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Token-Mol 1.0: Tokenized drug design with large language model

arXiv.org Artificial Intelligence

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D) structures, thereby limiting their effectiveness in tasks that explicitly involve molecular conformations. In this study, we introduced Token-Mol, a token-only 3D drug design model. This model encodes all molecular information, including 2D and 3D structures, as well as molecular property data, into tokens, which transforms classification and regression tasks in drug discovery into probabilistic prediction problems, thereby enabling learning through a unified paradigm. Token-Mol is built on the transformer decoder architecture and trained using random causal masking techniques. Additionally, we proposed the Gaussian cross-entropy (GCE) loss function to overcome the challenges in regression tasks, significantly enhancing the capacity of LLMs to learn continuous numerical values. Through a combination of fine-tuning and reinforcement learning (RL), Token-Mol achieves performance comparable to or surpassing existing task-specific methods across various downstream tasks, including pocket-based molecular generation, conformation generation, and molecular property prediction. Compared to existing molecular pre-trained models, Token-Mol exhibits superior proficiency in handling a wider range of downstream tasks essential for drug design. Notably, our approach improves regression task accuracy by approximately 30% compared to similar token-only methods. Token-Mol overcomes the precision limitations of token-only models and has the potential to integrate seamlessly with general models such as ChatGPT, paving the way for the development of a universal artificial intelligence drug design model that facilitates rapid and high-quality drug design by experts.


Cooperate or Collapse: Emergence of Sustainable Cooperation in a Society of LLM Agents

arXiv.org Artificial Intelligence

As AI systems pervade human life, ensuring that large language models (LLMs) make safe decisions remains a significant challenge. We introduce the Governance of the Commons Simulation (GovSim), a generative simulation platform designed to study strategic interactions and cooperative decision-making in LLMs. In GovSim, a society of AI agents must collectively balance exploiting a common resource with sustaining it for future use. This environment enables the study of how ethical considerations, strategic planning, and negotiation skills impact cooperative outcomes. We develop an LLM-based agent architecture and test it with the leading open and closed LLMs. We find that all but the most powerful LLM agents fail to achieve a sustainable equilibrium in GovSim, with the highest survival rate below 54%. Ablations reveal that successful multi-agent communication between agents is critical for achieving cooperation in these cases. Furthermore, our analyses show that the failure to achieve sustainable cooperation in most LLMs stems from their inability to formulate and analyze hypotheses about the long-term effects of their actions on the equilibrium of the group. Finally, we show that agents that leverage "Universalization"-based reasoning, a theory of moral thinking, are able to achieve significantly better sustainability. Taken together, GovSim enables us to study the mechanisms that underlie sustainable self-government with specificity and scale. We open source the full suite of our research results, including the simulation environment, agent prompts, and a comprehensive web interface.


Search, Examine and Early-Termination: Fake News Detection with Annotation-Free Evidences

arXiv.org Artificial Intelligence

Pioneer researches recognize evidences as crucial elements in fake news detection apart from patterns. Existing evidence-aware methods either require laborious pre-processing procedures to assure relevant and high-quality evidence data, or incorporate the entire spectrum of available evidences in all news cases, regardless of the quality and quantity of the retrieved data. In this paper, we propose an approach named \textbf{SEE} that retrieves useful information from web-searched annotation-free evidences with an early-termination mechanism. The proposed SEE is constructed by three main phases: \textbf{S}earching online materials using the news as a query and directly using their titles as evidences without any annotating or filtering procedure, sequentially \textbf{E}xamining the news alongside with each piece of evidence via attention mechanisms to produce new hidden states with retrieved information, and allowing \textbf{E}arly-termination within the examining loop by assessing whether there is adequate confidence for producing a correct prediction. We have conducted extensive experiments on datasets with unprocessed evidences, i.e., Weibo21, GossipCop, and pre-processed evidences, namely Snopes and PolitiFact. The experimental results demonstrate that the proposed method outperforms state-of-the-art approaches.


