The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. While modern biological pre-trained models have achieved great success in analyzing these macromolecules individually, their interconnected nature remains under-explored. In this paper, we follow the guidance of the central dogma to redesign both the data and model pipeline and offer a comprehensive framework, Life-Code, that spans different biological functions. As for data flow, we propose a unified pipeline to integrate multi-omics data by reverse-transcribing RNA and reverse-translating amino acids into nucleotide-based sequences. As for the model, we design a codon tokenizer and a hybrid long-sequence architecture to encode the interactions of both coding and non-coding regions with masked modeling pre-training. To model the translation and folding process with coding sequences, Life-Code learns protein structures of the corresponding amino acids by knowledge distillation from off-the-shelf protein language models. Such designs enable Life-Code to capture complex interactions within genetic sequences, providing a more comprehensive understanding of multi-omics with the central dogma. Extensive Experiments show that Life-Code achieves state-of-the-art performance on various tasks across three omics, highlighting its potential for advancing multi-omics analysis and interpretation.

Federated Distillation (FD) has emerged as a popular federated training framework, enabling clients to collaboratively train models without sharing private data. Public Dataset-Assisted Federated Distillation (PDA-FD), which leverages public datasets for knowledge sharing, has become widely adopted. Although PDA-FD enhances privacy compared to traditional Federated Learning, we demonstrate that the use of public datasets still poses significant privacy risks to clients' private training data. This paper presents the first comprehensive privacy analysis of PDA-FD in presence of an honest-but-curious server. We show that the server can exploit clients' inference results on public datasets to extract two critical types of private information: label distributions and membership information of the private training dataset. To quantify these vulnerabilities, we introduce two novel attacks specifically designed for the PDA-FD setting: a label distribution inference attack and innovative membership inference methods based on Likelihood Ratio Attack (LiRA). Through extensive evaluation of three representative PDA-FD frameworks (FedMD, DS-FL, and Cronus), our attacks achieve state-of-the-art performance, with label distribution attacks reaching minimal KL-divergence and membership inference attacks maintaining high True Positive Rates under low False Positive Rate constraints. Our findings reveal significant privacy risks in current PDA-FD frameworks and emphasize the need for more robust privacy protection mechanisms in collaborative learning systems.

This study investigates the stylistic differences among various Bible translations using a Variational Autoencoder (VAE) model. By embedding textual data into high-dimensional vectors, the study aims to detect and analyze stylistic variations between translations, with a specific focus on distinguishing the American Standard Version (ASV) from other translations. The results demonstrate that each translation exhibits a unique stylistic distribution, which can be effectively identified using the VAE model. These findings suggest that the VAE model is proficient in capturing and differentiating textual styles, although it is primarily optimized for distinguishing a single style. The study highlights the model's potential for broader applications in AI-based text generation and stylistic analysis, while also acknowledging the need for further model refinement to address the complexity of multi-dimensional stylistic relationships. Future research could extend this methodology to other text domains, offering deeper insights into the stylistic features embedded within various types of textual data.

The technique of "testing by betting" frames nonparametric sequential hypothesis testing as a multiple-round game, where a player bets on future observations that arrive in a streaming fashion, accumulates wealth that quantifies evidence against the null hypothesis, and rejects the null once the wealth exceeds a specified threshold while controlling the false positive error. Designing an online learning algorithm that achieves a small regret in the game can help rapidly accumulate the bettor's wealth, which in turn can shorten the time to reject the null hypothesis under the alternative $H_1$. However, many of the existing works employ the Online Newton Step (ONS) to update within a halved decision space to avoid a gradient explosion issue, which is potentially conservative for rapid wealth accumulation. In this paper, we introduce a novel strategy utilizing interior-point methods in optimization that allows updates across the entire interior of the decision space without the risk of gradient explosion. Our approach not only maintains strong statistical guarantees but also facilitates faster null hypothesis rejection in critical scenarios, overcoming the limitations of existing approaches.

The Transiting Exoplanet Survey Satellite (TESS) is surveying a large fraction of the sky, generating a vast database of photometric time series data that requires thorough analysis to identify exoplanetary transit signals. Automated learning approaches have been successfully applied to identify transit signals. However, most existing methods focus on the classification and validation of candidates, while few efforts have explored new techniques for the search of candidates. To search for new exoplanet transit candidates, we propose an approach to identify exoplanet transit signals without the need for phase folding or assuming periodicity in the transit signals, such as those observed in multi-transit light curves. To achieve this, we implement a new neural network inspired by Transformers to directly process Full Frame Image (FFI) light curves to detect exoplanet transits. Transformers, originally developed for natural language processing, have recently demonstrated significant success in capturing long-range dependencies compared to previous approaches focused on sequential data. This ability allows us to employ multi-head self-attention to identify exoplanet transit signals directly from the complete light curves, combined with background and centroid time series, without requiring prior transit parameters. The network is trained to learn characteristics of the transit signal, like the dip shape, which helps distinguish planetary transits from other variability sources. Our model successfully identified 214 new planetary system candidates, including 122 multi-transit light curves, 88 single-transit and 4 multi-planet systems from TESS sectors 1-26 with a radius > 0.27 $R_{\mathrm{Jupiter}}$, demonstrating its ability to detect transits regardless of their periodicity.

