Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

ising机器是一个有前途的非von-neumann用于神经网络训练和组合优化的计算概念。然而，虽然可以用诸如展示机器实现各种神经网络，但是它们无法执行快速统计采样使得它们与数字计算机相比训练这些神经网络的效率低。在这里，我们通过注入模拟噪声来介绍一个通用概念，以实现具有ising机器的超快统计抽样。通过光电型机，我们证明这可用于精确采样Boltzmann分布和无监督的神经网络训练，具有与基于软件的培训等于准确性。通过模拟，我们发现ising机器可以比基于软件的方法更快地执行统计采样顺序。这使得Ising Machines成为机器学习的有效工具和超出组合优化的其他应用。

Many problems in machine learning involve bilevel optimization (BLO), including hyperparameter optimization, meta-learning, and dataset distillation. Bilevel problems consist of two nested sub-problems, called the outer and inner problems, respectively. In practice, often at least one of these sub-problems is overparameterized. In this case, there are many ways to choose among optima that achieve equivalent objective values. Inspired by recent studies of the implicit bias induced by optimization algorithms in single-level optimization, we investigate the implicit bias of gradient-based algorithms for bilevel optimization. We delineate two standard BLO methods -- cold-start and warm-start -- and show that the converged solution or long-run behavior depends to a large degree on these and other algorithmic choices, such as the hypergradient approximation. We also show that the inner solutions obtained by warm-start BLO can encode a surprising amount of information about the outer objective, even when the outer parameters are low-dimensional. We believe that implicit bias deserves as central a role in the study of bilevel optimization as it has attained in the study of single-level neural net optimization.

We improve the understanding of the $\textit{golden ratio algorithm}$, which solves monotone variational inequalities (VI) and convex-concave min-max problems via the distinctive feature of adapting the step sizes to the local Lipschitz constants. Adaptive step sizes not only eliminate the need to pick hyperparameters, but they also remove the necessity of global Lipschitz continuity and can increase from one iteration to the next. We first establish the equivalence of this algorithm with popular VI methods such as reflected gradient, Popov or optimistic gradient descent-ascent in the unconstrained case with constant step sizes. We then move on to the constrained setting and introduce a new analysis that allows to use larger step sizes, to complete the bridge between the golden ratio algorithm and the existing algorithms in the literature. Doing so, we actually eliminate the link between the golden ratio $\frac{1+\sqrt{5}}{2}$ and the algorithm. Moreover, we improve the adaptive version of the algorithm, first by removing the maximum step size hyperparameter (an artifact from the analysis) to improve the complexity bound, and second by adjusting it to nonmonotone problems with weak Minty solutions, with superior empirical performance.

By optimizing the rate-distortion-realism trade-off, generative compression approaches produce detailed, realistic images, even at low bit rates, instead of the blurry reconstructions produced by rate-distortion optimized models. However, previous methods do not explicitly control how much detail is synthesized, which results in a common criticism of these methods: users might be worried that a misleading reconstruction far from the input image is generated. In this work, we alleviate these concerns by training a decoder that can bridge the two regimes and navigate the distortion-realism trade-off. From a single compressed representation, the receiver can decide to either reconstruct a low mean squared error reconstruction that is close to the input, a realistic reconstruction with high perceptual quality, or anything in between. With our method, we set a new state-of-the-art in distortion-realism, pushing the frontier of achievable distortion-realism pairs, i.e., our method achieves better distortions at high realism and better realism at low distortion than ever before.

In this paper, we introduce neural texture learning for 6D object pose estimation from synthetic data and a few unlabelled real images. Our major contribution is a novel learning scheme which removes the drawbacks of previous works, namely the strong dependency on co-modalities or additional refinement. These have been previously necessary to provide training signals for convergence. We formulate such a scheme as two sub-optimisation problems on texture learning and pose learning. We separately learn to predict realistic texture of objects from real image collections and learn pose estimation from pixel-perfect synthetic data. Combining these two capabilities allows then to synthesise photorealistic novel views to supervise the pose estimator with accurate geometry. To alleviate pose noise and segmentation imperfection present during the texture learning phase, we propose a surfel-based adversarial training loss together with texture regularisation from synthetic data. We demonstrate that the proposed approach significantly outperforms the recent state-of-the-art methods without ground-truth pose annotations and demonstrates substantial generalisation improvements towards unseen scenes. Remarkably, our scheme improves the adopted pose estimators substantially even when initialised with much inferior performance.

Fine-grained semantic segmentation of a person's face and head, including facial parts and head components, has progressed a great deal in recent years. However, it remains a challenging task, whereby considering ambiguous occlusions and large pose variations are particularly difficult. To overcome these difficulties, we propose a novel framework termed Mask-FPAN. It uses a de-occlusion module that learns to parse occluded faces in a semi-supervised way. In particular, face landmark localization, face occlusionstimations, and detected head poses are taken into account. A 3D morphable face model combined with the UV GAN improves the robustness of 2D face parsing. In addition, we introduce two new datasets named FaceOccMask-HQ and CelebAMaskOcc-HQ for face paring work. The proposed Mask-FPAN framework addresses the face parsing problem in the wild and shows significant performance improvements with MIOU from 0.7353 to 0.9013 compared to the state-of-the-art on challenging face datasets.

Deep unfolding networks (DUNs) have proven to be a viable approach to compressive sensing (CS). In this work, we propose a DUN called low-rank CS network (LR-CSNet) for natural image CS. Real-world image patches are often well-represented by low-rank approximations. LR-CSNet exploits this property by adding a low-rank prior to the CS optimization task. We derive a corresponding iterative optimization procedure using variable splitting, which is then translated to a new DUN architecture. The architecture uses low-rank generation modules (LRGMs), which learn low-rank matrix factorizations, as well as gradient descent and proximal mappings (GDPMs), which are proposed to extract high-frequency features to refine image details. In addition, the deep features generated at each reconstruction stage in the DUN are transferred between stages to boost the performance. Our extensive experiments on three widely considered datasets demonstrate the promising performance of LR-CSNet compared to state-of-the-art methods in natural image CS.

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.

Modern machine learning pipelines are limited due to data availability, storage quotas, privacy regulations, and expensive annotation processes. These constraints make it difficult or impossible to maintain a large-scale model trained on growing annotation sets. Continual learning directly approaches this problem, with the ultimate goal of devising methods where a neural network effectively learns relevant patterns for new (unseen) classes without significantly altering its performance on previously learned ones. In this paper, we address the problem of continual learning for video data. We introduce PIVOT, a novel method that leverages the extensive knowledge in pre-trained models from the image domain, thereby reducing the number of trainable parameters and the associated forgetting. Unlike previous methods, ours is the first approach that effectively uses prompting mechanisms for continual learning without any in-domain pre-training. Our experiments show that PIVOT improves state-of-the-art methods by a significant 27% on the 20-task ActivityNet setup.