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The rising popularity of deep learning (DL) methods and techniques has invigorated interest in the topic of SE4DL, the application of software engineering (SE) practices on deep learning software. Despite the novel engineering challenges brought on by the data-driven and non-deterministic paradigm of DL software, little work has been invested into developing AI-targeted SE tools. On the other hand, tools tackling more general engineering issues in DL are actively used and referred to under the umbrella term of ``MLOps tools''. Furthermore, the available literature supports the utility of conventional SE tooling in DL software development. Building upon previous MSR research on tool usage in open-source software works, we identify conventional and MLOps tools adopted in popular applied DL projects that use Python as the main programming language. About 70% of the GitHub repositories mined contained at least one conventional SE tool. Software configuration management tools are the most adopted, while the opposite applies to maintenance tools. Substantially fewer MLOps tools were in use, with only 9 tools out of a sample of 80 used in at least one repository. The majority of them were open-source rather than proprietary. One of these tools, TensorBoard, was found to be adopted in about half of the repositories in our study. Consequently, the use of conventional SE tooling demonstrates its relevance to DL software. Further research is recommended on the adoption of MLOps tooling by open-source projects, focusing on the relevance of particular tool types, the development of required tools, as well as ways to promote the use of already available tools.

As advancements in artificial intelligence (AI) propel progress in the life sciences, they may also enable the weaponisation and misuse of biological agents. This article differentiates two classes of AI tools that could pose such biosecurity risks: large language models (LLMs) and biological design tools (BDTs). LLMs, such as GPT-4 and its successors, might provide dual-use information and thus remove some barriers encountered by historical biological weapons efforts. As LLMs are turned into multi-modal lab assistants and autonomous science tools, this will increase their ability to support non-experts in performing laboratory work. Thus, LLMs may in particular lower barriers to biological misuse. In contrast, BDTs will expand the capabilities of sophisticated actors. Concretely, BDTs may enable the creation of pandemic pathogens substantially worse than anything seen to date and could enable forms of more predictable and targeted biological weapons. In combination, the convergence of LLMs and BDTs could raise the ceiling of harm from biological agents and could make them broadly accessible. A range of interventions would help to manage risks. Independent pre-release evaluations could help understand the capabilities of models and the effectiveness of safeguards. Options for differentiated access to such tools should be carefully weighed with the benefits of openly releasing systems. Lastly, essential for mitigating risks will be universal and enhanced screening of gene synthesis products.

This paper introduces the Budding Ensemble Architecture (BEA), a novel reduced ensemble architecture for anchor-based object detection models. Object detection models are crucial in vision-based tasks, particularly in autonomous systems. They should provide precise bounding box detections while also calibrating their predicted confidence scores, leading to higher-quality uncertainty estimates. However, current models may make erroneous decisions due to false positives receiving high scores or true positives being discarded due to low scores. BEA aims to address these issues. The proposed loss functions in BEA improve the confidence score calibration and lower the uncertainty error, which results in a better distinction of true and false positives and, eventually, higher accuracy of the object detection models. Both Base-YOLOv3 and SSD models were enhanced using the BEA method and its proposed loss functions. The BEA on Base-YOLOv3 trained on the KITTI dataset results in a 6% and 3.7% increase in mAP and AP50, respectively. Utilizing a well-balanced uncertainty estimation threshold to discard samples in real-time even leads to a 9.6% higher AP50 than its base model. This is attributed to a 40% increase in the area under the AP50-based retention curve used to measure the quality of calibration of confidence scores. Furthermore, BEA-YOLOV3 trained on KITTI provides superior out-of-distribution detection on Citypersons, BDD100K, and COCO datasets compared to the ensembles and vanilla models of YOLOv3 and Gaussian-YOLOv3.

In Computer Vision, self-supervised contrastive learning enforces similar representations between different views of the same image. The pre-training is most often performed on image classification datasets, like ImageNet, where images mainly contain a single class of objects. However, when dealing with complex scenes with multiple items, it becomes very unlikely for several views of the same image to represent the same object category. In this setting, we propose SAMCLR, an add-on to SimCLR which uses SAM to segment the image into semantic regions, then sample the two views from the same region. Preliminary results show empirically that when pre-training on Cityscapes and ADE20K, then evaluating on classification on CIFAR-10, STL10 and ImageNette, SAMCLR performs at least on par with, and most often significantly outperforms not only SimCLR, but also DINO and MoCo.

