Christian Borgs

Zhiling Zheng, Oufan Zhang, Christian Borgs et al.

We use prompt engineering to guide ChatGPT in the automation of text mining of metal-organic frameworks (MOFs) synthesis conditions from diverse formats and styles of the scientific literature. This effectively mitigates ChatGPT's tendency to hallucinate information -- an issue that previously made the use of Large Language Models (LLMs) in scientific fields challenging. Our approach involves the development of a workflow implementing three different processes for text mining, programmed by ChatGPT itself. All of them enable parsing, searching, filtering, classification, summarization, and data unification with different tradeoffs between labor, speed, and accuracy. We deploy this system to extract 26,257 distinct synthesis parameters pertaining to approximately 800 MOFs sourced from peer-reviewed research articles. This process incorporates our ChemPrompt Engineering strategy to instruct ChatGPT in text mining, resulting in impressive precision, recall, and F1 scores of 90-99%. Furthermore, with the dataset built by text mining, we constructed a machine-learning model with over 86% accuracy in predicting MOF experimental crystallization outcomes and preliminarily identifying important factors in MOF crystallization. We also developed a reliable data-grounded MOF chatbot to answer questions on chemical reactions and synthesis procedures. Given that the process of using ChatGPT reliably mines and tabulates diverse MOF synthesis information in a unified format, while using only narrative language requiring no coding expertise, we anticipate that our ChatGPT Chemistry Assistant will be very useful across various other chemistry sub-disciplines.

Zhiling Zheng, Zichao Rong, Nakul Rampal et al.

We present a new framework integrating the AI model GPT-4 into the iterative process of reticular chemistry experimentation, leveraging a cooperative workflow of interaction between AI and a human researcher. This GPT-4 Reticular Chemist is an integrated system composed of three phases. Each of these utilizes GPT-4 in various capacities, wherein GPT-4 provides detailed instructions for chemical experimentation and the human provides feedback on the experimental outcomes, including both success and failures, for the in-context learning of AI in the next iteration. This iterative human-AI interaction enabled GPT-4 to learn from the outcomes, much like an experienced chemist, by a prompt-learning strategy. Importantly, the system is based on natural language for both development and operation, eliminating the need for coding skills, and thus, make it accessible to all chemists. Our collaboration with GPT-4 Reticular Chemist guided the discovery of an isoreticular series of MOFs, with each synthesis fine-tuned through iterative feedback and expert suggestions. This workflow presents a potential for broader applications in scientific research by harnessing the capability of large language models like GPT-4 to enhance the feasibility and efficiency of research activities.

Shengchao Liu, Weitao Du, Yanjing Li et al.

Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these scientific problems, molecules serve as the fundamental building blocks, and machine learning has emerged as a highly effective and powerful tool for modeling their geometric structures. Nevertheless, due to the rapidly evolving process of the field and the knowledge gap between science (e.g., physics, chemistry, & biology) and machine learning communities, a benchmarking study on geometrical representation for such data has not been conducted. To address such an issue, in this paper, we first provide a unified view of the current symmetry-informed geometric methods, classifying them into three main categories: invariance, equivariance with spherical frame basis, and equivariance with vector frame basis. Then we propose a platform, coined Geom3D, which enables benchmarking the effectiveness of geometric strategies. Geom3D contains 16 advanced symmetry-informed geometric representation models and 14 geometric pretraining methods over 46 diverse datasets, including small molecules, proteins, and crystalline materials. We hope that Geom3D can, on the one hand, eliminate barriers for machine learning researchers interested in exploring scientific problems; and, on the other hand, provide valuable guidance for researchers in computational chemistry, structural biology, and materials science, aiding in the informed selection of representation techniques for specific applications.

Shengchao Liu, Divin Yan, Weitao Du et al.

Artificial intelligence models have shown great potential in structure-based drug design, generating ligands with high binding affinities. However, existing models have often overlooked a crucial physical constraint: atoms must maintain a minimum pairwise distance to avoid separation violation, a phenomenon governed by the balance of attractive and repulsive forces. To mitigate such separation violations, we propose NucleusDiff. It models the interactions between atomic nuclei and their surrounding electron clouds by enforcing the distance constraint between the nuclei and manifolds. We quantitatively evaluate NucleusDiff using the CrossDocked2020 dataset and a COVID-19 therapeutic target, demonstrating that NucleusDiff reduces violation rate by up to 100.00% and enhances binding affinity by up to 22.16%, surpassing state-of-the-art models for structure-based drug design. We also provide qualitative analysis through manifold sampling, visually confirming the effectiveness of NucleusDiff in reducing separation violations and improving binding affinities.

