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Applications · Chemistry and Drug Discovery

Miruna Cretu, Charles Harris, Ilia Igashov, Arne Schneuing, Marwin Segler, Bruno Correia, Julien Roy, Emmanuel Bengio, Pietro Lio

Generative models see increasing use in computer-aided drug design. However, while performing well at capturing distributions of molecular motifs, they often produce synthetically inaccessible molecules. To address this, we introduce SynFlowNet, a GFlowNet model whose action space uses chemical reactions and buyable reactants to sequentially build new molecules. By incorporating forward synthesis as an explicit constraint of the generative mechanism, we aim at bridging the gap between in silico molecular generation and real world synthesis capabilities. We evaluate our approach using synthetic accessibility scores and an independent retrosynthesis tool to assess the synthesizability of our compounds, and motivate the choice of GFlowNets through considerable improvement in sample diversity compared to baselines. Additionally, we identify challenges with reaction encodings that can complicate traversal of the MDP in the backward direction. To address this, we introduce various strategies for learning the GFlowNet backward policy and thus demonstrate how additional constraints can be integrated into the GFlowNet MDP framework. This approach enables our model to successfully identify synthesis pathways for previously unseen molecules.

Applications · Chemistry and Drug Discovery

KISHALAY DAS, Subhojyoti Khastagir, Pawan Goyal, Seung-Cheol Lee, Satadeep Bhattacharjee, Niloy Ganguly

Equivariant diffusion models have emerged as the prevailing approach for generat-ing novel crystal materials due to their ability to leverage the physical symmetriesof periodic material structures. However, current models do not effectively learn thejoint distribution of atom types, fractional coordinates, and lattice structure of thecrystal material in a cohesive end-to-end diffusion framework. Also, none of thesemodels work under realistic setups, where users specify the desired characteristicsthat the generated structures must match. In this work, we introduce TGDMat, anovel text-guided diffusion model designed for 3D periodic material generation.Our approach integrates global structural knowledge through textual descriptionsat each denoising step while jointly generating atom coordinates, types, and latticestructure using a periodic-E(3)-equivariant graph neural network (GNN). Extensiveexperiments using popular datasets on benchmark tasks reveal that TGDMat out-performs existing baseline methods by a good margin. Notably, for the structureprediction task, with just one generated sample, TGDMat outperforms all baselinemodels, highlighting the importance of text-guided diffusion. Further, in the genera-tion task, TGDMat surpasses all baselines and their text-fusion variants, showcasingthe effectiveness of the joint diffusion paradigm. Additionally, incorporating textualknowledge reduces overall training and sampling computational overhead whileenhancing generative performance when utilizing real-world textual prompts fromexperts. Code is available at https://github.com/kdmsit/TGDMat

Social Aspects · Everything Else

Erik Jones, Arjun Patrawala, Jacob Steinhardt

Humans often rely on subjective natural language to direct language models (LLMs); for example, users might instruct the LLM to write an *enthusiastic* blogpost, while developers might train models to be *helpful* and *harmless* using LLM-based edits. The LLM’s *operational semantics* of such subjective phrases---how it adjusts its behavior when each phrase is included in the prompt---thus dictates how aligned it is with human intent. In this work, we uncover instances of *misalignment* between LLMs' actual operational semantics and what humans expect. Our method, TED (thesaurus error detector), first constructs a thesaurus that captures whether two phrases have similar operational semantics according to the LLM. It then elicits failures by unearthing disagreements between this thesaurus and a human-constructed reference. TED routinely produces surprising instances of misalignment; for example, Mistral 7B Instruct produces more *harassing* outputs when it edits text to be *witty*, and Llama 3 8B Instruct produces *dishonest* articles when instructed to make the articles *enthusiastic*. Our results demonstrate that humans can uncover unexpected LLM behavior by scrutinizing relationships between abstract concepts, without supervising outputs directly.

