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Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous chromosomes of the human genome reveals allele-specific gene expression and allele-specific gene regulation by assessing allelic imbalance of read counts at individual sites. Here we formally describe an advanced statistical framework for detecting the allelic imbalance in allelic read counts at single-nucleotide variants detected in diverse omics studies (ChIP-Seq, ATAC-Seq, DNase-Seq, CAGE-Seq, and others). MIXALIME accounts for copy-number variants and aneuploidy, reference read mapping bias, and provides several scoring models to balance between sensitivity and specificity when scoring data with varying levels of experimental noise-caused overdispersion.

Memory corruption attacks (MCAs) refer to malicious behaviors of system intruders that modify the contents of a memory location to disrupt the normal operation of computing systems, causing leakage of sensitive data or perturbations to ongoing processes. Unlike general-purpose systems, unmanned systems cannot deploy complete security protection schemes, due to their limitations in size, cost and performance. MCAs in unmanned systems are particularly difficult to defend against. Furthermore, MCAs have diverse and unpredictable attack interfaces in unmanned systems, severely impacting digital and physical sectors. In this paper, we first generalize, model and taxonomize MCAs found in unmanned systems currently, laying the foundation for designing a portable and general defense approach. According to different attack mechanisms, we found that MCAs are mainly categorized into two types--return2libc and return2shellcode. To tackle return2libc attacks, we model the erratic operation of unmanned systems with cycles and then propose a cycle-task-oriented memory protection (CToMP) approach to protect control flows from tampering. To defend against return2shellcode attacks, we introduce a secure process stack with a randomized memory address by leveraging the memory pool to prevent Shellcode from being executed. Moreover, we discuss the mechanism by which CToMP resists the ROP attack, a novel variant of return2libc attacks. Finally, we implement CToMP on CUAV V5+ with Ardupilot and Crazyflie. The evaluation and security analysis results demonstrate that the proposed approach CToMP is resilient to various MCAs in unmanned systems with low footprints and system overhead.

Current research on cross-modal retrieval is mostly English-oriented, as the availability of a large number of English-oriented human-labeled vision-language corpora. In order to break the limit of non-English labeled data, cross-lingual cross-modal retrieval (CCR) has attracted increasing attention. Most CCR methods construct pseudo-parallel vision-language corpora via Machine Translation (MT) to achieve cross-lingual transfer. However, the translated sentences from MT are generally imperfect in describing the corresponding visual contents. Improperly assuming the pseudo-parallel data are correctly correlated will make the networks overfit to the noisy correspondence. Therefore, we propose Dual-view Curricular Optimal Transport (DCOT) to learn with noisy correspondence in CCR. In particular, we quantify the confidence of the sample pair correlation with optimal transport theory from both the cross-lingual and cross-modal views, and design dual-view curriculum learning to dynamically model the transportation costs according to the learning stage of the two views. Extensive experiments are conducted on two multilingual image-text datasets and one video-text dataset, and the results demonstrate the effectiveness and robustness of the proposed method. Besides, our proposed method also shows a good expansibility to cross-lingual image-text baselines and a decent generalization on out-of-domain data.

We generalize K\"ahler information manifolds of complex-valued signal processing filters by introducing weighted Hardy spaces and smooth transformations of transfer functions. We prove that the Riemannian geometry of a linear filter induced from weighted Hardy norms for the smooth transformations of its transfer function is a K\"ahler manifold. Additionally, the K\"ahler potential of the linear system geometry corresponds to the square of the weighted Hardy norms of its composite transfer functions. Based on properties of K\"ahler manifolds, geometric objects on the manifolds of the linear systems in weighted Hardy spaces are computed in much simpler ways. Moreover, K\"ahler information manifolds of signal filters in weighted Hardy spaces incorporate various well-known information manifolds under the unified framework. We also cover several examples from time series models of which metric tensor, Levi-Civita connection, and K\"ahler potentials are represented with polylogarithms of poles and zeros from the transfer functions with weight vectors in exponential forms.

Spiking Neural Networks (SNNs) have received considerable attention not only for their superiority in energy efficiency with discrete signal processing but also for their natural suitability to integrate multi-scale biological plasticity. However, most SNNs directly adopt the structure of the well-established Deep Neural Networks (DNNs), and rarely automatically design Neural Architecture Search (NAS) for SNNs. The neural motifs topology, modular regional structure and global cross-brain region connection of the human brain are the product of natural evolution and can serve as a perfect reference for designing brain-inspired SNN architecture. In this paper, we propose a Multi-Scale Evolutionary Neural Architecture Search (MSE-NAS) for SNN, simultaneously considering micro-, meso- and macro-scale brain topologies as the evolutionary search space. MSE-NAS evolves individual neuron operation, self-organized integration of multiple circuit motifs, and global connectivity across motifs through a brain-inspired indirect evaluation function, Representational Dissimilarity Matrices (RDMs). This training-free fitness function could greatly reduce computational consumption and NAS's time, and its task-independent property enables the searched SNNs to exhibit excellent transferability on multiple datasets. Furthermore, MSE-NAS show robustness against the training method and noise. Extensive experiments demonstrate that the proposed algorithm achieves state-of-the-art (SOTA) performance with shorter simulation steps on static datasets (CIFAR10, CIFAR100) and neuromorphic datasets (CIFAR10-DVS and DVS128-Gesture). The thorough analysis also illustrates the significant performance improvement and consistent bio-interpretability deriving from the topological evolution at different scales and the RDMs fitness function.