Nakul Rampal, Kaiyu Wang, Matthew Burigana et al.

The rapid advancement in artificial intelligence and natural language processing has led to the development of large-scale datasets aimed at benchmarking the performance of machine learning models. Herein, we introduce 'RetChemQA,' a comprehensive benchmark dataset designed to evaluate the capabilities of such models in the domain of reticular chemistry. This dataset includes both single-hop and multi-hop question-answer pairs, encompassing approximately 45,000 Q&As for each type. The questions have been extracted from an extensive corpus of literature containing about 2,530 research papers from publishers including NAS, ACS, RSC, Elsevier, and Nature Publishing Group, among others. The dataset has been generated using OpenAI's GPT-4 Turbo, a cutting-edge model known for its exceptional language understanding and generation capabilities. In addition to the Q&A dataset, we also release a dataset of synthesis conditions extracted from the corpus of literature used in this study. The aim of RetChemQA is to provide a robust platform for the development and evaluation of advanced machine learning algorithms, particularly for the reticular chemistry community. The dataset is structured to reflect the complexities and nuances of real-world scientific discourse, thereby enabling nuanced performance assessments across a variety of tasks. The dataset is available at the following link: https://github.com/nakulrampal/RetChemQA

Yeganeh Alimohammadi, Karissa Huang, Christian Borgs et al.

Online social platforms increasingly rely on crowd-sourced systems to label misleading content at scale, but these systems must both aggregate users' evaluations and decide whose evaluations to trust. To address the latter, many platforms audit users by rewarding agreement with the final aggregate outcome, a design we term consensus-based auditing. We analyze the consequences of this design in X's Community Notes, which in September 2022 adopted consensus-based auditing that ties users' eligibility for participation to agreement with the eventual platform outcome. We find evidence of strategic conformity: minority contributors' evaluations drift toward the majority and their participation share falls on controversial topics, where independent signals matter most. We formalize this mechanism in a behavioral model in which contributors trade off private beliefs against anticipated penalties for disagreement. Motivated by these findings, we propose a two-stage auditing and aggregation algorithm that weights contributors by the stability of their past residuals rather than by agreement with the majority. The method first accounts for differences across content and contributors, and then measures how predictable each contributor's evaluations are relative to the latent-factor model. Contributors whose evaluations are consistently informative receive greater influence in aggregation, even when they disagree with the prevailing consensus. In the Community Notes data, this approach improves out-of-sample predictive performance while avoiding penalization of disagreement.

Zhiling Zheng, Zhiguo He, Omar Khattab et al.

The integration of artificial intelligence into scientific research has reached a new pinnacle with GPT-4V, a large language model featuring enhanced vision capabilities, accessible through ChatGPT or an API. This study demonstrates the remarkable ability of GPT-4V to navigate and obtain complex data for metal-organic frameworks, especially from graphical sources. Our approach involved an automated process of converting 346 scholarly articles into 6240 images, which represents a benchmark dataset in this task, followed by deploying GPT-4V to categorize and analyze these images using natural language prompts. This methodology enabled GPT-4V to accurately identify and interpret key plots integral to MOF characterization, such as nitrogen isotherms, PXRD patterns, and TGA curves, among others, with accuracy and recall above 93%. The model's proficiency in extracting critical information from these plots not only underscores its capability in data mining but also highlights its potential in aiding the creation of comprehensive digital databases for reticular chemistry. In addition, the extracted nitrogen isotherm data from the selected literature allowed for a comparison between theoretical and experimental porosity values for over 200 compounds, highlighting certain discrepancies and underscoring the importance of integrating computational and experimental data. This work highlights the potential of AI in accelerating scientific discovery and innovation, bridging the gap between computational tools and experimental research, and paving the way for more efficient, inclusive, and comprehensive scientific inquiry.

Theo Jaffrelot Inizan, Sherry Yang, Aaron Kaplan et al.

Generative models and machine learning promise accelerated material discovery in MOFs for CO2 capture and water harvesting but face significant challenges navigating vast chemical spaces while ensuring synthetizability. Here, we present MOFGen, a system of Agentic AI comprising interconnected agents: a large language model that proposes novel MOF compositions, a diffusion model that generates crystal structures, quantum mechanical agents that optimize and filter candidates, and synthetic-feasibility agents guided by expert rules and machine learning. Trained on all experimentally reported MOFs and computational databases, MOFGen generated hundreds of thousands of novel MOF structures and synthesizable organic linkers. Our methodology was validated through high-throughput experiments and the successful synthesis of five "AI-dreamt" MOFs, representing a major step toward automated synthesizable material discovery.

