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Social Aspects · Accountability, Transparency and Interpretability

David Steinmann, Wolfgang Stammer, Felix Friedrich, Kristian Kersting

While deep learning models often lack interpretability, concept bottleneck models (CBMs) provide inherent explanations via their concept representations. Moreover, they allow users to perform interventional interactions on these concepts by updating the concept values and thus correcting the predictive output of the model. Up to this point, these interventions were typically applied to the model just once and then discarded. To rectify this, we present concept bottleneck memory models (CB2Ms), which keep a memory of past interventions. Specifically, CB2Ms leverage a two-fold memory to generalize interventions to appropriate novel situations, enabling the model to identify errors and reapply previous interventions. This way, a CB2M learns to automatically improve model performance from a few initially obtained interventions. If no prior human interventions are available, a CB2M can detect potential mistakes of the CBM bottleneck and request targeted interventions. Our experimental evaluations on challenging scenarios like handling distribution shifts and confounded data demonstrate that CB2Ms are able to successfully generalize interventions to unseen data and can indeed identify wrongly inferred concepts. Hence, CB2Ms are a valuable tool for users to provide interactive feedback on CBMs, by guiding a user's interaction and requiring fewer interventions.

Applications · Chemistry and Drug Discovery

Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi Jaakkola

A significant amount of protein function requires binding small molecules, including enzymatic catalysis. As such, designing binding pockets for small molecules has several impactful applications ranging from drug synthesis to energy storage. Towards this goal, we first develop HarmonicFlow, an improved generative process over 3D protein-ligand binding structures based on our self-conditioned flow matching objective. FlowSite extends this flow model to jointly generate a protein pocket's discrete residue types and the molecule's binding 3D structure. We show that HarmonicFlow improves upon state-of-the-art generative processes for docking in simplicity, generality, and average sample quality in pocket-level docking. Enabled by this structure modeling, FlowSite designs binding sites substantially better than baseline approaches.

Applications · Chemistry and Drug Discovery

Henry W. Sprueill, Carl Edwards, Khushbu Agarwal, Mariefel Olarte, Udishnu Sanyal, Conrad Johnston, Hongbin Liu, Heng Ji, Sutanay Choudhury

The discovery of new catalysts is essential for the design of new and more efficient chemical processes in order to transition to a sustainable future. We introduce an AI-guided computational screening framework unifying linguistic reasoning with quantum-chemistry based feedback from 3D atomistic representations. Our approach formulates catalyst discovery as an uncertain environment where an agent actively searches for highly effective catalysts via the iterative combination of large language model (LLM)-derived hypotheses and atomistic graph neural network (GNN)-derived feedback. Identified catalysts in intermediate search steps undergo structural evaluation based on spatial orientation, reaction pathways, and stability. Scoring functions based on adsorption energies and reaction energy barriers steer the exploration in the LLM's knowledge space toward energetically favorable, high-efficiency catalysts. We introduce planning methods that automatically guide the exploration without human input, providing competitive performance against expert-enumerated chemical descriptor-based implementations. By integrating language-guided reasoning with computational chemistry feedback, our work pioneers AI-accelerated, trustworthy catalyst discovery.

Social Aspects · Trustworthy Machine Learning

Taylor Sorensen, Jared Moore, Jillian Fisher, Mitchell Gordon, Niloofar Mireshghallah, Christopher Rytting, Andre Ye, Liwei Jiang, Ximing Lu, Nouha Dziri 等

With increased power and prevalence of AI systems, it is ever more critical that AI systems are designed to serve *all*, i.e., people with diverse values and perspectives. However, aligning models to serve *pluralistic* human values remains an open research question. In this piece, we propose a roadmap to pluralistic alignment, specifically using large language models as a test bed. We identify and formalize three possible ways to define and operationalize pluralism in AI systems: 1) *Overton pluralistic* models that present a spectrum of reasonable responses; 2) *Steerably pluralistic* models that can steer to reflect certain perspectives; and 3) *Distributionally pluralistic* models that are well-calibrated to a given population in distribution. We also formalize and discuss three possible classes of *pluralistic benchmarks*: 1) *Multi-objective* benchmarks, 2) *Trade-off steerable* benchmarks that incentivize models to steer to arbitrary trade-offs, and 3) *Jury-pluralistic* benchmarks that explicitly model diverse human ratings. We use this framework to argue that current alignment techniques may be fundamentally limited for pluralistic AI; indeed, we highlight empirical evidence, both from our own experiments and from other work, that standard alignment procedures might *reduce* distributional pluralism in models, motivating the need for further research on pluralistic alignment.

