Towards Early Prediction of Human iPSC Reprogramming Success

This paper presents advancements in automated early-stage prediction of the success of reprogramming human induced pluripotent stem cells (iPSCs) as a potential source for regenerative cell therapies.The minuscule success rate of iPSC-reprogramming of around $ 0.01% $ to $ 0.1% $ makes it labor-intensive, time-consuming, and exorbitantly expensive to generate a stable iPSC line. Since that requires culturing of millions of cells and intense biological scrutiny of multiple clones to identify a single optimal clone. The ability to reliably predict which cells are likely to establish as an optimal iPSC line at an early stage of pluripotency would therefore be ground-breaking in rendering this a practical and cost-effective approach to personalized medicine. Temporal information about changes in cellular appearance over time is crucial for predicting its future growth outcomes. In order to generate this data, we first performed continuous time-lapse imaging of iPSCs in culture using an ultra-high resolution microscope. We then annotated the locations and identities of cells in late-stage images where reliable manual identification is possible. Next, we propagated these labels backwards in time using a semi-automated tracking system to obtain labels for early stages of growth. Finally, we used this data to train deep neural networks to perform automatic cell segmentation and classification. Our code and data are available at https://github.com/abhineet123/ipsc_prediction.

Sophia: A Scalable Stochastic Second-order Optimizer for Language Model Pre-training

Given the massive cost of language model pre-training, a non-trivial improvement of the optimization algorithm would lead to a material reduction on the time and cost of training. Adam and its variants have been state-of-the-art for years, and more sophisticated second-order (Hessian-based) optimizers often incur too much per-step overhead. In this paper, we propose Sophia, Second-order Clipped Stochastic Optimization, a simple scalable second-order optimizer that uses a light-weight estimate of the diagonal Hessian as the pre-conditioner. The update is the moving average of the gradients divided by the moving average of the estimated Hessian, followed by element-wise clipping. The clipping controls the worst-case update size and tames the negative impact of non-convexity and rapid change of Hessian along the trajectory. Sophia only estimates the diagonal Hessian every handful of iterations, which has negligible average per-step time and memory overhead. On language modeling with GPT-2 models of sizes ranging from 125M to 770M, Sophia achieves a 2x speed-up compared with Adam in the number of steps, total compute, and wall-clock time. Theoretically, we show that Sophia adapts to the curvature in different components of the parameters, which can be highly heterogeneous for language modeling tasks. Our run-time bound does not depend on the condition number of the loss.

R-TOSS: A Framework for Real-Time Object Detection using Semi-Structured Pruning

Object detectors used in autonomous vehicles can have high memory and computational overheads. In this paper, we introduce a novel semi-structured pruning framework called R-TOSS that overcomes the shortcomings of state-of-the-art model pruning techniques. Experimental results on the JetsonTX2 show that R-TOSS has a compression rate of 4.4x on the YOLOv5 object detector with a 2.15x speedup in inference time and 57.01% decrease in energy usage. R-TOSS also enables 2.89x compression on RetinaNet with a 1.86x speedup in inference time and 56.31% decrease in energy usage. We also demonstrate significant improvements compared to various state-of-the-art pruning techniques.

LMD: Light-weight Prediction Quality Estimation for Object Detection in Lidar Point Clouds

Object detection on Lidar point cloud data is a promising technology for autonomous driving and robotics which has seen a significant rise in performance and accuracy during recent years. Particularly uncertainty estimation is a crucial component for down-stream tasks and deep neural networks remain error-prone even for predictions with high confidence. Previously proposed methods for quantifying prediction uncertainty tend to alter the training scheme of the detector or rely on prediction sampling which results in vastly increased inference time. In order to address these two issues, we propose LidarMetaDetect (LMD), a light-weight post-processing scheme for prediction quality estimation. Our method can easily be added to any pre-trained Lidar object detector without altering anything about the base model and is purely based on post-processing, therefore, only leading to a negligible computational overhead. Our experiments show a significant increase of statistical reliability in separating true from false predictions. We propose and evaluate an additional application of our method leading to the detection of annotation errors. Explicit samples and a conservative count of annotation error proposals indicates the viability of our method for large-scale datasets like KITTI and nuScenes. On the widely-used nuScenes test dataset, 43 out of the top 100 proposals of our method indicate, in fact, erroneous annotations.

LOVM: Language-Only Vision Model Selection

Pre-trained multi-modal vision-language models (VLMs) are becoming increasingly popular due to their exceptional performance on downstream vision applications, particularly in the few- and zero-shot settings. However, selecting the best-performing VLM for some downstream applications is non-trivial, as it is dataset and task-dependent. Meanwhile, the exhaustive evaluation of all available VLMs on a novel application is not only time and computationally demanding but also necessitates the collection of a labeled dataset for evaluation. As the number of open-source VLM variants increases, there is a need for an efficient model selection strategy that does not require access to a curated evaluation dataset. This paper proposes a novel task and benchmark for efficiently evaluating VLMs' zero-shot performance on downstream applications without access to the downstream task dataset. Specifically, we introduce a new task LOVM: Language-Only Vision Model Selection, where methods are expected to perform both model selection and performance prediction based solely on a text description of the desired downstream application. We then introduced an extensive LOVM benchmark consisting of ground-truth evaluations of 35 pre-trained VLMs and 23 datasets, where methods are expected to rank the pre-trained VLMs and predict their zero-shot performance.