Social Aspects · Fairness, Equity, Justice and Safety

Yaowen Ye, Cassidy Laidlaw, Jacob Steinhardt

Language model (LM) post-training relies on two stages of human supervision: task demonstrations for supervised finetuning (SFT), followed by preference comparisons for reinforcement learning from human feedback (RLHF). As LMs become more capable, the tasks they are given become harder to supervise. Will post-training remain effective under unreliable supervision? To test this, we simulate unreliable demonstrations and comparison feedback using small LMs and time-constrained humans. We find that in the presence of unreliable supervision, SFT still retains some effectiveness, but DPO (a common RLHF algorithm) fails to improve the model beyond SFT. To address this, we propose *iterative label refinement* (ILR) as an alternative to RLHF. ILR improves the SFT data by using comparison feedback to decide whether human demonstrations should be replaced by model-generated alternatives, then retrains the model via SFT on the updated data. SFT+ILR outperforms SFT+DPO on several tasks with unreliable supervision (math, coding, and safe instruction-following). Our findings suggest that as LMs are used for complex tasks where human supervision is unreliable, RLHF may no longer be the best use of human comparison feedback; instead, it is better to direct feedback towards improving the training *data* rather than continually training the *model*. Our code and data are available at https://github.com/helloelwin/iterative-label-refinement.

Applications · Physics

Yusei Ito, Tatsunori Taniai, Ryo Igarashi, Yoshitaka Ushiku, Kanta Ono

Crystal structure modeling with graph neural networks is essential for various applications in materials informatics, and capturing SE(3)-invariant geometric features is a fundamental requirement for these networks. A straightforward approach is to model with orientation-standardized structures through structure-aligned coordinate systems, or “frames.” However, unlike molecules, determining frames for crystal structures is challenging due to their infinite and highly symmetric nature. In particular, existing methods rely on a statically fixed frame for each structure, determined solely by its structural information, regardless of the task under consideration. Here, we rethink the role of frames, *questioning whether such simplistic alignment with the structure is sufficient*, and propose the concept of *dynamic frames*. While accommodating the infinite and symmetric nature of crystals, these frames provide each atom with a dynamic view of its local environment, focusing on actively interacting atoms. We demonstrate this concept by utilizing the attention mechanism in a recent transformer-based crystal encoder, resulting in a new architecture called **CrystalFramer**. Extensive experiments show that CrystalFramer outperforms conventional frames and existing crystal encoders in various crystal property prediction tasks.

Pablo Lemos, Sammy Sharief, Nikolay Malkin, Salma Salhi, Connor Stone, Laurence Perreault-Levasseur, Yashar Hezaveh

We propose a likelihood-free method for comparing two distributions given samples from each, with the goal of assessing the quality of generative models. The proposed approach, PQMass, provides a statistically rigorous method for assessing the performance of a single generative model or the comparison of multiple competing models. PQMass divides the sample space into non-overlapping regions and applies chi-squared tests to the number of data samples that fall within each region, giving a $p$-value that measures the probability that the bin counts derived from two sets of samples are drawn from the same multinomial distribution. PQMass does not depend on assumptions regarding the density of the true distribution, nor does it rely on training or fitting any auxiliary models. We evaluate PQMass on data of various modalities and dimensions, demonstrating its effectiveness in assessing the quality, novelty, and diversity of generated samples. We further show that PQMass scales well to moderately high-dimensional data and thus obviates the need for feature extraction in practical applications.

Deep Learning · Large Language Models

Ayan Sengupta, Siddhant Chaudhary, Tanmoy Chakraborty

The ever-increasing size of large language models (LLMs) presents significant challenges for deployment due to their heavy computational and memory requirements. Current model pruning techniques attempt to alleviate these issues by relying heavily on external calibration datasets to determine which parameters to prune or compress, thus limiting their flexibility and scalability across different compression ratios. Moreover, these methods often cause severe performance degradation, particularly in downstream tasks, when subjected to higher compression rates. In this paper, we propose *PruneNet*, a novel model compression method that addresses these limitations by reformulating model pruning as a policy learning process. PruneNet decouples the pruning process from the model architecture, eliminating the need for calibration datasets. It learns a stochastic pruning policy to assess parameter importance solely based on intrinsic model properties while preserving the spectral structure to minimize information loss. PruneNet can compress the LLaMA-2-7B model in just 15 minutes, achieving over 80\% retention of its zero-shot performance with a 30\% compression ratio, outperforming existing methods that retain only 75\% performance. Furthermore, on complex multitask language understanding tasks, PruneNet demonstrates its robustness by preserving up to 80\% performance of the original model, proving itself a superior alternative to conventional structured compression techniques.