A Review of the Challenges with Massive Web-mined Corpora Used in Large Language Models Pre-Training

arXiv.org Artificial Intelligence

The advent of large language models (LLMs) has heralded a new era in natural language processing (NLP), offering capabilities that range from sophisticated text generation to nuanced language understanding. These advancements have been propelled by significant improvements in model architectures, algorithms, and, crucially, the availability of extensive datasets for training. Given the data-intensive nature of these models, the quest for high-quality, diverse, and substantial datasets has become paramount. In this context, massive web-mined corpora have emerged as a vital resource, offering an abundance of textual data that mirrors the vastness and variety of human language and interaction [22, 35, 37, 42]. The internet, with its exponential growth and dynamic content, presents a near-infinite source of text data, spanning every conceivable topic, language, and style. This richness makes web-mined data an attractive foundation for training LLMs, aiming to equip them with a broad understanding of language and its applications. However, the use of such data is not without its challenges. The process of web mining--extracting data from websites--entails navigating a complex landscape of technical, legal, ethical, and quality-related issues [12, 13, 15, 43, 46]. By critically examining the use of web-mined corpora in the pre-training of LLMs, this article contributes to a nuanced understanding of the current landscape and future directions in large-scale language model development.


Virtual Agents for Alcohol Use Counseling: Exploring LLM-Powered Motivational Interviewing

arXiv.org Artificial Intelligence

We introduce a novel application of large language models (LLMs) in developing a virtual counselor capable of conducting motivational interviewing (MI) for alcohol use counseling. Access to effective counseling remains limited, particularly for substance abuse, and virtual agents offer a promising solution by leveraging LLM capabilities to simulate nuanced communication techniques inherent in MI. Our approach combines prompt engineering and integration into a user-friendly virtual platform to facilitate realistic, empathetic interactions. We evaluate the effectiveness of our virtual agent through a series of studies focusing on replicating MI techniques and human counselor dialog. Initial findings suggest that our LLM-powered virtual agent matches human counselors' empathetic and adaptive conversational skills, presenting a significant step forward in virtual health counseling and providing insights into the design and implementation of LLM-based therapeutic interactions.


African Democracy in the Era of Generative Disinformation: Challenges and Countermeasures against AI-Generated Propaganda

arXiv.org Artificial Intelligence

In light of prominent discourse around the negative implications of generative AI, an emerging area of research is investigating the current and estimated impacts of AI-generated propaganda on African citizens participating in elections. Throughout Africa, there have already been suspected cases of AI-generated propaganda influencing electoral outcomes or precipitating coups in countries like Nigeria, Burkina Faso, and Gabon, underscoring the need for comprehensive research in this domain. This paper aims to highlight the risks associated with the spread of generative AI-driven disinformation within Africa while concurrently examining the roles of government, civil society, academia, and the general public in the responsible development, practical use, and robust governance of AI. To understand how African governments might effectively counteract the impact of AI-generated propaganda, this paper presents case studies illustrating the current usage of generative AI for election-related propaganda in Africa. Subsequently, this paper discusses efforts by fact-checking organisations to mitigate the negative impacts of disinformation, explores the potential for new initiatives to actively engage citizens in literacy efforts to combat disinformation spread, and advocates for increased governmental regulatory measures. Overall, this research seeks to increase comprehension of the potential ramifications of AI-generated propaganda on democratic processes within Africa and propose actionable strategies for stakeholders to address these multifaceted challenges.


ChatGPT Doesn't Trust Chargers Fans: Guardrail Sensitivity in Context

arXiv.org Artificial Intelligence

While the biases of language models in production are extensively documented, the biases of their guardrails have been neglected. This paper studies how contextual information about the user influences the likelihood of an LLM to refuse to execute a request. By generating user biographies that offer ideological and demographic information, we find a number of biases in guardrail sensitivity on GPT-3.5. Younger, female, and Asian-American personas are more likely to trigger a refusal guardrail when requesting censored or illegal information. Guardrails are also sycophantic, refusing to comply with requests for a political position the user is likely to disagree with. We find that certain identity groups and seemingly innocuous information, e.g., sports fandom, can elicit changes in guardrail sensitivity similar to direct statements of political ideology. For each demographic category and even for American football team fandom, we find that ChatGPT appears to infer a likely political ideology and modify guardrail behavior accordingly.


