Gupta, Prateek
OASIS: Open Agent Social Interaction Simulations with One Million Agents
Yang, Ziyi, Zhang, Zaibin, Zheng, Zirui, Jiang, Yuxian, Gan, Ziyue, Wang, Zhiyu, Ling, Zijian, Chen, Jinsong, Ma, Martz, Dong, Bowen, Gupta, Prateek, Hu, Shuyue, Yin, Zhenfei, Li, Guohao, Jia, Xu, Wang, Lijun, Ghanem, Bernard, Lu, Huchuan, Lu, Chaochao, Ouyang, Wanli, Qiao, Yu, Torr, Philip, Shao, Jing
There has been a growing interest in enhancing rule-based agent-based models (ABMs) for social media platforms (i.e., X, Reddit) with more realistic large language model (LLM) agents, thereby allowing for a more nuanced study of complex systems. As a result, several LLM-based ABMs have been proposed in the past year. While they hold promise, each simulator is specifically designed to study a particular scenario, making it time-consuming and resource-intensive to explore other phenomena using the same ABM. Additionally, these models simulate only a limited number of agents, whereas real-world social media platforms involve millions of users. To this end, we propose OASIS, a generalizable and scalable social media simulator. OASIS is designed based on real-world social media platforms, incorporating dynamically updated environments (i.e., dynamic social networks and post information), diverse action spaces (i.e., following, commenting), and recommendation systems (i.e., interest-based and hot-score-based). Additionally, OASIS supports large-scale user simulations, capable of modeling up to one million users. With these features, OASIS can be easily extended to different social media platforms to study large-scale group phenomena and behaviors. We replicate various social phenomena, including information spreading, group polarization, and herd effects across X and Reddit platforms. Moreover, we provide observations of social phenomena at different agent group scales. We observe that the larger agent group scale leads to more enhanced group dynamics and more diverse and helpful agents' opinions. These findings demonstrate OASIS's potential as a powerful tool for studying complex systems in digital environments.
Machine learning and optimization-based approaches to duality in statistical physics
Ferrari, Andrea E. V., Gupta, Prateek, Iqbal, Nabil
The notion of duality -- that a given physical system can have two different mathematical descriptions -- is a key idea in modern theoretical physics. Establishing a duality in lattice statistical mechanics models requires the construction of a dual Hamiltonian and a map from the original to the dual observables. By using simple neural networks to parameterize these maps and introducing a loss function that penalises the difference between correlation functions in original and dual models, we formulate the process of duality discovery as an optimization problem. We numerically solve this problem and show that our framework can rediscover the celebrated Kramers-Wannier duality for the 2d Ising model, reconstructing the known mapping of temperatures. We also discuss an alternative approach which uses known features of the mapping of topological lines to reduce the problem to optimizing the couplings in a dual Hamiltonian, and explore next-to-nearest neighbour deformations of the 2d Ising duality. We discuss future directions and prospects for discovering new dualities within this framework.
Generative Active Learning for the Search of Small-molecule Protein Binders
Korablyov, Maksym, Liu, Cheng-Hao, Jain, Moksh, van der Sloot, Almer M., Jolicoeur, Eric, Ruediger, Edward, Nica, Andrei Cristian, Bengio, Emmanuel, Lapchevskyi, Kostiantyn, St-Cyr, Daniel, Schuetz, Doris Alexandra, Butoi, Victor Ion, Rector-Brooks, Jarrid, Blackburn, Simon, Feng, Leo, Nekoei, Hadi, Gottipati, SaiKrishna, Vijayan, Priyesh, Gupta, Prateek, Rampรกลกek, Ladislav, Avancha, Sasikanth, Bacon, Pierre-Luc, Hamilton, William L., Paige, Brooks, Misra, Sanchit, Jastrzebski, Stanislaw Kamil, Kaul, Bharat, Precup, Doina, Hernรกndez-Lobato, Josรฉ Miguel, Segler, Marwin, Bronstein, Michael, Marinier, Anne, Tyers, Mike, Bengio, Yoshua
Despite substantial progress in machine learning for scientific discovery in recent years, truly de novo design of small molecules which exhibit a property of interest remains a significant challenge. We introduce LambdaZero, a generative active learning approach to search for synthesizable molecules. Powered by deep reinforcement learning, LambdaZero learns to search over the vast space of molecules to discover candidates with a desired property. We apply LambdaZero with molecular docking to design novel small molecules that inhibit the enzyme soluble Epoxide Hydrolase 2 (sEH), while enforcing constraints on synthesizability and drug-likeliness. LambdaZero provides an exponential speedup in terms of the number of calls to the expensive molecular docking oracle, and LambdaZero de novo designed molecules reach docking scores that would otherwise require the virtual screening of a hundred billion molecules. Importantly, LambdaZero discovers novel scaffolds of synthesizable, drug-like inhibitors for sEH. In in vitro experimental validation, a series of ligands from a generated quinazoline-based scaffold were synthesized, and the lead inhibitor N-(4,6-di(pyrrolidin-1-yl)quinazolin-2-yl)-N-methylbenzamide (UM0152893) displayed sub-micromolar enzyme inhibition of sEH.
