FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning

Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, the large feasible model space of MRL poses significant challenges to benchmarking, and existing MRL frameworks face limitations in flexibility and scope. To address these challenges, avoid repetitive coding efforts, and ensure fair comparison of models, we introduce FlexMol, a comprehensive toolkit designed to facilitate the construction and evaluation of diverse model architectures across various datasets and performance metrics. FlexMol offers a robust suite of preset model components, including 16 drug encoders, 13 protein sequence encoders, 9 protein structure encoders, and 7 interaction layers. With its easy-to-use API and flexibility, FlexMol supports the dynamic construction of over 70, 000 distinct combinations of model architectures. Additionally, we provide detailed benchmark results and code examples to demonstrate FlexMol's effectiveness in simplifying and standardizing MRL model development and comparison.

Generative Artificial Intelligence (GAI) for Mobile Communications: A Diffusion Model Perspective

This article targets at unlocking the potentials of a class of prominent generative artificial intelligence (GAI) method, namely diffusion model (DM), for mobile communications. First, a DM-driven communication architecture is proposed, which introduces two key paradigms, i.e., conditional DM and DMdriven deep reinforcement learning (DRL), for wireless data generation and communication management, respectively. Then, we discuss the key advantages of DM-driven communication paradigms. To elaborate further, we explore DM-driven channel generation mechanisms for channel estimation, extrapolation, and feedback in multiple-input multiple-output (MIMO) systems. We showcase the numerical performance of conditional DM using the accurate DeepMIMO channel datasets, revealing its superiority in generating high-fidelity channels and mitigating unforeseen distribution shifts in sophisticated scenes. Furthermore, several DM-driven communication management designs are conceived, which is promising to deal with imperfect channels and taskoriented communications. To inspire future research developments, we highlight the potential applications and open research challenges of DM-driven communications. Code is available at https://github.com/xiaoxiaxusummer/GAI_COMM/

FlipAttack: Jailbreak LLMs via Flipping

This paper proposes a simple yet effective jailbreak attack named FlipAttack against black-box LLMs. First, from the autoregressive nature, we reveal that LLMs tend to understand the text from left to right and find that they struggle to comprehend the text when noise is added to the left side. Motivated by these insights, we propose to disguise the harmful prompt by constructing left-side noise merely based on the prompt itself, then generalize this idea to 4 flipping modes. Second, we verify the strong ability of LLMs to perform the text-flipping task, and then develop 4 variants to guide LLMs to denoise, understand, and execute harmful behaviors accurately. These designs keep FlipAttack universal, stealthy, and simple, allowing it to jailbreak black-box LLMs within only 1 query. Experiments on 8 LLMs demonstrate the superiority of FlipAttack. Remarkably, it achieves $\sim$98\% attack success rate on GPT-4o, and $\sim$98\% bypass rate against 5 guardrail models on average. The codes are available at GitHub\footnote{https://github.com/yueliu1999/FlipAttack}.

Vision Calorimeter for Anti-neutron Reconstruction: A Baseline

In high-energy physics, anti-neutrons ($\bar{n}$) are fundamental particles that frequently appear as final-state particles, and the reconstruction of their kinematic properties provides an important probe for understanding the governing principles. However, this confronts significant challenges instrumentally with the electromagnetic calorimeter (EMC), a typical experimental sensor but recovering the information of incident $\bar{n}$ insufficiently. In this study, we introduce Vision Calorimeter (ViC), a baseline method for anti-neutron reconstruction that leverages deep learning detectors to analyze the implicit relationships between EMC responses and incident $\bar{n}$ characteristics. Our motivation lies in that energy distributions of $\bar{n}$ samples deposited in the EMC cell arrays embody rich contextual information. Converted to 2-D images, such contextual energy distributions can be used to predict the status of $\bar{n}$ ($i.e.$, incident position and momentum) through a deep learning detector along with pseudo bounding boxes and a specified training objective. Experimental results demonstrate that ViC substantially outperforms the conventional reconstruction approach, reducing the prediction error of incident position by 42.81% (from 17.31$^{\circ}$ to 9.90$^{\circ}$). More importantly, this study for the first time realizes the measurement of incident $\bar{n}$ momentum, underscoring the potential of deep learning detectors for particle reconstruction. Code is available at https://github.com/yuhongtian17/ViC.

Blockchain-Enabled Accountability in Data Supply Chain: A Data Bill of Materials Approach

In the era of advanced artificial intelligence, highlighted by large-scale generative models like GPT-4, ensuring the traceability, verifiability, and reproducibility of datasets throughout their lifecycle is paramount for research institutions and technology companies. These organisations increasingly rely on vast corpora to train and fine-tune advanced AI models, resulting in intricate data supply chains that demand effective data governance mechanisms. In addition, the challenge intensifies as diverse stakeholders may use assorted tools, often without adequate measures to ensure the accountability of data and the reliability of outcomes. In this study, we adapt the concept of ``Software Bill of Materials" into the field of data governance and management to address the above challenges, and introduce ``Data Bill of Materials" (DataBOM) to capture the dependency relationship between different datasets and stakeholders by storing specific metadata. We demonstrate a platform architecture for providing blockchain-based DataBOM services, present the interaction protocol for stakeholders, and discuss the minimal requirements for DataBOM metadata. The proposed solution is evaluated in terms of feasibility and performance via case study and quantitative analysis respectively.