Elena Rohde, Jonas Klingwort, Christian Borgs

This paper presents a meta-analysis evaluating ML performance in sentiment analysis for Twitter data. The study aims to estimate the average performance, assess heterogeneity between and within studies, and analyze how study characteristics influence model performance. Using PRISMA guidelines, we searched academic databases and selected 195 trials from 20 studies with 12 study features. Overall accuracy, the most reported performance metric, was analyzed using double arcsine transformation and a three-level random effects model. The average overall accuracy of the AIC-optimized model was 0.80 [0.76, 0.84]. This paper provides two key insights: 1) Overall accuracy is widely used but often misleading due to its sensitivity to class imbalance and the number of sentiment classes, highlighting the need for normalization. 2) Standardized reporting of model performance, including reporting confusion matrices for independent test sets, is essential for reliable comparisons of ML classifiers across studies, which seems far from common practice.

Shengchao Liu, Weitao Du, Hannan Xu et al.

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of improving the efficiency of MD simulations through better numerical methods and, more recently, by utilizing machine learning (ML) methods. Yet, challenges remain, such as accurate modeling of extended-timescale simulations. To address this issue, we propose NeuralMD, the first ML surrogate that can facilitate numerical MD and provide accurate simulations in protein-ligand binding dynamics. We propose a principled approach that incorporates a novel physics-informed multi-grained group symmetric framework. Specifically, we propose (1) the BindingNet model that satisfies group symmetry using vector frames and captures the multi-level protein-ligand interactions, and (2) an augmented neural differential equation solver that learns the trajectory under Newtonian mechanics. For the experiment, we design ten single-trajectory and three multi-trajectory binding simulation tasks. We demonstrate the efficiency and effectiveness of NeuralMD, achieving over 1K$\times$ speedup compared to standard numerical MD simulations. NeuralMD also outperforms all other ML approaches, achieving up to 15$\times$ reduction in reconstruction error and 70% increase in validity. Additionally, we qualitatively illustrate that the oscillations in the predicted trajectories align more closely with ground-truth dynamics than those of other machine-learning methods. We believe NeuralMD paves the foundation for a new research paradigm in simulating protein-ligand dynamics.

Christian Borgs, Jennifer Chayes, Christian Ikeokwu et al.

On social networks, algorithmic personalization drives users into filter bubbles where they rarely see content that deviates from their interests. We present a model for content curation and personalization that avoids filter bubbles, along with algorithmic guarantees and nearly matching lower bounds. In our model, the platform interacts with $n$ users over $T$ timesteps, choosing content for each user from $k$ categories. The platform receives stochastic rewards as in a multi-arm bandit. To avoid filter bubbles, we draw on the intuition that if some users are shown some category of content, then all users should see at least a small amount of that content. We first analyze a naive formalization of this intuition and show it has unintended consequences: it leads to ``tyranny of the majority'' with the burden of diversification borne disproportionately by those with minority interests. This leads us to our model which distributes this burden more equitably. We require that the probability any user is shown a particular type of content is at least $γ$ times the average probability all users are shown that type of content. Full personalization corresponds to $γ= 0$ and complete homogenization corresponds to $γ= 1$; hence, $γ$ encodes a hard cap on the level of personalization. We also analyze additional formulations where the platform can exceed its cap but pays a penalty proportional to its constraint violation. We provide algorithmic guarantees for optimizing recommendations subject to these constraints. These include nearly matching upper and lower bounds for the entire range of $γ\in [0,1]$ showing that the reward of a multi-agent variant of UCB is nearly optimal. Using real-world preference data, we empirically verify that under our model, users share the burden of diversification with only minor utility loss under our constraints.

Lydia T. Liu, Nikhil Garg, Christian Borgs

Strategic classification studies the design of a classifier robust to the manipulation of input by strategic individuals. However, the existing literature does not consider the effect of competition among individuals as induced by the algorithm design. Motivated by constrained allocation settings such as college admissions, we introduce strategic ranking, in which the (designed) individual reward depends on an applicant's post-effort rank in a measurement of interest. Our results illustrate how competition among applicants affects the resulting equilibria and model insights. We analyze how various ranking reward designs, belonging to a family of step functions, trade off applicant, school, and societal utility, as well as how ranking design counters inequities arising from disparate access to resources. In particular, we find that randomization in the reward design can mitigate two measures of disparate impact, welfare gap and access.