AI For Global Climate Cooperation 2023 Competition Proceedings
Bengio, Yoshua, Gupta, Prateek, Li, Lu, Phade, Soham, Srinivasa, Sunil, Williams, Andrew, Zhang, Tianyu, Zhang, Yang, Zheng, Stephan
The international community must collaborate to mitigate climate change and sustain economic growth. However, collaboration is hard to achieve, partly because no global authority can ensure compliance with international climate agreements. Combining AI with climate-economic simulations offers a promising solution to design international frameworks, including negotiation protocols and climate agreements, that promote and incentivize collaboration. In addition, these frameworks should also have policy goals fulfillment, and sustained commitment, taking into account climate-economic dynamics and strategic behaviors. These challenges require an interdisciplinary approach across machine learning, economics, climate science, law, policy, ethics, and other fields. Towards this objective, we organized AI for Global Climate Cooperation, a Mila competition in which teams submitted proposals and analyses of international frameworks, based on (modifications of) RICE-N, an AI-driven integrated assessment model (IAM). In particular, RICE-N supports modeling regional decision-making using AI agents. Furthermore, the IAM then models the climate-economic impact of those decisions into the future. Whereas the first track focused only on performance metrics, the proposals submitted to the second track were evaluated both quantitatively and qualitatively. The quantitative evaluation focused on a combination of (i) the degree of mitigation of global temperature rise and (ii) the increase in economic productivity. On the other hand, an interdisciplinary panel of human experts in law, policy, sociology, economics and environmental science, evaluated the solutions qualitatively. In particular, the panel considered the effectiveness, simplicity, feasibility, ethics, and notions of climate justice of the protocols. In the third track, the participants were asked to critique and improve RICE-N.
GNN-Assisted Phase Space Integration with Application to Atomistics
Saxena, Shashank, Bastek, Jan-Hendrik, Spinola, Miguel, Gupta, Prateek, Kochmann, Dennis M.
Overcoming the time scale limitations of atomistics can be achieved by switching from the state-space representation of Molecular Dynamics (MD) to a statistical-mechanics-based representation in phase space, where approximations such as maximum-entropy or Gaussian phase packets (GPP) evolve the atomistic ensemble in a time-coarsened fashion. In practice, this requires the computation of expensive high-dimensional integrals over all of phase space of an atomistic ensemble. This, in turn, is commonly accomplished efficiently by low-order numerical quadrature. We show that numerical quadrature in this context, unfortunately, comes with a set of inherent problems, which corrupt the accuracy of simulations -- especially when dealing with crystal lattices with imperfections. As a remedy, we demonstrate that Graph Neural Networks, trained on Monte-Carlo data, can serve as a replacement for commonly used numerical quadrature rules, overcoming their deficiencies and significantly improving the accuracy. This is showcased by three benchmarks: the thermal expansion of copper, the martensitic phase transition of iron, and the energy of grain boundaries. We illustrate the benefits of the proposed technique over classically used third- and fifth-order Gaussian quadrature, we highlight the impact on time-coarsened atomistic predictions, and we discuss the computational efficiency. The latter is of general importance when performing frequent evaluation of phase space or other high-dimensional integrals, which is why the proposed framework promises applications beyond the scope of atomistics.