Local Causal Discovery with Background Knowledge

Causality plays a pivotal role in various fields of study. Based on the framework of causal graphical models, previous works have proposed identifying whether a variable is a cause or non-cause of a target in every Markov equivalent graph solely by learning a local structure. However, the presence of prior knowledge, often represented as a partially known causal graph, is common in many causal modeling applications. Leveraging this prior knowledge allows for the further identification of causal relationships. In this paper, we first propose a method for learning the local structure using all types of causal background knowledge, including direct causal information, non-ancestral information and ancestral information. Then we introduce criteria for identifying causal relationships based solely on the local structure in the presence of prior knowledge. We also apply out method to fair machine learning, and experiments involving local structure learning, causal relationship identification, and fair machine learning demonstrate that our method is both effective and efficient.

Integrating ESG and AI: A Comprehensive Responsible AI Assessment Framework

Artificial Intelligence (AI) is a widely developed and adopted technology across entire industry sectors. Integrating environmental, social, and governance (ESG) considerations with AI investments is crucial for ensuring ethical and sustainable technological advancement. Particularly from an investor perspective, this integration not only mitigates risks but also enhances long-term value creation by aligning AI initiatives with broader societal goals. Yet, this area has been less explored in both academia and industry. To bridge the gap, we introduce a novel ESG-AI framework, which is developed based on insights from engagements with 28 companies and comprises three key components. The framework provides a structured approach to this integration, developed in collaboration with industry practitioners. The ESG-AI framework provides an overview of the environmental and social impacts of AI applications, helping users such as investors assess the materiality of AI use. Moreover, it enables investors to evaluate a company's commitment to responsible AI through structured engagements and thorough assessment of specific risk areas. We have publicly released the framework and toolkit in April 2024, which has received significant attention and positive feedback from the investment community. This paper details each component of the framework, demonstrating its applicability in real-world contexts and its potential to guide ethical AI investments.

Responsible AI Question Bank: A Comprehensive Tool for AI Risk Assessment

The rapid growth of Artificial Intelligence (AI) has underscored the urgent need for responsible AI practices. Despite increasing interest, a comprehensive AI risk assessment toolkit remains lacking. This study introduces our Responsible AI (RAI) Question Bank, a comprehensive framework and tool designed to support diverse AI initiatives. By integrating AI ethics principles such as fairness, transparency, and accountability into a structured question format, the RAI Question Bank aids in identifying potential risks, aligning with emerging regulations like the EU AI Act, and enhancing overall AI governance. A key benefit of the RAI Question Bank is its systematic approach to linking lower-level risk questions to higher-level ones and related themes, preventing siloed assessments and ensuring a cohesive evaluation process. Case studies illustrate the practical application of the RAI Question Bank in assessing AI projects, from evaluating risk factors to informing decision-making processes. The study also demonstrates how the RAI Question Bank can be used to ensure compliance with standards, mitigate risks, and promote the development of trustworthy AI systems. This work advances RAI by providing organizations with a valuable tool to navigate the complexities of ethical AI development and deployment while ensuring comprehensive risk management.

Dynamic Dimension Wrapping (DDW) Algorithm: A Novel Approach for Efficient Cross-Dimensional Search in Dynamic Multidimensional Spaces

In the real world, as the complexity of optimization problems continues to increase, there is an urgent need to research more efficient optimization methods. Current optimization algorithms excel in solving problems with a fixed number of dimensions. However, their efficiency in searching dynamic multi-dimensional spaces is unsatisfactory. In response to the challenge of cross-dimensional search in multi-dimensional spaces with varying numbers of dimensions, this study proposes a new optimization algorithm-Dynamic Dimension Wrapping (DDW) algorithm. Firstly, by utilizing the Dynamic Time Warping (DTW) algorithm and Euclidean distance, a mapping relationship between different time series across dimensions is established, thus creating a fitness function suitable for dimensionally dynamic multi-dimensional space. Additionally, DDW introduces a novel, more efficient cross-dimensional search mechanism for dynamic multidimensional spaces. Finally, through comparative tests with 31 optimization algorithms in dynamic multidimensional space search, the results demonstrate that DDW exhibits outstanding search efficiency and provides search results closest to the actual optimal solution.

NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for \emph{de novo} peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and $\pi$-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark will be open-sourced to facilitate future research and application.