Equitable Multi-task Learning

Multi-task learning (MTL) has achieved great success in various research domains, such as CV, NLP and IR etc. Due to the complex and competing task correlation, na\"ive training all tasks may lead to inequitable learning, \textit{i.e.} some tasks are learned well while others are overlooked. Multi-task optimization (MTO) aims to improve all tasks at same time, but conventional methods often perform poor when tasks with large loss scale or gradient norm magnitude difference. To solve the issue, we in-depth investigate the equity problem for MTL and find that regularizing relative contribution of different tasks (\textit{i.e.} value of task-specific loss divides its raw gradient norm) in updating shared parameter can improve generalization performance of MTL. Based on our theoretical analysis, we propose a novel multi-task optimization method, named \textit{EMTL}, to achieve equitable MTL. Specifically, we efficiently add variance regularization to make different tasks' relative contribution closer. Extensive experiments have been conduct to evaluate EMTL, our method stably outperforms state-of-the-art methods on the public benchmark datasets of two different research domains. Furthermore, offline and online A/B test on multi-task recommendation are conducted too. EMTL improves multi-task recommendation significantly, demonstrating the superiority and practicability of our method in industrial landscape.

OMS-DPM: Optimizing the Model Schedule for Diffusion Probabilistic Models

Diffusion probabilistic models (DPMs) are a new class of generative models that have achieved state-of-the-art generation quality in various domains. Despite the promise, one major drawback of DPMs is the slow generation speed due to the large number of neural network evaluations required in the generation process. In this paper, we reveal an overlooked dimension -- model schedule -- for optimizing the trade-off between generation quality and speed. More specifically, we observe that small models, though having worse generation quality when used alone, could outperform large models in certain generation steps. Therefore, unlike the traditional way of using a single model, using different models in different generation steps in a carefully designed \emph{model schedule} could potentially improve generation quality and speed \emph{simultaneously}. We design OMS-DPM, a predictor-based search algorithm, to optimize the model schedule given an arbitrary generation time budget and a set of pre-trained models. We demonstrate that OMS-DPM can find model schedules that improve generation quality and speed than prior state-of-the-art methods across CIFAR-10, CelebA, ImageNet, and LSUN datasets. When applied to the public checkpoints of the Stable Diffusion model, we are able to accelerate the sampling by 2$\times$ while maintaining the generation quality.

Online Heavy-tailed Change-point detection

We study algorithms for online change-point detection (OCPD), where samples that are potentially heavy-tailed, are presented one at a time and a change in the underlying mean must be detected as early as possible. We present an algorithm based on clipped Stochastic Gradient Descent (SGD), that works even if we only assume that the second moment of the data generating process is bounded. We derive guarantees on worst-case, finite-sample false-positive rate (FPR) over the family of all distributions with bounded second moment. Thus, our method is the first OCPD algorithm that guarantees finite-sample FPR, even if the data is high dimensional and the underlying distributions are heavy-tailed. The technical contribution of our paper is to show that clipped-SGD can estimate the mean of a random vector and simultaneously provide confidence bounds at all confidence values. We combine this robust estimate with a union bound argument and construct a sequential change-point algorithm with finite-sample FPR guarantees. We show empirically that our algorithm works well in a variety of situations, whether the underlying data are heavy-tailed, light-tailed, high dimensional or discrete. No other algorithm achieves bounded FPR theoretically or empirically, over all settings we study simultaneously.

Towards Faster Non-Asymptotic Convergence for Diffusion-Based Generative Models

Diffusion models, which convert noise into new data instances by learning to reverse a Markov diffusion process, have become a cornerstone in contemporary generative modeling. While their practical power has now been widely recognized, the theoretical underpinnings remain far from mature. In this work, we develop a suite of non-asymptotic theory towards understanding the data generation process of diffusion models in discrete time, assuming access to reliable estimates of the (Stein) score functions. For a popular deterministic sampler (based on the probability flow ODE), we establish a convergence rate proportional to $1/T$ (with $T$ the total number of steps), improving upon past results; for another mainstream stochastic sampler (i.e., a type of the denoising diffusion probabilistic model (DDPM)), we derive a convergence rate proportional to $1/\sqrt{T}$, matching the state-of-the-art theory. Our theory imposes only minimal assumptions on the target data distribution (e.g., no smoothness assumption is imposed), and is developed based on an elementary yet versatile non-asymptotic approach without resorting to toolboxes for SDEs and ODEs. Further, we design two accelerated variants, improving the convergence to $1/T^2$ for the ODE-based sampler and $1/T$ for the DDPM-type sampler, which might be of independent theoretical and empirical interest.

Map Reconstruction of radio observations with Conditional Invertible Neural Networks

In radio astronomy, the challenge of reconstructing a sky map from time ordered data (TOD) is known as an inverse problem. Standard map-making techniques and gridding algorithms are commonly employed to address this problem, each offering its own benefits such as producing minimum-variance maps. However, these approaches also carry limitations such as computational inefficiency and numerical instability in map-making and the inability to remove beam effects in grid-based methods. To overcome these challenges, this study proposes a novel solution through the use of the conditional invertible neural network (cINN) for efficient sky map reconstruction. With the aid of forward modeling, where the simulated TODs are generated from a given sky model with a specific observation, the trained neural network can produce accurate reconstructed sky maps. Using the five-hundred-meter aperture spherical radio telescope (FAST) as an example, cINN demonstrates remarkable performance in map reconstruction from simulated TODs, achieving a mean squared error of $2.29\pm 2.14 \times 10^{-4}~\rm K^2$, a structural similarity index of $0.968\pm0.002$, and a peak signal-to-noise ratio of $26.13\pm5.22$ at the $1\sigma$ level. Furthermore, by sampling in the latent space of cINN, the reconstruction errors for each pixel can be accurately quantified.