Protein inverse folding is a fundamental problem in bioinformatics, aiming to recover the amino acid sequences from a given protein backbone structure. Despite the success of existing methods, they struggle to fully capture the intricate inter-residue relationships critical for accurate sequence prediction. We propose a novel method that leverages diffusion models with representation alignment (DMRA), which enhances diffusion-based inverse folding by (1) proposing a shared center that aggregates contextual information from the entire protein structure and selectively distributes it to each residue; and (2) aligning noisy hidden representations with clean semantic representations during the denoising process. This is achieved by predefined semantic representations for amino acid types and a representation alignment method that utilizes type embeddings as semantic feedback to normalize each residue. In experiments, we conduct extensive evaluations on the CATH4.2 dataset to demonstrate that DMRA outperforms leading methods, achieving state-of-the-art performance and exhibiting strong generalization capabilities on the TS50 and TS500 datasets.

We applied machine learning to the entire data history of ESO's High Accuracy Radial Velocity Planet Searcher (HARPS) instrument. Our primary goal was to recover the physical properties of the observed objects, with a secondary emphasis on simulating spectra. We systematically investigated the impact of various factors on the accuracy and fidelity of the results, including the use of simulated data, the effect of varying amounts of real training data, network architectures, and learning paradigms. Our approach integrates supervised and unsupervised learning techniques within autoencoder frameworks. Our methodology leverages an existing simulation model that utilizes a library of existing stellar spectra in which the emerging flux is computed from first principles rooted in physics and a HARPS instrument model to generate simulated spectra comparable to observational data. We trained standard and variational autoencoders on HARPS data to predict spectral parameters and generate spectra. Our models excel at predicting spectral parameters and compressing real spectra, and they achieved a mean prediction error of approximately 50 K for effective temperatures, making them relevant for most astrophysical applications. Furthermore, the models predict metallicity ([M/H]) and surface gravity (log g) with an accuracy of approximately 0.03 dex and 0.04 dex, respectively, underscoring their broad applicability in astrophysical research. The models' computational efficiency, with processing times of 779.6 ms on CPU and 3.97 ms on GPU, makes them valuable for high-throughput applications like massive spectroscopic surveys and large archival studies. By achieving accuracy comparable to classical methods with significantly reduced computation time, our methodology enhances the scope and efficiency of spectroscopic analysis.

Recent advancement in deep-neural network performance led to the development of new state-of-the-art approaches in numerous areas. However, the black-box nature of neural networks often prohibits their use in areas where model explainability and model transparency are crucial. Over the years, researchers proposed many algorithms to aid neural network understanding and provide additional information to the human expert. One of the most popular methods being Layer-Wise Relevance Propagation (LRP). This method assigns local relevance based on the pixel-wise decomposition of nonlinear classifiers. With the rise of attribution method research, there has emerged a pressing need to assess and evaluate their performance. Numerous metrics have been proposed, each assessing an individual property of attribution methods such as faithfulness, robustness or localization. Unfortunately, no single metric is deemed optimal for every case, and researchers often use several metrics to test the quality of the attribution maps. In this work, we address the shortcomings of the current LRP formulations and introduce a novel method for determining the relevance of input neurons through layer-wise relevance propagation. Furthermore, we apply this approach to the recently developed Vision Transformer architecture and evaluate its performance against existing methods on two image classification datasets, namely ImageNet and PascalVOC. Our results clearly demonstrate the advantage of our proposed method. Furthermore, we discuss the insufficiencies of current evaluation metrics for attribution-based explainability and propose a new evaluation metric that combines the notions of faithfulness, robustness and contrastiveness. We utilize this new metric to evaluate the performance of various attribution-based methods. Our code is available at: https://github.com/davor10105/relative-absolute-magnitude-propagation

Position bias poses a persistent challenge in recommender systems, with much of the existing research focusing on refining ranking relevance and driving user engagement. However, in practical applications, the mitigation of position bias does not always result in detectable short-term improvements in ranking relevance. This paper provides an alternative, practically useful view of what position bias reduction methods can achieve. It demonstrates that position debiasing can spread visibility and interactions more evenly across the assortment, effectively reducing a skew in the popularity of items induced by the position bias through a feedback loop. We offer an explanation of how position bias affects item popularity. This includes an illustrative model of the item popularity histogram and the effect of the position bias on its skewness. Through offline and online experiments on our large-scale e-commerce platform, we show that position debiasing can significantly improve assortment utilization, without any degradation in user engagement or financial metrics. This makes the ranking fairer and helps attract more partners or content providers, benefiting the customers and the business in the long term.

The rapid advancement of multi-agent reinforcement learning (MARL) has given rise to diverse training paradigms to learn the policies of each agent in the multi-agent system. The paradigms of decentralized training and execution (DTDE) and centralized training with decentralized execution (CTDE) have been proposed and widely applied. However, as the number of agents increases, the inherent limitations of these frameworks significantly degrade the performance metrics, such as win rate, total reward, etc. To reduce the influence of the increasing number of agents on the performance metrics, we propose a novel training paradigm of grouped training decentralized execution (GTDE). This framework eliminates the need for a centralized module and relies solely on local information, effectively meeting the training requirements of large-scale multi-agent systems. Specifically, we first introduce an adaptive grouping module, which divides each agent into different groups based on their observation history. To implement end-to-end training, GTDE uses Gumbel-Sigmoid for efficient point-to-point sampling on the grouping distribution while ensuring gradient backpropagation. To adapt to the uncertainty in the number of members in a group, two methods are used to implement a group information aggregation module that merges member information within the group. Empirical results show that in a cooperative environment with 495 agents, GTDE increased the total reward by an average of 382\% compared to the baseline. In a competitive environment with 64 agents, GTDE achieved a 100\% win rate against the baseline.