Applications · Chemistry and Drug Discovery

Zhenqiao Song, Yunlong Zhao, Wenxian Shi, Wengong Jin, Yang Yang, Lei Li

Enzymes are genetically encoded biocatalysts capable of accelerating chemical reactions. How can we automatically design functional enzymes? In this paper, we propose EnzyGen, an approach to learn a unified model to design enzymes across all functional families. Our key idea is to generate an enzyme's amino acid sequence and their three-dimensional (3D) coordinates based on functionally important sites and substrates corresponding to a desired catalytic function. These sites are automatically mined from enzyme databases. EnzyGen consists of a novel interleaving network of attention and neighborhood equivariant layers, which captures both long-range correlation in an entire protein sequence and local influence from nearest amino acids in 3D space. To learn the generative model, we devise a joint training objective, including a sequence generation loss, a position prediction loss and an enzyme-substrate interaction loss. We further construct EnzyBench, a dataset with 3157 enzyme families, covering all available enzymes within the protein data bank (PDB). Experimental results show that our EnzyGen consistently achieves the best performance across all 323 testing families, surpassing the best baseline by 10.79% in terms of substrate binding affinity. These findings demonstrate EnzyGen's superior capability in designing well-folded and effective enzymes binding to specific substrates with high affinities. Our code, model and dataset are provided at https://github.com/LeiLiLab/EnzyGen.

Zitao Song, Chao Yang, Chaojie Wang, Bo An, Shuang Li

Modern high-stakes systems, such as healthcare or robotics, often generate vast streaming event sequences. Our goal is to design an efficient, plug-and-play tool to elicit logic tree-based explanations from Large Language Models (LLMs) to provide customized insights into each observed event sequence. Built on the temporal point process model for events, our method employs the likelihood function as a score to evaluate generated logic trees. We propose an amortized Expectation-Maximization (EM) learning framework and treat the logic tree as latent variables. In the E-step, we evaluate the posterior distribution over the latent logic trees using an LLM prior and the likelihood of the observed event sequences. LLM provides a high-quality prior for the latent logic trees, however, since the posterior is built over a discrete combinatorial space, we cannot get the closed-form solution. We propose to generate logic tree samples from the posterior using a learnable GFlowNet, which is a diversity-seeking generator for structured discrete variables. The M-step employs the generated logic rules to approximate marginalization over the posterior, facilitating the learning of model parameters and refining the tunable LLM prior parameters. In the online setting, our locally built, lightweight model will iteratively extract the most relevant rules from LLMs for each sequence using only a few iterations. Empirical demonstrations showcase the promising performance and adaptability of our framework.

Optimization · Zero-order and Black-box Optimization

Xingyou Song, Yingtao Tian, Robert Lange, Chansoo Lee, Yujin Tang, Yutian Chen

Undeniably, Large Language Models (LLMs) have stirred an extraordinary wave of innovation in the machine learning research domain, resulting in substantial impact across diverse fields such as reinforcement learning, robotics, and computer vision. Their incorporation has been rapid and transformative, marking a significant paradigm shift in the field of machine learning research. However, the field of experimental design, grounded on black-box optimization, has been much less affected by such a paradigm shift, even though integrating LLMs with optimization presents a unique landscape ripe for exploration. In this position paper, we frame the field of black-box optimization around sequence-based foundation models and organize their relationship with previous literature. We discuss the most promising ways foundational language models can revolutionize optimization, which include harnessing the vast wealth of information encapsulated in free-form text to enrich task comprehension, utilizing highly flexible sequence models such as Transformers to engineer superior optimization strategies, and enhancing performance prediction over previously unseen search spaces.

