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.

Because of the widespread existence of noise and data corruption, recovering the true regression parameters with a certain proportion of corrupted response variables is an essential task. Methods to overcome this problem often involve robust least-squares regression, but few methods perform well when confronted with severe adaptive adversarial attacks. In many applications, prior knowledge is often available from historical data or engineering experience, and by incorporating prior information into a robust regression method, we develop an effective robust regression method that can resist adaptive adversarial attacks. First, we propose the novel TRIP (hard Thresholding approach to Robust regression with sImple Prior) algorithm, which improves the breakdown point when facing adaptive adversarial attacks. Then, to improve the robustness and reduce the estimation error caused by the inclusion of priors, we use the idea of Bayesian reweighting to construct the more robust BRHT (robust Bayesian Reweighting regression via Hard Thresholding) algorithm. We prove the theoretical convergence of the proposed algorithms under mild conditions, and extensive experiments show that under different types of dataset attacks, our algorithms outperform other benchmark ones. Finally, we apply our methods to a data-recovery problem in a real-world application involving a space solar array, demonstrating their good applicability.

One of the key challenges in deploying RL to real-world applications is to adapt to variations of unknown environment contexts, such as changing terrains in robotic tasks and fluctuated bandwidth in congestion control. Existing works on adaptation to unknown environment contexts either assume the contexts are the same for the whole episode or assume the context variables are Markovian. However, in many real-world applications, the environment context usually stays stable for a stochastic period and then changes in an abrupt and unpredictable manner within an episode, resulting in a segment structure, which existing works fail to address. To leverage the segment structure of piecewise stable context in real-world applications, in this paper, we propose a \textit{\textbf{Se}gmented \textbf{C}ontext \textbf{B}elief \textbf{A}ugmented \textbf{D}eep~(SeCBAD)} RL method. Our method can jointly infer the belief distribution over latent context with the posterior over segment length and perform more accurate belief context inference with observed data within the current context segment. The inferred belief context can be leveraged to augment the state, leading to a policy that can adapt to abrupt variations in context. We demonstrate empirically that SeCBAD can infer context segment length accurately and outperform existing methods on a toy grid world environment and Mujuco tasks with piecewise-stable context.

While mislabeled or ambiguously-labeled samples in the training set could negatively affect the performance of deep models, diagnosing the dataset and identifying mislabeled samples helps to improve the generalization power. Training dynamics, i.e., the traces left by iterations of optimization algorithms, have recently been proved to be effective to localize mislabeled samples with hand-crafted features. In this paper, beyond manually designed features, we introduce a novel learning-based solution, leveraging a noise detector, instanced by an LSTM network, which learns to predict whether a sample was mislabeled using the raw training dynamics as input. Specifically, the proposed method trains the noise detector in a supervised manner using the dataset with synthesized label noises and can adapt to various datasets (either naturally or synthesized label-noised) without retraining. We conduct extensive experiments to evaluate the proposed method. We train the noise detector based on the synthesized label-noised CIFAR dataset and test such noise detector on Tiny ImageNet, CUB-200, Caltech-256, WebVision and Clothing1M. Results show that the proposed method precisely detects mislabeled samples on various datasets without further adaptation, and outperforms state-of-the-art methods. Besides, more experiments demonstrate that the mislabel identification can guide a label correction, namely data debugging, providing orthogonal improvements of algorithm-centric state-of-the-art techniques from the data aspect.

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.

Massively multi-task learning with large language models has recently made substantial progress on few-shot generalization. However, this is usually performed in a centralized learning fashion, ignoring the privacy sensitivity issue of (annotated) data used in multiple tasks. To mitigate this issue, we propose FewFedWeight, a few-shot federated learning framework across multiple tasks, to achieve the best of both worlds: privacy preservation and cross-task generalization. FewFedWeight trains client models in isolated devices without sharing data. It broadcasts the global model in the server to each client and produces pseudo data for clients so that knowledge from the global model can be explored to enhance few-shot learning of each client model. An energy-based algorithm is further proposed to weight pseudo samples in order to reduce the negative impact of noise from the generated pseudo data. Adaptive model weights of client models are also tuned according to their performance. We use these model weights to dynamically aggregate client models to update the global model. Experiments on 118 NLP tasks show that FewFedWeight can significantly improve the performance of client models on 61% tasks with an average performance improvement rate of 30.5% over the baseline and substantially outperform FedAvg and other decentralized learning methods.