Score-based Generative Models (SGMs) have demonstrated remarkable generalization abilities, e.g. generating unseen, but natural data. However, the greater the generalization power, the more likely the unintended generalization, and the more dangerous the abuse. Research on moderated generalization in SGMs remains limited. To fill this gap, we first examine the current 'gold standard' in Machine Unlearning (MU), i.e., re-training the model after removing the undesirable training data, and find it does not work in SGMs. Further analysis of score functions reveals that the MU 'gold standard' does not alter the original score function, which explains its ineffectiveness. Based on this insight, we propose the first Moderated Score-based Generative Model (MSGM), which introduces a novel score adjustment strategy that redirects the score function away from undesirable data during the continuous-time stochastic differential equation process. Extensive experimental results demonstrate that MSGM significantly reduces the likelihood of generating undesirable content while preserving high visual quality for normal image generation. Albeit designed for SGMs, MSGM is a general and flexible MU framework that is compatible with diverse diffusion architectures (SGM and DDPM) and training strategies (re-training and fine-tuning), and enables zero-shot transfer of the pre-trained models to downstream tasks, e.g. image inpainting and reconstruction. The code will be shared upon acceptance.

A brain-computer interface (BCI) enables direct communication between the brain and an external device. Electroencephalogram (EEG) is a common input signal for BCIs, due to its convenience and low cost. Most research on EEG-based BCIs focuses on the accurate decoding of EEG signals, while ignoring their security. Recent studies have shown that machine learning models in BCIs are vulnerable to adversarial attacks. This paper proposes adversarial filtering based evasion and backdoor attacks to EEG-based BCIs, which are very easy to implement. Experiments on three datasets from different BCI paradigms demonstrated the effectiveness of our proposed attack approaches. To our knowledge, this is the first study on adversarial filtering for EEG-based BCIs, raising a new security concern and calling for more attention on the security of BCIs.

Standard deep learning architectures used for classification generate label predictions with a projection head and softmax activation function. Although successful, these methods fail to leverage the relational information between samples in the batch for generating label predictions. In recent works, graph-based learning techniques, namely Laplace learning, have been heuristically combined with neural networks for both supervised and semi-supervised learning (SSL) tasks. However, prior works approximate the gradient of the loss function with respect to the graph learning algorithm or decouple the processes; end-to-end integration with neural networks is not achieved. In this work, we derive backpropagation equations, via the adjoint method, for inclusion of a general family of graph learning layers into a neural network. This allows us to precisely integrate graph Laplacian-based label propagation into a neural network layer, replacing a projection head and softmax activation function for classification tasks. Using this new framework, our experimental results demonstrate smooth label transitions across data, improved robustness to adversarial attacks, improved generalization, and improved training dynamics compared to the standard softmax-based approach.

Normalizing Flows (NFs) are likelihood-based models for continuous inputs. They have demonstrated promising results on both density estimation and generative modeling tasks, but have received relatively little attention in recent years. In this work, we demonstrate that NFs are more powerful than previously believed. We present TarFlow: a simple and scalable architecture that enables highly performant NF models. TarFlow can be thought of as a Transformer-based variant of Masked Autoregressive Flows (MAFs): it consists of a stack of autoregressive Transformer blocks on image patches, alternating the autoregression direction between layers. TarFlow is straightforward to train end-to-end, and capable of directly modeling and generating pixels. We also propose three key techniques to improve sample quality: Gaussian noise augmentation during training, a post training denoising procedure, and an effective guidance method for both class-conditional and unconditional settings. Putting these together, TarFlow sets new state-of-the-art results on likelihood estimation for images, beating the previous best methods by a large margin, and generates samples with quality and diversity comparable to diffusion models, for the first time with a stand-alone NF model. We make our code available at https://github.com/apple/ml-tarflow.

Large Language Models (LLMs) have emerged as a transformative AI paradigm, profoundly influencing daily life through their exceptional language understanding and contextual generation capabilities. Despite their remarkable performance, LLMs face a critical challenge: the propensity to produce unreliable outputs due to the inherent limitations of their learning-based nature. Formal methods (FMs), on the other hand, are a well-established computation paradigm that provides mathematically rigorous techniques for modeling, specifying, and verifying the correctness of systems. FMs have been extensively applied in mission-critical software engineering, embedded systems, and cybersecurity. However, the primary challenge impeding the deployment of FMs in real-world settings lies in their steep learning curves, the absence of user-friendly interfaces, and issues with efficiency and adaptability. This position paper outlines a roadmap for advancing the next generation of trustworthy AI systems by leveraging the mutual enhancement of LLMs and FMs. First, we illustrate how FMs, including reasoning and certification techniques, can help LLMs generate more reliable and formally certified outputs. Subsequently, we highlight how the advanced learning capabilities and adaptability of LLMs can significantly enhance the usability, efficiency, and scalability of existing FM tools. Finally, we show that unifying these two computation paradigms -- integrating the flexibility and intelligence of LLMs with the rigorous reasoning abilities of FMs -- has transformative potential for the development of trustworthy AI software systems. We acknowledge that this integration has the potential to enhance both the trustworthiness and efficiency of software engineering practices while fostering the development of intelligent FM tools capable of addressing complex yet real-world challenges.