Deep Learning · Large Language Models

Weixi Song, Zuchao Li, Lefei Zhang, hai zhao, Bo Du

With the prevalence of pre-training-fine-tuning paradigm, how to efficiently adapt the pre-trained model to the downstream tasks has been an intriguing issue. $\textbf{P}$arameter-$\textbf{E}$fficient $\textbf{F}$ine-$\textbf{T}$uning(PEFT) methods have been proposed for low-cost adaptation. Although PEFT has demonstrated effectiveness and been widely applied, the underlying principles are still unclear. In this paper, we adopt the PAC-Bayesian generalization error bound, viewing pre-training as a shift of prior distribution which leads to a tighter bound for generalization error. We validate this shift from the perspectives of oscillations in the loss landscape and the quasi-sparsity in gradient distribution. Based on this, we propose a gradient-based sparse fine-tuning algorithm, named $\textbf{S}$parse $\textbf{I}$ncrement $\textbf{F}$ine-$\textbf{T}$uning(SIFT), and validate its effectiveness on a range of tasks including the GLUE Benchmark and Instruction-tuning. The code is accessible at https://github.com/song-wx/SIFT/.

Applications · Computer Vision

Ziyang Song, Jinxi Li, Bo Yang

It has long been challenging to recover the underlying dynamic 3D scene representations from a monocular RGB video. Existing works formulate this problem into finding a single most plausible solution by adding various constraints such as depth priors and strong geometry constraints, ignoring the fact that there could be infinitely many 3D scene representations corresponding to a single dynamic video. In this paper, we aim to learn all plausible 3D scene configurations that match the input video, instead of just inferring a specific one. To achieve this ambitious goal, we introduce a new framework, called OSN. The key to our approach is a simple yet innovative object scale network together with a joint optimization module to learn an accurate scale range for every dynamic 3D object. This allows us to sample as many faithful 3D scene configurations as possible. Extensive experiments show that our method surpasses all baselines and achieves superior accuracy in dynamic novel view synthesis on multiple synthetic and real-world datasets. Most notably, our method demonstrates a clear advantage in learning fine-grained 3D scene geometry.

Applications · Chemistry and Drug Discovery

Zhenqiao Song, Tinglin Huang, Lei Li, Wengong Jin

How can we design proteins with desired functions? We are motivated by a chemical intuition that both geometric structure and biochemical properties are critical to a protein's function. In this paper, we propose SurfPro, a new method to generate functional proteins given a desired surface and its associated biochemical properties. SurfPro comprises a hierarchical encoder that progressively models the geometric shape and biochemical features of a protein surface, and an autoregressive decoder to produce an amino acid sequence. We evaluate SurfPro on a standard inverse folding benchmark CATH 4.2 and two functional protein design tasks: protein binder design and enzyme design. Our SurfPro consistently surpasses previous state-of-the-art inverse folding methods, achieving a recovery rate of 57.78% on CATH 4.2 and higher success rates in terms of protein-protein binding and enzyme-substrate interaction scores

Reinforcement Learning

Yuda Song, J. Bagnell, Aarti Singh

We consider the hybrid reinforcement learning setting where the agent has access to both offline data and online interactive access. While RL research typically assumes offline data contains complete action, reward and transition information, datasets with only state information (also known as *observation-only* datasets) are more general, abundant and practical. This motivates our study of the *hybrid RL with observation-only offline dataset* framework. While the task of competing with the best policy ``covered'' by the offline data can be solved if a *reset* model of the environment is provided (i.e., one that can be reset to any state), we show evidence of hardness of competing when only given the weaker *trace* model (i.e., one can only reset to the initial states and must produce full traces through the environment), without further assumption of *admissibility* of the offline data. Under the admissibility assumptions-- that the offline data could actually be produced by the policy class we consider-- we propose the first algorithm in the trace model setting that provably matches the performance of algorithms that leverage a reset model. We also perform proof-of-concept experiments that suggest the effectiveness of our algorithm in practice.