Knowledge distillation (KD) has been widely used for model compression and knowledge transfer. Typically, a big teacher model trained on sufficient data transfers knowledge to a small student model. However, despite the success of KD, little effort has been made to study whether KD leaks the training data of the teacher model. In this paper, we experimentally reveal that KD suffers from the risk of privacy leakage. To alleviate this issue, we propose a novel knowledge distillation method, swing distillation, which can effectively protect the private information of the teacher model from flowing to the student model. In our framework, the temperature coefficient is dynamically and adaptively adjusted according to the degree of private information contained in the data, rather than a predefined constant hyperparameter. It assigns different temperatures to tokens according to the likelihood that a token in a position contains private information. In addition, we inject noise into soft targets provided to the student model, in order to avoid unshielded knowledge transfer. Experiments on multiple datasets and tasks demonstrate that the proposed swing distillation can significantly reduce (by over 80% in terms of canary exposure) the risk of privacy leakage in comparison to KD with competitive or better performance. Furthermore, swing distillation is robust against the increasing privacy budget.

Causal chain reasoning (CCR) is an essential ability for many decision-making AI systems, which requires the model to build reliable causal chains by connecting causal pairs. However, CCR suffers from two main transitive problems: threshold effect and scene drift. In other words, the causal pairs to be spliced may have a conflicting threshold boundary or scenario. To address these issues, we propose a novel Reliable Causal chain reasoning framework~(ReCo), which introduces exogenous variables to represent the threshold and scene factors of each causal pair within the causal chain, and estimates the threshold and scene contradictions across exogenous variables via structural causal recurrent neural networks~(SRNN). Experiments show that ReCo outperforms a series of strong baselines on both Chinese and English CCR datasets. Moreover, by injecting reliable causal chain knowledge distilled by ReCo, BERT can achieve better performances on four downstream causal-related tasks than BERT models enhanced by other kinds of knowledge.

Multi-player multi-armed bandit is an increasingly relevant decision-making problem, motivated by applications to cognitive radio systems. Most research for this problem focuses exclusively on the settings that players have \textit{full access} to all arms and receive no reward when pulling the same arm. Hence all players solve the same bandit problem with the goal of maximizing their cumulative reward. However, these settings neglect several important factors in many real-world applications, where players have \textit{limited access} to \textit{a dynamic local subset of arms} (i.e., an arm could sometimes be ``walking'' and not accessible to the player). To this end, this paper proposes a \textit{multi-player multi-armed walking bandits} model, aiming to address aforementioned modeling issues. The goal now is to maximize the reward, however, players can only pull arms from the local subset and only collect a full reward if no other players pull the same arm. We adopt Upper Confidence Bound (UCB) to deal with the exploration-exploitation tradeoff and employ distributed optimization techniques to properly handle collisions. By carefully integrating these two techniques, we propose a decentralized algorithm with near-optimal guarantee on the regret, and can be easily implemented to obtain competitive empirical performance.

Fusing camera with LiDAR is a promising technique to improve the accuracy of 3D detection due to the complementary physical properties. While most existing methods focus on fusing camera features directly with raw LiDAR point clouds or shallow 3D features, it is observed that direct deep 3D feature fusion achieves inferior accuracy due to feature misalignment. The misalignment that originates from the feature aggregation across large receptive fields becomes increasingly severe for deep network stages. In this paper, we propose PathFusion to enable path-consistent LiDAR-camera deep feature fusion. PathFusion introduces a path consistency loss between shallow and deep features, which encourages the 2D backbone and its fusion path to transform 2D features in a way that is semantically aligned with the transform of the 3D backbone. We apply PathFusion to the prior-art fusion baseline, Focals Conv, and observe more than 1.2\% mAP improvements on the nuScenes test split consistently with and without testing-time augmentations. Moreover, PathFusion also improves KITTI AP3D (R11) by more than 0.6% on moderate level.