Lookback for Learning to Branch
Gupta, Prateek, Khalil, Elias B., Chetรฉlat, Didier, Gasse, Maxime, Bengio, Yoshua, Lodi, Andrea, Kumar, M. Pawan
The expressive and computationally inexpensive bipartite Graph Neural Networks (GNN) have been shown to be an important component of deep learning based Mixed-Integer Linear Program (MILP) solvers. Recent works have demonstrated the effectiveness of such GNNs in replacing the branching (variable selection) heuristic in branch-and-bound (B&B) solvers. These GNNs are trained, offline and on a collection of MILPs, to imitate a very good but computationally expensive branching heuristic, strong branching. Given that B&B results in a tree of sub-MILPs, we ask (a) whether there are strong dependencies exhibited by the target heuristic among the neighboring nodes of the B&B tree, and (b) if so, whether we can incorporate them in our training procedure. Specifically, we find that with the strong branching heuristic, a child node's best choice was often the parent's second-best choice. We call this the "lookback" phenomenon. Surprisingly, the typical branching GNN of Gasse et al. (2019) often misses this simple "answer". To imitate the target behavior more closely by incorporating the lookback phenomenon in GNNs, we propose two methods: (a) target smoothing for the standard cross-entropy loss function, and (b) adding a Parent-as-Target (PAT) Lookback regularizer term. Finally, we propose a model selection framework to incorporate harder-to-formulate objectives such as solving time in the final models. Through extensive experimentation on standard benchmark instances, we show that our proposal results in up to 22% decrease in the size of the B&B tree and up to 15% improvement in the solving times.
Ship Performance Monitoring using Machine-learning
Gupta, Prateek, Rasheed, Adil, Steen, Sverre
The hydrodynamic performance of a sea-going ship varies over its lifespan due to factors like marine fouling and the condition of the anti-fouling paint system. In order to accurately estimate the power demand and fuel consumption for a planned voyage, it is important to assess the hydrodynamic performance of the ship. The current work uses machine-learning (ML) methods to estimate the hydrodynamic performance of a ship using the onboard recorded in-service data. Three ML methods, NL-PCR, NL-PLSR and probabilistic ANN, are calibrated using the data from two sister ships. The calibrated models are used to extract the varying trend in ship's hydrodynamic performance over time and predict the change in performance through several propeller and hull cleaning events. The predicted change in performance is compared with the corresponding values estimated using the fouling friction coefficient ($\Delta C_F$). The ML methods are found to be performing well while modelling the hydrodynamic state variables of the ships with probabilistic ANN model performing the best, but the results from NL-PCR and NL-PLSR are not far behind, indicating that it may be possible to use simple methods to solve such problems with the help of domain knowledge.
Hybrid Models for Learning to Branch
Gupta, Prateek, Gasse, Maxime, Khalil, Elias B., Kumar, M. Pawan, Lodi, Andrea, Bengio, Yoshua
A recent Graph Neural Network (GNN) approach for learning to branch has been shown to successfully reduce the running time of branch-and-bound algorithms for Mixed Integer Linear Programming (MILP). While the GNN relies on a GPU for inference, MILP solvers are purely CPU-based. This severely limits its application as many practitioners may not have access to high-end GPUs. In this work, we ask two key questions. First, in a more realistic setting where only a CPU is available, is the GNN model still competitive? Second, can we devise an alternate computationally inexpensive model that retains the predictive power of the GNN architecture? We answer the first question in the negative, and address the second question by proposing a new hybrid architecture for efficient branching on CPU machines. The proposed architecture combines the expressive power of GNNs with computationally inexpensive multi-layer perceptrons (MLP) for branching. We evaluate our methods on four classes of MILP problems, and show that they lead to up to 26% reduction in solver running time compared to state-of-the-art methods without a GPU, while extrapolating to harder problems than it was trained on. The code for this project is publicly available at https://github.com/pg2455/Hybrid-learn2branch.