Applications · Physics

Ning Liu, Yiming Fan, Xianyi Zeng, Milan Klöwer, LU ZHANG, Yue Yu

Neural operators (NOs) have emerged as effective tools for modeling complex physical systems in scientific machine learning. In NOs, a central characteristic is to learn the governing physical laws directly from data. In contrast to other machine learning applications, partial knowledge is often known a priori about the physical system at hand whereby quantities such as mass, energy and momentum are exactly conserved. Currently, NOs have to learn these conservation laws from data and can only approximately satisfy them due to finite training data and random noise. In this work, we introduce conservation law-encoded neural operators (clawNOs), a suite of NOs that endow inference with automatic satisfaction of such conservation laws. ClawNOs are built with a divergence-free prediction of the solution field, with which the continuity equation is automatically guaranteed. As a consequence, clawNOs are compliant with the most fundamental and ubiquitous conservation laws essential for correct physical consistency. As demonstrations, we consider a wide variety of scientific applications ranging from constitutive modeling of material deformation, incompressible fluid dynamics, to atmospheric simulation. ClawNOs significantly outperform the state-of-the-art NOs in learning efficacy, especially in small-data regimes.

Probabilistic Methods · Bayesian Models and Methods

Emanuel Sommer, Lisa Wimmer, Theodore Papamarkou, Ludwig Bothmann, Bernd Bischl, David Rügamer

A major challenge in sample-based inference (SBI) for Bayesian neural networks is the size and structure of the networks’ parameter space. Our work shows that successful SBI is possible by embracing the characteristic relationship between weight and function space, uncovering a systematic link between overparameterization and the difficulty of the sampling problem. Through extensive experiments, we establish practical guidelines for sampling and convergence diagnosis. As a result, we present a deep ensemble initialized approach as an effective solution with competitive performance and uncertainty quantification.

Probabilistic Methods · Bayesian Models and Methods

Paulo Soares, Adarsh Pyarelal, Meghavarshini Krishnaswamy, Emily Butler, Kobus Barnard

We develop a novel probabilistic model for interpersonal coordination as a latent phenomenon explaining statistical temporal influence between multiple components in a system. For example, the state of one person can influence that of another at a later time, as indicated by their observed behaviors. We characterize coordination as the degree to which the distributions for such states at one time point are merged for the next salient time point. We evaluate our model in the context of three-person teams executing a virtual search and rescue (SAR) mission. We first use synthetic data to confirm that our technical definition of coordination is consistent with expectations and that we can recover generated coordination despite noise. We then show that captured coordination can be predictive of team performance on real data. Here we use speech vocalics and semantics to infer coordination for 36 teams carrying out two successive SAR missions. In two different datasets, we find that coordination is generally predictive of team score for the second mission, but not for the first, where teams are largely learning to play the game. In addition, we found that including a semantic modality improves prediction in some scenarios. This shows that our intuitive technical definition can capture useful explanatory aspects of team behavior.

Optimization · Non-Convex

Oscar Smee, Fred Roosta

We consider solving large scale nonconvex optimisation problems with nonnegativity constraints. Such problems arise frequently in machine learning, such as nonnegative least-squares, nonnegative matrix factorisation, as well as problems with sparsity-inducing regularisation. In such settings, first-order methods, despite their simplicity, can be prohibitively slow on ill-conditioned problems or become trapped near saddle regions, while most second-order alternatives involve non-trivially challenging subproblems. The two-metric projection framework, initially proposed by Bertsekas (1982), alleviates these issues and achieves the best of both worlds by combining projected gradient steps at the boundary of the feasible region with Newton steps in the interior in such a way that feasibility can be maintained by simple projection onto the nonnegative orthant. We develop extensions of the two-metric projection framework, which by inexactly solving the subproblems as well as employing non-positive curvature directions, are suitable for large scale and nonconvex settings. We obtain state-of-the-art convergence rates for various classes of non-convex problems and demonstrate competitive practical performance on a variety of problems.

Reinforcement Learning · Multi-agent

Amutheezan Sivagnanam, Ava Pettet, Hunter Lee, Ayan Mukhopadhyay, Abhishek Dubey, Aron Laszka