Deep Learning · Large Language Models

Guibin Zhang, Yanwei Yue, Zhixun Li, Sukwon Yun, Guancheng Wan, Kun Wang, Dawei Cheng, Jeffrey Yu, Tianlong Chen

Recent advancements in large language model (LLM)-powered agents have shown that collective intelligence can significantly outperform individual capabilities, largely attributed to the meticulously designed inter-agent communication topologies. Though impressive in performance, existing multi-agent pipelines inherently introduce substantial token overhead, as well as increased economic costs, which pose challenges for their large-scale deployments. In response to this challenge, we propose an economical, simple, and robust multi-agent communication framework, termed $\texttt{AgentPrune}$, which can seamlessly integrate into mainstream multi-agent systems and prunes redundant or even malicious communication messages. Technically, $\texttt{AgentPrune}$ is the first to identify and formally define the $\textit{Communication Redundancy}$ issue present in current LLM-based multi-agent pipelines, and efficiently performs one-shot pruning on the spatial-temporal message-passing graph, yielding a token-economic and high-performing communication topology.Extensive experiments across six benchmarks demonstrate that $\texttt{AgentPrune}$ $\textbf{(I)}$ achieves comparable results as state-of-the-art topologies at merely $\\$5.6$ cost compared to their $\\$43.7$, $\textbf{(II)}$ integrates seamlessly into existing multi-agent frameworks with $28.1\\%\sim72.8\\%\downarrow$ token reduction, and $\textbf{(III)}$ successfully defend against two types of agent-based adversarial attacks with $3.5\\%\sim10.8\\%\uparrow$ performance boost. The source code is available at \url{https://github.com/yanweiyue/AgentPrune}.

Probabilistic Methods · Everything Else

Rui Xu, Chao Chen, Yue Sun, Parvathinathan Venkitasubramaniam, Sihong Xie

Conformal prediction yields a prediction set with guaranteed $1-\alpha$ coverage of the true target under the i.i.d. assumption, which can fail and lead to a gap between $1-\alpha$ and the actual coverage. Prior studies bound the gap using total variation distance, which cannot identify the gap changes under distribution shift at different $\alpha$, thus serving as a weak indicator of prediction set validity. Besides, existing methods are mostly limited to covariate shifts, while general joint distribution shifts are more common in practice but less researched. In response, we first propose a Wasserstein distance-based upper bound of the coverage gap and analyze the bound using probability measure pushforwards between the shifted joint data and conformal score distributions, enabling a separation of the effect of covariate and concept shifts over the coverage gap. We exploit the separation to design algorithms based on importance weighting and regularized representation learning (WR-CP) to reduce the Wasserstein bound with a finite-sample error bound. WR-CP achieves a controllable balance between conformal prediction accuracy and efficiency. Experiments on six datasets prove that WR-CP can reduce coverage gaps to 3.2% across different confidence levels and outputs prediction sets 37% smaller than the worst-case approach on average.

Applications · Robotics

Muhan Li, Lingji Kong, Sam Kriegman

The automatic design of embodied agents (e.g. robots) has existed for 31 years and is experiencing a renaissance of interest in the literature. To date however, the field has remained narrowly focused on two kinds of anatomically simple robots: (1) fully rigid, jointed bodies; and (2) fully soft, jointless bodies. Here we bridge these two extremes with the open ended creation of terrestrial endoskeletal robots: deformable soft bodies that leverage jointed internal skeletons to move efficiently across land. Simultaneous de novo generation of external and internal structures is achieved by (i) modeling 3D endoskeletal body plans as integrated collections of elastic and rigid cells that directly attach to form soft tissues anchored to compound rigid bodies; (ii) encoding these discrete mechanical subsystems into a continuous yet coherent latent embedding; (iii) optimizing the sensorimotor coordination of each decoded design using model-free reinforcement learning; and (iv) navigating this smooth yet highly non-convex latent manifold using evolutionary strategies. This yields an endless stream of novel species of ``higher robots'' that, like all higher animals, harness the mechanical advantages of both elastic tissues and skeletal levers for terrestrial travel. It also provides a plug-and-play experimental platform for benchmarking evolutionary design and representation learning algorithms in complex hierarchical embodied systems.

