed past data to jointly optimize the model with current data to alleviate catastrophic forgetting. During optimization, we additionally perform domain-sensitive feature whitening to suppress model's dependency on features that are sensitive to domain changes (e.g., domain-distinctive style features) to assist domain-invariant feature exploration and gradually improve the generalization performance of the network. We have extensively evaluated our approach with the M&Ms Dataset in single-domain and compound-domain incremental learning settings with improved performance over other comparison approaches.

Federated learning provides an effective paradigm to jointly optimize a model benefited from rich distributed data while protecting data privacy. Nonetheless, the heterogeneity nature of distributed data makes it challenging to define and ensure fairness among local agents. For instance, it is intuitively "unfair" for agents with data of high quality to sacrifice their performance due to other agents with low quality data. Currently popular egalitarian and weighted equity-based fairness measures suffer from the aforementioned pitfall. In this work, we aim to formally represent this problem and address these fairness issues using concepts from co-operative game theory and social choice theory. We model the task of learning a shared predictor in the federated setting as a fair public decision making problem, and then define the notion of core-stable fairness: Given $N$ agents, there is no subset of agents $S$ that can benefit significantly by forming a coalition among themselves based on their utilities $U_N$ and $U_S$ (i.e., $\frac{|S|}{N} U_S \geq U_N$). Core-stable predictors are robust to low quality local data from some agents, and additionally they satisfy Proportionality and Pareto-optimality, two well sought-after fairness and efficiency notions within social choice. We then propose an efficient federated learning protocol CoreFed to optimize a core stable predictor. CoreFed determines a core-stable predictor when the loss functions of the agents are convex. CoreFed also determines approximate core-stable predictors when the loss functions are not convex, like smooth neural networks. We further show the existence of core-stable predictors in more general settings using Kakutani's fixed point theorem. Finally, we empirically validate our analysis on two real-world datasets, and we show that CoreFed achieves higher core-stability fairness than FedAvg while having similar accuracy.

在训练之前对神经网络进行修剪不仅会压缩原始模型，还可以加速其具有实质性应用值的网络培训阶段。当前的工作着重于细粒修剪，该修剪使用指标来计算重量筛查的重量评分，并从初始的单阶修剪到迭代修剪。通过这些作品，我们认为可以将网络修剪总结为权重的表达力传递过程，其中保留权重将从被删除的力量中占据表达力，以维持原始网络的性能。为了实现最佳的表达力调度，我们在训练名为神经网络Pannaging之前提出了一种修剪计划，该方案通过多指数和多进程步骤指导表达力转移，并设计一种基于强化学习以自动化过程的平移代理。实验结果表明，平平在训练方法之前的性能优于各种可用的修剪。