An emergency responder management (ERM) system dispatches responders, such as ambulances, when it receives requests for medical aid. ERM systems can also proactively reposition responders between predesignated waiting locations to cover any gaps that arise due to the prior dispatch of responders or significant changes in the distribution of anticipated requests. Optimal repositioning is computationally challenging due to the exponential number of ways to allocate responders between locations and the uncertainty in future requests. The state-of-the-art approach in proactive repositioning is a hierarchical approach based on spatial decomposition and online Monte Carlo tree search, which may require minutes of computation for each decision in a domain where seconds can save lives. We address the issue of long decision times by introducing a novel reinforcement learning (RL) approach, based on the same hierarchical decomposition, but replacing online search with learning. To address the computational challenges posed by large, variable-dimensional, and discrete state and action spaces, we propose: (1) actor-critic based agents that incorporate transformers to handle variable-dimensional states and actions, (2) projections to fixed-dimensional observations to handle complex states, and (3) combinatorial techniques to map continuous actions to discrete allocations. We evaluate our approach using real-world data from two U.S. cities, Nashville, TN and Seattle, WA. Our experiments show that compared to the state of the art, our approach reduces computation time per decision by three orders of magnitude, while also slightly reducing average ambulance response time by 5 seconds.

Reinforcement Learning · Deep RL

Viacheslav Sinii, Alexander Nikulin, Vladislav Kurenkov, Ilya Zisman, Sergey Kolesnikov

Recently, it has been shown that transformers pre-trained on diverse datasets with multi-episode contexts can generalize to new reinforcement learning tasks in-context. A key limitation of previously proposed models is their reliance on a predefined action space size and structure. The introduction of a new action space often requires data re-collection and model re-training, which can be costly for some applications. In our work, we show that it is possible to mitigate this issue by proposing the Headless-AD model that, despite being trained only once, is capable of generalizing to discrete action spaces of variable size, semantic content and order. By experimenting with Bernoulli and contextual bandits, as well as a gridworld environment, we show that Headless-AD exhibits significant capability to generalize to action spaces it has never encountered, even outperforming specialized models trained for a specific set of actions on several environment configurations.

Deep Learning · Generative Models and Autoencoders

Gautam Singh, Yue Wang, Jiawei Yang, Boris Ivanovic, Sungjin Ahn, Marco Pavone, Tong Che

While modern best practices advocate for scalable architectures that support long-range interactions, object-centric models are yet to fully embrace these architectures. In particular, existing object-centric models for handling sequential inputs, due to their reliance on RNN-based implementation, show poor stability and capacity and are slow to train on long sequences. We introduce Parallelizable Spatiotemporal Binder or PSB, the first temporally-parallelizable slot learning architecture for sequential inputs. Unlike conventional RNN-based approaches, PSB produces object-centric representations, known as slots, for all time-steps in parallel. This is achieved by refining the initial slots across all time-steps through a fixed number of layers equipped with causal attention. By capitalizing on the parallelism induced by our architecture, the proposed model exhibits a significant boost in efficiency. In experiments, we test PSB extensively as an encoder within an auto-encoding framework paired with a wide variety of decoder options. Compared to the state-of-the-art, our architecture demonstrates stable training on longer sequences, achieves parallelization that results in a 60% increase in training speed, and yields performance that is on par with or better on unsupervised 2D and 3D object-centric scene decomposition and understanding.

Social Aspects · Trustworthy Machine Learning

Ankit Pratap Singh, Namrata Vaswani

This work introduces a Byzantine resilient solution for learning low-dimensional linear representation. Our main contribution is the development of a provably Byzantine-resilient AltGDmin algorithm for solving this problem in a federated setting. We argue that our solution is sample-efficient, fast, and communicationefficient. In solving this problem, we also introduce a novel secure solution to the federated subspace learning meta-problem that occurs in many different applications.

Theory · Domain Adaptation and Transfer Learning

Anurag Singh, Siu Lun Chau, Shahine Bouabid, Krikamol Muandet

Out-of-distribution (OOD) generalisation is challenging because it involves not only learning from empirical data, but also deciding among various notions of generalisation, e.g. optimise based on the average-case risk, worst-case risk, or interpolations thereof. While this decision should in principle be decided by the model operator like medical doctors in practice, this information might not always be available at training time. This situation leads to arbitrary commitments to specific generalisation strategies by machine learners due to these deployment uncertainties. We introduce the Imprecise Domain Generalisation framework to mitigate this, featuring an imprecise risk optimisation that allows learners to stay imprecise by optimising against a continuous spectrum of generalisation strategies during training, and a model framework that allows operators to specify their generalisation preference at deployment. Our work, supported by theoretical and empirical evidence, showcases the benefits of integrating imprecision into domain generalisation.