Optimization · Large Scale, Parallel and Distributed

Yury Demidovich, Grigory Malinovsky, Egor Shulgin, Peter Richtarik

We introduce a novel optimization problem formulation that departs from the conventional way of minimizing machine learning model loss as a black-box function. Unlike traditional formulations, the proposed approach explicitly incorporates an initially pre-trained model and random sketch operators, allowing for sparsification of both the model and gradient during training. We establish insightful properties of the proposed objective function and highlight its connections to the standard formulation. Furthermore, we present several variants of the Stochastic Gradient Descent (SGD) method adapted to the new problem formulation, including SGD with general sampling, a distributed version, and SGD with variance reduction techniques. We achieve tighter convergence rates and relax assumptions, bridging the gap between theoretical principles and practical applications, covering several important techniques such as Dropout and Sparse training. This work presents promising opportunities to enhance the theoretical understanding of model training through a sparsification-aware optimization approach.

Optimization · Large Scale, Parallel and Distributed

Yury Demidovich, Petr Ostroukhov, Grigory Malinovsky, Samuel Horváth, Martin Takáč, Peter Richtarik, Eduard Gorbunov

Non-convex Machine Learning problems typically do not adhere to the standard smoothness assumption. Based on empirical findings, Zhang et al. (2020b) proposed a more realistic generalized $(L_0,L_1)$-smoothness assumption, though it remains largely unexplored. Many existing algorithms designed for standard smooth problems need to be revised. However, in the context of Federated Learning, only a few works address this problem but rely on additional limiting assumptions. In this paper, we address this gap in the literature: we propose and analyze new methods with local steps, partial participation of clients, and Random Reshuffling without extra restrictive assumptions beyond generalized smoothness. The proposed methods are based on the proper interplay between clients' and server's stepsizes and gradient clipping. Furthermore, we perform the first analysis of these methods under the Polyak-Łojasiewicz condition. Our theory is consistent with the known results for standard smooth problems, and our experimental results support the theoretical insights.

Esben Kran, Hieu Minh Nguyen, Akash Kundu, Sami Jawhar, Jinsuk Park, Mateusz Jurewicz

We introduce DarkBench, a comprehensive benchmark for detecting dark design patterns—manipulative techniques that influence user behavior—in interactions with large language models (LLMs). Our benchmark comprises 660 prompts across six categories: brand bias, user retention, sycophancy, anthropomorphism, harmful generation, and sneaking. We evaluate models from five leading companies (OpenAI, Anthropic, Meta, Mistral, Google) and find that some LLMs are explicitly designed to favor their developers' products and exhibit untruthful communication, among other manipulative behaviors. Companies developing LLMs should recognize and mitigate the impact of dark design patterns to promote more ethical Al.

Social Aspects · Fairness, Equity, Justice and Safety

Esben Kran, Hieu Minh Nguyen, Akash Kundu, Sami Jawhar, Jinsuk Park, Mateusz Jurewicz

We introduce DarkBench, a comprehensive benchmark for detecting dark design patterns—manipulative techniques that influence user behavior—in interactions with large language models (LLMs). Our benchmark comprises 660 prompts across six categories: brand bias, user retention, sycophancy, anthropomorphism, harmful generation, and sneaking. We evaluate models from five leading companies (OpenAI, Anthropic, Meta, Mistral, Google) and find that some LLMs are explicitly designed to favor their developers' products and exhibit untruthful communication, among other manipulative behaviors. Companies developing LLMs should recognize and mitigate the impact of dark design patterns to promote more ethical Al.