We introduce JAX FDM, a differentiable solver to design mechanically efficient shapes for 3D structures conditioned on target architectural, fabrication and structural properties. Examples of such structures are domes, cable nets and towers. JAX FDM solves these inverse form-finding problems by combining the force density method, differentiable sparsity and gradient-based optimization. Our solver can be paired with other libraries in the JAX ecosystem to facilitate the integration of form-finding simulations with neural networks. We showcase the features of JAX FDM with two design examples. JAX FDM is available as an open-source library at //github.com/arpastrana/jax_fdm.

To check the accuracy of Bayesian computations, it is common to use rank-based simulation-based calibration (SBC). However, SBC has drawbacks: The test statistic is somewhat ad-hoc, interactions are difficult to examine, multiple testing is a challenge, and the resulting p-value is not a divergence metric. We propose to replace the marginal rank test with a flexible classification approach that learns test statistics from data. This measure typically has a higher statistical power than the SBC rank test and returns an interpretable divergence measure of miscalibration, computed from classification accuracy. This approach can be used with different data generating processes to address likelihood-free inference or traditional inference methods like Markov chain Monte Carlo or variational inference. We illustrate an automated implementation using neural networks and statistically-inspired features, and validate the method with numerical and real data experiments.

TorchAudio is an open-source audio and speech processing library built for PyTorch. It aims to accelerate the research and development of audio and speech technologies by providing well-designed, easy-to-use, and performant PyTorch components. Its contributors routinely engage with users to understand their needs and fulfill them by developing impactful features. Here, we survey TorchAudio's development principles and contents and highlight key features we include in its latest version (2.1): self-supervised learning pre-trained pipelines and training recipes, high-performance CTC decoders, speech recognition models and training recipes, advanced media I/O capabilities, and tools for performing forced alignment, multi-channel speech enhancement, and reference-less speech assessment. For a selection of these features, through empirical studies, we demonstrate their efficacy and show that they achieve competitive or state-of-the-art performance.

Neural networks are seeing increased use in diverse Internet of Things (IoT) applications such as healthcare, smart homes and industrial monitoring. Their widespread use makes neural networks a lucrative target for theft. An attacker can obtain a model without having access to the training data or incurring the cost of training. Also, networks trained using private data (e.g., medical records) can reveal information about this data. Networks can be stolen by leveraging side channels such as power traces of the IoT device when it is running the network. Existing attacks require operations to occur in the same order each time; an attacker must collect and analyze several traces of the device to steal the network. Therefore, to prevent this type of attack, we randomly shuffle the order of operations each time. With shuffling, each operation can now happen at many different points in each execution, making the attack intractable. However, we show that shuffling in software can leak information which can be used to subvert this solution. Therefore, to perform secure shuffling and reduce latency, we present BlackJack, hardware added as a functional unit within the CPU. BlackJack secures neural networks on IoT devices by increasing the time needed for an attack to centuries, while adding just 2.46% area, 3.28% power and 0.56% latency overhead on an ARM M0+ SoC.

We present ResMLP, an architecture built entirely upon multi-layer perceptrons for image classification. It is a simple residual network that alternates (i) a linear layer in which image patches interact, independently and identically across channels, and (ii) a two-layer feed-forward network in which channels interact independently per patch. When trained with a modern training strategy using heavy data-augmentation and optionally distillation, it attains surprisingly good accuracy/complexity trade-offs on ImageNet. We will share our code based on the Timm library and pre-trained models.

In this paper, we focus on three problems in deep learning based medical image segmentation. Firstly, U-net, as a popular model for medical image segmentation, is difficult to train when convolutional layers increase even though a deeper network usually has a better generalization ability because of more learnable parameters. Secondly, the exponential ReLU (ELU), as an alternative of ReLU, is not much different from ReLU when the network of interest gets deep. Thirdly, the Dice loss, as one of the pervasive loss functions for medical image segmentation, is not effective when the prediction is close to ground truth and will cause oscillation during training. To address the aforementioned three problems, we propose and validate a deeper network that can fit medical image datasets that are usually small in the sample size. Meanwhile, we propose a new loss function to accelerate the learning process and a combination of different activation functions to improve the network performance. Our experimental results suggest that our network is comparable or superior to state-of-the-art methods.