Alexey Romanov, Maria De-Arteaga, Hanna Wallach et al.

There is a growing body of work that proposes methods for mitigating bias in machine learning systems. These methods typically rely on access to protected attributes such as race, gender, or age. However, this raises two significant challenges: (1) protected attributes may not be available or it may not be legal to use them, and (2) it is often desirable to simultaneously consider multiple protected attributes, as well as their intersections. In the context of mitigating bias in occupation classification, we propose a method for discouraging correlation between the predicted probability of an individual's true occupation and a word embedding of their name. This method leverages the societal biases that are encoded in word embeddings, eliminating the need for access to protected attributes. Crucially, it only requires access to individuals' names at training time and not at deployment time. We evaluate two variations of our proposed method using a large-scale dataset of online biographies. We find that both variations simultaneously reduce race and gender biases, with almost no reduction in the classifier's overall true positive rate.

Maria De-Arteaga, Alexey Romanov, Hanna Wallach et al.

We present a large-scale study of gender bias in occupation classification, a task where the use of machine learning may lead to negative outcomes on peoples' lives. We analyze the potential allocation harms that can result from semantic representation bias. To do so, we study the impact on occupation classification of including explicit gender indicators---such as first names and pronouns---in different semantic representations of online biographies. Additionally, we quantify the bias that remains when these indicators are "scrubbed," and describe proxy behavior that occurs in the absence of explicit gender indicators. As we demonstrate, differences in true positive rates between genders are correlated with existing gender imbalances in occupations, which may compound these imbalances.

Christian Borgs, Jennifer Chayes, Adam Smith et al.

We consider the following fundamental question on $ε$-differential privacy. Consider an arbitrary $ε$-differentially private algorithm defined on a subset of the input space. Is it possible to extend it to an $ε'$-differentially private algorithm on the whole input space for some $ε'$ comparable with $ε$? In this note we answer affirmatively this question for $ε'=2ε$. Our result applies to every input metric space and space of possible outputs. This result originally appeared in a recent paper by the authors [BCSZ18]. We present a self-contained version in this note, in the hopes that it will be broadly useful.

Christian Borgs, Jennifer Chayes, Adam Smith et al.

Motivated by growing concerns over ensuring privacy on social networks, we develop new algorithms and impossibility results for fitting complex statistical models to network data subject to rigorous privacy guarantees. We consider the so-called node-differentially private algorithms, which compute information about a graph or network while provably revealing almost no information about the presence or absence of a particular node in the graph. We provide new algorithms for node-differentially private estimation for a popular and expressive family of network models: stochastic block models and their generalization, graphons. Our algorithms improve on prior work, reducing their error quadratically and matching, in many regimes, the optimal nonprivate algorithm. We also show that for the simplest random graph models ($G(n,p)$ and $G(n,m)$), node-private algorithms can be qualitatively more accurate than for more complex models---converging at a rate of $\frac{1}{ε^2 n^{3}}$ instead of $\frac{1}{ε^2 n^2}$. This result uses a new extension lemma for differentially private algorithms that we hope will be broadly useful.

Pratik Chaudhari, Anna Choromanska, Stefano Soatto et al.

This paper proposes a new optimization algorithm called Entropy-SGD for training deep neural networks that is motivated by the local geometry of the energy landscape. Local extrema with low generalization error have a large proportion of almost-zero eigenvalues in the Hessian with very few positive or negative eigenvalues. We leverage upon this observation to construct a local-entropy-based objective function that favors well-generalizable solutions lying in large flat regions of the energy landscape, while avoiding poorly-generalizable solutions located in the sharp valleys. Conceptually, our algorithm resembles two nested loops of SGD where we use Langevin dynamics in the inner loop to compute the gradient of the local entropy before each update of the weights. We show that the new objective has a smoother energy landscape and show improved generalization over SGD using uniform stability, under certain assumptions. Our experiments on convolutional and recurrent networks demonstrate that Entropy-SGD compares favorably to state-of-the-art techniques in terms of generalization error and training time.

Carlo Baldassi, Christian Borgs, Jennifer Chayes et al.