TriQXNet: Forecasting Dst Index from Solar Wind Data Using an Interpretable Parallel Classical-Quantum Framework with Uncertainty Quantification

arXiv.org Artificial Intelligence

Geomagnetic storms, caused by solar wind energy transfer to Earth's magnetic field, can disrupt critical infrastructure like GPS, satellite communications, and power grids. The disturbance storm-time (Dst) index measures storm intensity. Despite advancements in empirical, physics-based, and machine-learning models using real-time solar wind data, accurately forecasting extreme geomagnetic events remains challenging due to noise and sensor failures. This research introduces TriQXNet, a novel hybrid classical-quantum neural network for Dst forecasting. Our model integrates classical and quantum computing, conformal prediction, and explainable AI (XAI) within a hybrid architecture. To ensure high-quality input data, we developed a comprehensive preprocessing pipeline that included feature selection, normalization, aggregation, and imputation. TriQXNet processes preprocessed solar wind data from NASA's ACE and NOAA's DSCOVR satellites, predicting the Dst index for the current hour and the next, providing vital advance notice to mitigate geomagnetic storm impacts. TriQXNet outperforms 13 state-of-the-art hybrid deep-learning models, achieving a root mean squared error of 9.27 nanoteslas (nT). Rigorous evaluation through 10-fold cross-validated paired t-tests confirmed its superior performance with 95% confidence. Conformal prediction techniques provide quantifiable uncertainty, which is essential for operational decisions, while XAI methods like ShapTime enhance interpretability. Comparative analysis shows TriQXNet's superior forecasting accuracy, setting a new level of expectations for geomagnetic storm prediction and highlighting the potential of classical-quantum hybrid models in space weather forecasting.


Learning treatment effects while treating those in need

arXiv.org Machine Learning

Many social programs attempt to allocate scarce resources to people with the greatest need. Indeed, public services increasingly use algorithmic risk assessments motivated by this goal. However, targeting the highest-need recipients often conflicts with attempting to evaluate the causal effect of the program as a whole, as the best evaluations would be obtained by randomizing the allocation. We propose a framework to design randomized allocation rules which optimally balance targeting high-need individuals with learning treatment effects, presenting policymakers with a Pareto frontier between the two goals. We give sample complexity guarantees for the policy learning problem and provide a computationally efficient strategy to implement it. We then apply our framework to data from human services in Allegheny County, Pennsylvania. Optimized policies can substantially mitigate the tradeoff between learning and targeting. For example, it is often possible to obtain 90% of the optimal utility in targeting high-need individuals while ensuring that the average treatment effect can be estimated with less than 2 times the samples that a randomized controlled trial would require. Mechanisms for targeting public services often focus on measuring need as accurately as possible. However, our results suggest that algorithmic systems in public services can be most impactful if they incorporate program evaluation as an explicit goal alongside targeting.


Long-Term Fairness in Sequential Multi-Agent Selection with Positive Reinforcement

arXiv.org Machine Learning

While much of the rapidly growing literature on fair decision-making focuses on metrics for one-shot decisions, recent work has raised the intriguing possibility of designing sequential decision-making to positively impact long-term social fairness. In selection processes such as college admissions or hiring, biasing slightly towards applicants from under-represented groups is hypothesized to provide positive feedback that increases the pool of under-represented applicants in future selection rounds, thus enhancing fairness in the long term. In this paper, we examine this hypothesis and its consequences in a setting in which multiple agents are selecting from a common pool of applicants. We propose the Multi-agent Fair-Greedy policy, that balances greedy score maximization and fairness. Under this policy, we prove that the resource pool and the admissions converge to a long-term fairness target set by the agents when the score distributions across the groups in the population are identical. We provide empirical evidence of existence of equilibria under non-identical score distributions through synthetic and adapted real-world datasets. We then sound a cautionary note for more complex applicant pool evolution models, under which uncoordinated behavior by the agents can cause negative reinforcement, leading to a reduction in the fraction of under-represented applicants. Our results indicate that, while positive reinforcement is a promising mechanism for long-term fairness, policies must be designed carefully to be robust to variations in the evolution model, with a number of open issues that remain to be explored by algorithm designers, social scientists, and policymakers.