Prompt tuning (PT), where a small amount of trainable soft (continuous) prompt vectors is affixed to the input of language models (LM), has shown promising results across various tasks and models for parameter-efficient fine-tuning (PEFT). PT stands out from other PEFT approaches because it maintains competitive performance with fewer trainable parameters and does not drastically scale up its parameters as the model size expands. However, PT introduces additional soft prompt tokens, leading to longer input sequences, which significantly impacts training and inference time and memory usage due to the Transformer's quadratic complexity. Particularly concerning for Large Language Models (LLMs) that face heavy daily querying. To address this issue, we propose Decomposed Prompt Tuning (DePT), which decomposes the soft prompt into a shorter soft prompt and a pair of low-rank matrices that are then optimised with two different learning rates. This allows DePT to achieve better performance while saving over 20% memory and time costs compared to vanilla PT and its variants, without changing trainable parameter sizes. Through extensive experiments on 23 natural language processing (NLP) and vision-language (VL) tasks, we demonstrate that DePT outperforms state-of-the-art PEFT approaches, including the full fine-tuning baseline in some scenarios. Additionally, we empirically show that DEPT grows more efficient as the model size increases. Our further study reveals that DePT integrates seamlessly with parameter-efficient transfer learning in the few-shot learning setting and highlights its adaptability to various model architectures and sizes.

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper, rather than pursuing state-of-the-art performance, we aim to evaluate capabilities of LLMs in a wide range of tasks across the chemistry domain. We identify three key chemistry-related capabilities including understanding, reasoning and explaining to explore in LLMs and establish a benchmark containing eight chemistry tasks. Our analysis draws on widely recognized datasets facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Five LLMs (GPT-4, GPT-3.5, Davinci-003, Llama and Galactica) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. Our investigation found that GPT-4 outperformed other models and LLMs exhibit different competitive levels in eight chemistry tasks. In addition to the key findings from the comprehensive benchmark analysis, our work provides insights into the limitation of current LLMs and the impact of in-context learning settings on LLMs' performance across various chemistry tasks. The code and datasets used in this study are available at //github.com/ChemFoundationModels/ChemLLMBench.

Simulations are gaining increasingly significance in the field of autonomous driving due to the demand for rapid prototyping and extensive testing. Employing physics-based simulation brings several benefits at an affordable cost, while mitigating potential risks to prototypes, drivers, and vulnerable road users. However, there exit two primary limitations. Firstly, the reality gap which refers to the disparity between reality and simulation and prevents the simulated autonomous driving systems from having the same performance in the real world. Secondly, the lack of empirical understanding regarding the behavior of real agents, such as backup drivers or passengers, as well as other road users such as vehicles, pedestrians, or cyclists. Agent simulation is commonly implemented through deterministic or randomized probabilistic pre-programmed models, or generated from real-world data; but it fails to accurately represent the behaviors adopted by real agents while interacting within a specific simulated scenario. This paper extends the description of our proposed framework to enable real-time interaction between real agents and simulated environments, by means immersive virtual reality and human motion capture systems within the CARLA simulator for autonomous driving. We have designed a set of usability examples that allow the analysis of the interactions between real pedestrians and simulated autonomous vehicles and we provide a first measure of the user's sensation of presence in the virtual environment.

Social insects such as ants communicate via pheromones which allows them to coordinate their activity and solve complex tasks as a swarm, e.g. foraging for food. This behavior was shaped through evolutionary processes. In computational models, self-coordination in swarms has been implemented using probabilistic or simple action rules to shape the decision of each agent and the collective behavior. However, manual tuned decision rules may limit the behavior of the swarm. In this work we investigate the emergence of self-coordination and communication in evolved swarms without defining any explicit rule. We evolve a swarm of agents representing an ant colony. We use an evolutionary algorithm to optimize a spiking neural network (SNN) which serves as an artificial brain to control the behavior of each agent. The goal of the evolved colony is to find optimal ways to forage for food and return it to the nest in the shortest amount of time. In the evolutionary phase, the ants are able to learn to collaborate by depositing pheromone near food piles and near the nest to guide other ants. The pheromone usage is not manually encoded into the network; instead, this behavior is established through the optimization procedure. We observe that pheromone-based communication enables the ants to perform better in comparison to colonies where communication via pheromone did not emerge. We assess the foraging performance by comparing the SNN based model to a rule based system. Our results show that the SNN based model can efficiently complete the foraging task in a short amount of time. Our approach illustrates self coordination via pheromone emerges as a result of the network optimization. This work serves as a proof of concept for the possibility of creating complex applications utilizing SNNs as underlying architectures for multi-agent interactions where communication and self-coordination is desired.

We provide a construction of Gabor frames that encode local linearizations of a signal detected on a curved smooth manifold of arbitrary dimension, with Gabor filters that can detect the presence of higher-dimensional boundaries in the manifold signal. We describe an application in configuration spaces in robotics with sharp constrains. The construction is a higher-dimensional generalization of the geometric setting developed for the study of signal analysis in the visual cortex.