Applications · Chemistry and Drug Discovery

Yurou Liu, Jiahao Chen, Rui Jiao, Jiangmeng Li, Wenbing Huang, Bing Su

Denoising learning of 3D molecules learns molecular representations by imposing noises into the equilibrium conformation and predicting the added noises to recover the equilibrium conformation, which essentially captures the information of molecular force fields. Due to the specificity of Potential Energy Surfaces, the probabilities of physically reasonable noises for each atom in different molecules are different. However, existing methods apply the shared heuristic hand-crafted noise sampling strategy to all molecules, resulting in inaccurate force field learning. In this paper, we propose a novel 3D molecular pre-training method, namely DenoiseVAE, which employs a Noise Generator to acquire atom-specific noise distributions for different molecules. It utilizes the stochastic reparameterization technique to sample noisy conformations from the generated distributions, which are inputted into a Denoising Module for denoising. The Noise Generator and the Denoising Module are jointly learned in a manner conforming with the paradigm of Variational Auto Encoder. Consequently, the sampled noisy conformations can be more diverse, adaptive, and informative, and thus DenoiseVAE can learn representations that better reveal the molecular force fields. Extensive experiments show that DenoiseVAE outperforms the current state-of-the-art methods on various molecular property prediction tasks, demonstrating the effectiveness of it.

Miscellaneous Aspects of Machine Learning · Causality

Gideon Stein, Maha Shadaydeh, Jan Blunk, Niklas Penzel, Joachim Denzler

Causal discovery, or identifying causal relationships from observational data, is a notoriously challenging task, with numerous methods proposed to tackle it.Despite this, in-the-wild evaluation of these methods is still lacking, as works frequently rely on synthetic data evaluation and sparse real-world examples under critical theoretical assumptions.Real-world causal structures, however, are often complex, evolving over time, non-linear, and influenced by unobserved factors, makingit hard to decide on a proper causal discovery strategy.To bridge this gap, we introduce CausalRivers, the largest in-the-wild causal discovery benchmarking kit for time-series data to date.CausalRivers features an extensive dataset on river discharge that covers the eastern German territory (666 measurement stations) and the state of Bavaria (494 measurement stations).It spans the years 2019 to 2023 with a 15-minute temporal resolution.Further, we provide additional data from a flood around the Elbe River, as an event with a pronounced distributional shift.Leveraging multiple sources of information and time-series meta-data, we constructed two distinct causal ground truth graphs (Bavaria and eastern Germany).These graphs can be sampled to generate thousands of subgraphs to benchmark causal discovery across diverse and challenging settings.To demonstrate the utility of CausalRivers, we evaluate several causal discovery approaches through a set of experiments to identify areas for improvement.CausalRivers has the potential to facilitate robust evaluations and comparisons of causal discovery methods.Besides this primary purpose, we also expect that this dataset will be relevant for connected areas of research, such as time-series forecasting and anomaly detection.Based on this, we hope to push benchmark-driven method development that fosters advanced techniques for causal discovery, as is the case for many other areas of machine learning.

Deep Learning · Large Language Models

Jang Hyun Cho, Boris Ivanovic, Yulong Cao, Edward Schmerling, Yue Wang, Xinshuo Weng, Boyi Li, Yurong You, Philipp Krähenbühl, Yan Wang 等

Multi-modal large language models (MLLMs) have shown incredible capabilities in a variety of 2D vision and language tasks. We extend MLLMs’ perceptual capabilities to ground and reason about images in 3-dimensional space. To that end, we first develop a large-scale pretraining dataset for 2D and 3D called LV3D by combining multiple existing 2D and 3D recognition datasets under a common task formulation: as multi-turn question-answering. Next, we introduce a new MLLM named CUBE-LLM and pre-train it on LV3D. We show that pure data scaling makes a strong 3D perception capability without 3D specific architectural design or training objective. CUBE-LLM exhibits intriguing properties similar to LLMs: (1) CUBE-LLM can apply chain-of-thought prompting to improve 3D understanding from 2D context information. (2) CUBE-LLM can follow complex and diverse instructions and adapt to versatile input and output formats. (3) CUBE-LLM can be visually prompted such as 2D box or a set of candidate 3D boxes from specialists. Our experiments on outdoor benchmarks demonstrate that CUBE-LLM significantly outperforms existing baselines by 21.3 points of AP-BEV on the Talk2Car dataset for 3D grounded reasoning and 17.7 points on the DriveLM dataset for complex reasoning about driving scenarios, respectively. CUBE-LLM also shows competitive results in general MLLM benchmarks such as refCOCO for 2D grounding with (87.0) average score, as well as visual question answering benchmarks such as VQAv2, GQA, SQA, POPE, etc. for complex reasoning.