In artificial neural networks, learning from data is a computationally demanding task in which a large number of connection weights are iteratively tuned through stochastic-gradient-based heuristic processes over a cost-function. It is not well understood how learning occurs in these systems, in particular how they avoid getting trapped in configurations with poor computational performance. Here we study the difficult case of networks with discrete weights, where the optimization landscape is very rough even for simple architectures, and provide theoretical and numerical evidence of the existence of rare - but extremely dense and accessible - regions of configurations in the network weight space. We define a novel measure, which we call the "robust ensemble" (RE), which suppresses trapping by isolated configurations and amplifies the role of these dense regions. We analytically compute the RE in some exactly solvable models, and also provide a general algorithmic scheme which is straightforward to implement: define a cost-function given by a sum of a finite number of replicas of the original cost-function, with a constraint centering the replicas around a driving assignment. To illustrate this, we derive several powerful new algorithms, ranging from Markov Chains to message passing to gradient descent processes, where the algorithms target the robust dense states, resulting in substantial improvements in performance. The weak dependence on the number of precision bits of the weights leads us to conjecture that very similar reasoning applies to more conventional neural networks. Analogous algorithmic schemes can also be applied to other optimization problems.

Furong Huang, Animashree Anandkumar, Christian Borgs et al.

Cataloging the neuronal cell types that comprise circuitry of individual brain regions is a major goal of modern neuroscience and the BRAIN initiative. Single-cell RNA sequencing can now be used to measure the gene expression profiles of individual neurons and to categorize neurons based on their gene expression profiles. While the single-cell techniques are extremely powerful and hold great promise, they are currently still labor intensive, have a high cost per cell, and, most importantly, do not provide information on spatial distribution of cell types in specific regions of the brain. We propose a complementary approach that uses computational methods to infer the cell types and their gene expression profiles through analysis of brain-wide single-cell resolution in situ hybridization (ISH) imagery contained in the Allen Brain Atlas (ABA). We measure the spatial distribution of neurons labeled in the ISH image for each gene and model it as a spatial point process mixture, whose mixture weights are given by the cell types which express that gene. By fitting a point process mixture model jointly to the ISH images, we infer both the spatial point process distribution for each cell type and their gene expression profile. We validate our predictions of cell type-specific gene expression profiles using single cell RNA sequencing data, recently published for the mouse somatosensory cortex. Jointly with the gene expression profiles, cell features such as cell size, orientation, intensity and local density level are inferred per cell type.

Christian Borgs, Jennifer T. Chayes, Adam Smith

We design algorithms for fitting a high-dimensional statistical model to a large, sparse network without revealing sensitive information of individual members. Given a sparse input graph $G$, our algorithms output a node-differentially-private nonparametric block model approximation. By node-differentially-private, we mean that our output hides the insertion or removal of a vertex and all its adjacent edges. If $G$ is an instance of the network obtained from a generative nonparametric model defined in terms of a graphon $W$, our model guarantees consistency, in the sense that as the number of vertices tends to infinity, the output of our algorithm converges to $W$ in an appropriate version of the $L_2$ norm. In particular, this means we can estimate the sizes of all multi-way cuts in $G$. Our results hold as long as $W$ is bounded, the average degree of $G$ grows at least like the log of the number of vertices, and the number of blocks goes to infinity at an appropriate rate. We give explicit error bounds in terms of the parameters of the model; in several settings, our bounds improve on or match known nonprivate results.

Christian Borgs, Jennifer Chayes, Adrian Marple et al.

We provide the first social choice theory approach to the question of what constitutes a community in a social network. Inspired by the classic preferences models in social choice theory, we start from an abstract social network framework, called preference networks; these consist of a finite set of members where each member has a total-ranking preference of all members in the set. Within this framework, we develop two complementary approaches to axiomatically study the formation and structures of communities. (1) We apply social choice theory and define communities indirectly by postulating that they are fixed points of a preference aggregation function obeying certain desirable axioms. (2) We directly postulate desirable axioms for communities without reference to preference aggregation, leading to eight natural community axioms. These approaches allow us to formulate and analyze community rules. We prove a taxonomy theorem that provides a structural characterization of the family of community rules that satisfies all eight axioms. The structure is actually quite beautiful: these community rules form a bounded lattice under the natural intersection and union operations. Our structural theorem is complemented with a complexity result: while identifying a community by the most selective rule of the lattice is in P, deciding if a subset is a community by the most comprehensive rule of the lattice is coNP-complete. Our studies also shed light on the limitations of defining community rules solely based on preference aggregation: any aggregation function satisfying Arrow's IIA axiom, or based on commonly used aggregation schemes like the Borda count or generalizations thereof, lead to communities which violate at least one of our community axioms. Finally, we give a polynomial-time rule consistent with seven axioms and weakly satisfying the eighth axiom.