Anomaly detection in time series is essential for industrial monitoring and environmental sensing, yet distinguishing anomalies from complex patterns remains challenging. Existing methods like the Anomaly Transformer and DCdetector have progressed, but they face limitations such as sensitivity to short-term contexts and inefficiency in noisy, non-stationary environments. To overcome these issues, we introduce MAAT, an improved architecture that enhances association discrepancy modeling and reconstruction quality. MAAT features Sparse Attention, efficiently capturing long-range dependencies by focusing on relevant time steps, thereby reducing computational redundancy. Additionally, a Mamba-Selective State Space Model is incorporated into the reconstruction module, utilizing a skip connection and Gated Attention to improve anomaly localization and detection performance. Extensive experiments show that MAAT significantly outperforms previous methods, achieving better anomaly distinguishability and generalization across various time series applications, setting a new standard for unsupervised time series anomaly detection in real-world scenarios.

This paper presents a novel Natural Language Processing (NLP) framework for enhancing medical diagnosis through the integration of advanced techniques in data augmentation, feature extraction, and classification. The proposed approach employs back-translation to generate diverse paraphrased datasets, improving robustness and mitigating overfitting in classification tasks. Leveraging Decoding-enhanced BERT with Disentangled Attention (DeBERTa) with Dynamic Contextual Positional Gating (DCPG), the model captures fine-grained contextual and positional relationships, dynamically adjusting the influence of positional information based on semantic context to produce high-quality text embeddings. For classification, an Attention-Based Feedforward Neural Network (ABFNN) is utilized, effectively focusing on the most relevant features to improve decision-making accuracy. Applied to the classification of symptoms, clinical notes, and other medical texts, this architecture demonstrates its ability to address the complexities of medical data. The combination of data augmentation, contextual embedding generation, and advanced classification mechanisms offers a robust and accurate diagnostic tool, with potential applications in automated medical diagnosis and clinical decision support. This method demonstrates the effectiveness of the proposed NLP framework for medical diagnosis, achieving remarkable results with an accuracy of 99.78%, recall of 99.72%, precision of 99.79%, and an F1-score of 99.75%. These metrics not only underscore the model's robust performance in classifying medical texts with exceptional precision and reliability but also highlight its superiority over existing methods, making it a highly promising tool for automated diagnostic systems.

Permutation tests are a popular choice for distinguishing distributions and testing independence, due to their exact, finite-sample control of false positives and their minimax optimality when paired with U-statistics. However, standard permutation tests are also expensive, requiring a test statistic to be computed hundreds or thousands of times to detect a separation between distributions. In this work, we offer a simple approach to accelerate testing: group your datapoints into bins and permute only those bins. For U and V-statistics, we prove that these cheap permutation tests have two remarkable properties. First, by storing appropriate sufficient statistics, a cheap test can be run in time comparable to evaluating a single test statistic. Second, cheap permutation power closely approximates standard permutation power. As a result, cheap tests inherit the exact false positive control and minimax optimality of standard permutation tests while running in a fraction of the time. We complement these findings with improved power guarantees for standard permutation testing and experiments demonstrating the benefits of cheap permutations over standard maximum mean discrepancy (MMD), Hilbert-Schmidt independence criterion (HSIC), random Fourier feature, Wilcoxon-Mann-Whitney, cross-MMD, and cross-HSIC tests.

The ability to identify useful features or representations of the input data based on training data that achieves low prediction error on test data across multiple prediction tasks is considered the key to multitask learning success. In practice, however, one faces the issue of the choice of prediction tasks and the availability of test data from the chosen tasks while comparing the relative performance of different features. In this work, we develop a class of pseudometrics called Uniform Kernel Prober (UKP) for comparing features or representations learned by different statistical models such as neural networks when the downstream prediction tasks involve kernel ridge regression. The proposed pseudometric, UKP, between any two representations, provides a uniform measure of prediction error on test data corresponding to a general class of kernel ridge regression tasks for a given choice of a kernel without access to test data. Additionally, desired invariances in representations can be successfully captured by UKP only through the choice of the kernel function and the pseudometric can be efficiently estimated from $n$ input data samples with $O(\frac{1}{\sqrt{n}})$ estimation error. We also experimentally demonstrate the ability of UKP to discriminate between different types of features or representations based on their generalization performance on downstream kernel ridge regression tasks.

Recent advancements in language models have led to significant improvements in mathematical reasoning across various benchmarks. However, most of these benchmarks rely on automatic evaluation methods that only compare final answers using heuristics, without verifying the underlying reasoning steps. This limitation results in false positive solutions, where models may produce correct final answers but with flawed deduction paths. In this paper, we systematically examine the prevalence of false positive solutions in mathematical problem solving for language models. We analyze the characteristics and extent of this issue across different open-source models, datasets of varying difficulty levels, and decoding strategies. Specifically, we explore how false positives influence the inference time scaling behavior of language models. Our experimental results reveal that: (1) false positive solutions persist across different models, datasets, and decoding methods, (2) sampling-based inference time scaling methods do not alleviate the problem, and (3) the pass@N evaluation metric is more susceptible to false positives, suggesting a significantly lower scaling ceiling than what automatic evaluations indicate. Additionally, we analyze specific instances of false positives and discuss potential limitations in self-improvement techniques and synthetic data generation under such conditions.