Applications · Computer Vision

Tsung-Han Wu, Giscard Biamby, Jerome Quenum, Ritwik Gupta, Joseph E Gonzalez, trevor darrell, David Chan

Large Multimodal Models (LMMs) have made significant strides in visual question-answering for single images. Recent advancements like long-context LMMs have allowed them to ingest larger, or even multiple, images. However, the ability to process a large number of visual tokens does not guarantee effective retrieval and reasoning for multi-image question answering (MIQA), especially in real-world applications like photo album searches or satellite imagery analysis. In this work, we first assess the limitations of current benchmarks for long-context LMMs. We address these limitations by introducing a new vision-centric, long-context benchmark, "Visual Haystacks (VHs)". We comprehensively evaluate both open-source and proprietary models on VHs, and demonstrate that these models struggle when reasoning across potentially unrelated images, perform poorly on cross-image reasoning, as well as exhibit biases based on the placement of key information within the context window. Towards a solution, we introduce MIRAGE (Multi-Image Retrieval Augmented Generation), an open-source, lightweight visual-RAG framework that processes up to 10k images on a single 40G A100 GPU—far surpassing the 1k-image limit of contemporary models. MIRAGE demonstrates up to 13% performance improvement over existing open-source LMMs on VHs, sets a new state-of-the-art on the RetVQA multi-image QA benchmark, and achieves competitive performance on single-image QA with state-of-the-art LMMs. Our dataset, model, and code are available at: https://visual-haystacks.github.io.

Thieu Vo, Duy-Tung Pham, Xin Tong, Tan Nguyen

Selective state space models (SSM), such as Mamba, have gained prominence for their effectiveness in modeling sequential data. Despite their outstanding empirical performance, a comprehensive theoretical understanding of deep selective SSM remains elusive, hindering their further development and adoption for applications that need high fidelity. In this paper, we investigate the dynamical properties of tokens in a pre-trained Mamba model. In particular, we derive the dynamical system governing the continuous-time limit of the Mamba model and characterize the asymptotic behavior of its solutions. In the one-dimensional case, we prove that only one of the following two scenarios happens: either all tokens converge to zero, or all tokens diverge to infinity. We provide criteria based on model parameters to determine when each scenario occurs. For the convergent scenario, we empirically verify that this scenario negatively impacts the model's performance. For the divergent scenario, we prove that different tokens will diverge to infinity at different rates, thereby contributing unequally to the updates during model training. Based on these investigations, we propose two refinements for the model: excluding the convergent scenario and reordering tokens based on their importance scores, both aimed at improving practical performance. Our experimental results validate these refinements, offering insights into enhancing Mamba's effectiveness in real-world applications.

Applications · Chemistry and Drug Discovery

Yikun Zhang, Geyan Ye, Chaohao Yuan, Bo Han, Long-Kai Huang, Jianhua Yao, Wei Liu, Yu Rong

Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a global alignment approach to learn the knowledge from different modalities that may fail to capture fine-grained information, such as molecule-and-text fragments and stereoisomeric nuances, which is crucial for downstream tasks. Furthermore, it is incapable of modeling such information using a similar global alignment strategy due to the lack of annotations about the fine-grained fragments in the existing dataset.In this paper, we propose Atomas, a hierarchical molecular representation learning framework that jointly learns representations from SMILES strings and text. We design a Hierarchical Adaptive Alignment model to automatically learn the fine-grained fragment correspondence between two modalities and align these representations at three semantic levels. Atomas's end-to-end training framework supports understanding and generating molecules, enabling a wider range of downstream tasks. Atomas achieves superior performance across 12 tasks on 11 datasets, outperforming 11 baseline models thus highlighting the effectiveness and versatility of our method. Scaling experiments further demonstrate Atomas’s robustness and scalability. Moreover, visualization and qualitative analysis, validated by human experts, confirm the chemical relevance of our approach. Codes are released on ~\url{https://github.com/yikunpku/Atomas}.