Predicting Infectiousness for Proactive Contact Tracing
Bengio, Yoshua, Gupta, Prateek, Maharaj, Tegan, Rahaman, Nasim, Weiss, Martin, Deleu, Tristan, Muller, Eilif, Qu, Meng, Schmidt, Victor, St-Charles, Pierre-Luc, Alsdurf, Hannah, Bilanuik, Olexa, Buckeridge, David, Caron, Gรกetan Marceau, Carrier, Pierre-Luc, Ghosn, Joumana, Ortiz-Gagne, Satya, Pal, Chris, Rish, Irina, Schรถlkopf, Bernhard, Sharma, Abhinav, Tang, Jian, Williams, Andrew
The COVID-19 pandemic has spread rapidly worldwide, overwhelming manual contact tracing in many countries and resulting in widespread lockdowns for emergency containment. Various DCT methods have been proposed, each making tradeoffs between privacy, mobility restrictions, and public health. The most common approach, binary contact tracing (BCT), models infection as a binary event, informed only by an individual's test results, with corresponding binary recommendations that either all or none of the individual's contacts quarantine. BCT ignores the inherent uncertainty in contacts and the infection process, which could be used to tailor messaging to high-risk individuals, and prompt proactive testing or earlier warnings. It also does not make use of observations such as symptoms or preexisting medical conditions, which could be used to make more accurate infectiousness predictions. In this paper, we use a recently-proposed COVID-19 epidemiological simulator to develop and test methods that can be deployed to a smartphone to locally and proactively predict an individual's infectiousness (risk of infecting others) based on their contact history and other information, while respecting strong privacy constraints. Predictions are used to provide personalized recommendations to the individual via an app, as well as to send anonymized messages to the individual's contacts, who use this information to better predict their own infectiousness, an approach we call proactive contact tracing (PCT). Similarly to other works, we find that compared to no tracing, all DCT methods tested are able to reduce spread of the disease and thus save lives, even at low adoption rates, strongly supporting a role for DCT methods in managing the pandemic. Further, we find a deep-learning based PCT method which improves over BCT for equivalent average mobility, suggesting PCT could help in safe reopening and second-wave prevention. Until pharmaceutical interventions such as a vaccine become available, control of the COVID-19 pandemic relies on nonpharmaceutical interventions such as lockdown and social distancing. While these have often been successful in limiting spread of the disease in the short term, these restrictive measures have important negative social, mental health, and economic impacts. Digital contact tracing (DCT), a technique to track the spread of the virus among individuals in a population using smartphones, is an attractive potential solution to help reduce growth in the number of cases and thereby allow more economic and social activities to resume while keeping the number of cases low. All bolded terms are defined in the Glossary; Appendix 1.
COVI White Paper
Alsdurf, Hannah, Belliveau, Edmond, Bengio, Yoshua, Deleu, Tristan, Gupta, Prateek, Ippolito, Daphne, Janda, Richard, Jarvie, Max, Kolody, Tyler, Krastev, Sekoul, Maharaj, Tegan, Obryk, Robert, Pilat, Dan, Pisano, Valerie, Prud'homme, Benjamin, Qu, Meng, Rahaman, Nasim, Rish, Irina, Rousseau, Jean-Francois, Sharma, Abhinav, Struck, Brooke, Tang, Jian, Weiss, Martin, Yu, Yun William
The SARS-CoV-2 (Covid-19) pandemic has caused significant strain on public health institutions around the world. Contact tracing is an essential tool to change the course of the Covid-19 pandemic. Manual contact tracing of Covid-19 cases has significant challenges that limit the ability of public health authorities to minimize community infections. Personalized peer-to-peer contact tracing through the use of mobile apps has the potential to shift the paradigm. Some countries have deployed centralized tracking systems, but more privacy-protecting decentralized systems offer much of the same benefit without concentrating data in the hands of a state authority or for-profit corporations. Machine learning methods can circumvent some of the limitations of standard digital tracing by incorporating many clues and their uncertainty into a more graded and precise estimation of infection risk. The estimated risk can provide early risk awareness, personalized recommendations and relevant information to the user. Finally, non-identifying risk data can inform epidemiological models trained jointly with the machine learning predictor. These models can provide statistical evidence for the importance of factors involved in disease transmission. They can also be used to monitor, evaluate and optimize health policy and (de)confinement scenarios according to medical and economic productivity indicators. However, such a strategy based on mobile apps and machine learning should proactively mitigate potential ethical and privacy risks, which could have substantial impacts on society (not only impacts on health but also impacts such as stigmatization and abuse of personal data). Here, we present an overview of the rationale, design, ethical considerations and privacy strategy of `COVI,' a Covid-19 public peer-to-peer contact tracing and risk awareness mobile application developed in Canada.