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Applications

Kevin Yu, Jihye Roh, Ziang Li, Wenhao Gao, Runzhong Wang, Connor Coley

Computer-aided synthesis planning (CASP) algorithms have demonstrated expert-level abilities in planning retrosynthetic routes to molecules of low to moderate complexity. However, current search methods assume the sufficiency of reaching arbitrary building blocks, failing to address the common real-world constraint where using specific molecules is desired. To this end, we present a formulation of synthesis planning with starting material constraints. Under this formulation, we propose Double-Ended Synthesis Planning ($\texttt{DESP}$), a novel CASP algorithm under a _bidirectional graph search_ scheme that interleaves expansions from the target and from the goal starting materials to ensure constraint satisfiability. The search algorithm is guided by a goal-conditioned cost network learned offline from a partially observed hypergraph of valid chemical reactions. We demonstrate the utility of $\texttt{DESP}$ in improving solve rates and reducing the number of search expansions by biasing synthesis planning towards expert goals on multiple new benchmarks. $\texttt{DESP}$ can make use of existing one-step retrosynthesis models, and we anticipate its performance to scale as these one-step model capabilities improve.

Graph Neural Networks

Luis Müller, Daniel Kusuma, Blai Bonet, Christopher Morris

The expressive power of graph learning architectures based on the $k$-dimensional Weisfeiler-Leman ($k$-WL) hierarchy is well understood. However, such architectures often fail to deliver solid predictive performance on real-world tasks, limiting their practical impact. In contrast, global attention-based models such as graph transformers demonstrate strong performance in practice, but comparing their expressive power with the $k$-WL hierarchy remains challenging, particularly since these architectures rely on positional or structural encodings for their expressivity and predictive performance. To address this, we show that the recently proposed Edge Transformer, a global attention model operating on node pairs instead of nodes, has 3-WL expressive power when provided with the right tokenization. Empirically, we demonstrate that the Edge Transformer surpasses other theoretically aligned architectures regarding predictive performance while not relying on positional or structural encodings.

Computational Biology

Lingxiang Jia, Yuchen Ying, Zunlei Feng, Zipeng Zhong, Shaolun Yao, Jiacong Hu, Mingjiang Duan, Xingen Wang, Jie Song, Mingli Song

Deep learning-based methods significantly advance the exploration of associations among triple-wise biological entities (e.g., drug-target protein-adverse reaction), thereby facilitating drug discovery and safeguarding human health. However, existing researches only focus on entity-centric information mapping and aggregation, neglecting the crucial role of potential association patterns among different entities. To address the above limitation, we propose a novel association pattern-aware fusion method for biological entity relationship prediction, which effectively integrates the related association pattern information into entity representation learning. Additionally, to enhance the missing information of the low-order message passing, we devise a bind-relation module that considers the strong bind of low-order entity associations. Extensive experiments conducted on three biological datasets quantitatively demonstrate that the proposed method achieves about 4%-23% hit@1 improvements compared with state-of-the-art baselines. Furthermore, the interpretability of association patterns is elucidated in detail, thus revealing the intrinsic biological mechanisms and promoting it to be deployed in real-world scenarios. Our data and code are available at https://github.com/hry98kki/PatternBERP.

Computer Vision

Bavesh Balaji, Jerrin Bright, Yuhao Chen, Sirisha Rambhatla, John Zelek, David Clausi

Accurate estimation of human pose and the pose of interacting objects, like a hockey stick, is crucial for action recognition and performance analysis, particularly in sports. Existing methods capture the object along with the human in the bounding boxes, assuming all keypoints are visible within the bounding box. This necessitates larger bounding boxes to capture the object, introducing unnecessary visual features and hindering performance in real-world cluttered environments. We propose a simple image and text-based multimodal solution TokenCLIPose that addresses this limitation. Our approach focuses solely on human keypoints within the bounding box, treating objects as unseen. TokenCLIPose leverages the rich semantic representations endowed by language for inducing keypoint-specific context, even for occluded keypoints. We evaluate the performance of TokenCLIPose on a real-world Ice-Hockey dataset, and demonstrate its generalizability through zero-shot transfer to a smaller Lacrosse dataset. Additionally, we showcase its flexibility on CrowdPose, a popular occlusion benchmark with keypoints within the bounding box. Our method significantly improves over state-of-the-art approaches on all three datasets, with gains of 4.36\%, 2.35\%, and 3.8\%, respectively.

Privacy

Ruofan Wu, Guanhua Fang, Mingyang Zhang, Qiying Pan, Tengfei LIU, Weiqiang Wang

Graph representation learning (GRL) is critical for extracting insights from complex network structures, but it also raises security concerns due to potential privacy vulnerabilities in these representations. This paper investigates the structural vulnerabilities in graph neural models where sensitive topological information can be inferred through edge reconstruction attacks. Our research primarily addresses the theoretical underpinnings of similarity-based edge reconstruction attacks (SERA), furnishing a non-asymptotic analysis of their reconstruction capacities. Moreover, we present empirical corroboration indicating that such attacks can perfectly reconstruct sparse graphs as graph size increases. Conversely, we establish that sparsity is a critical factor for SERA's effectiveness, as demonstrated through analysis and experiments on (dense) stochastic block models. Finally, we explore the resilience of private graph representations produced via noisy aggregation (NAG) mechanism against SERA. Through theoretical analysis and empirical assessments, we affirm the mitigation of SERA using NAG . In parallel, we also empirically delineate instances wherein SERA demonstrates both efficacy and deficiency in its capacity to function as an instrument for elucidating the trade-off between privacy and utility.

Computer Vision

Dvir Samuel, Rami Ben-Ari, Matan Levy, Nir Darshan, Gal Chechik

Personalized retrieval and segmentation aim to locate specific instances within a dataset based on an input image and a short description of the reference instance. While supervised methods are effective, they require extensive labeled data for training. Recently, self-supervised foundation models have been introduced to these tasks showing comparable results to supervised methods. However, a significant flaw in these models is evident: they struggle to locate a desired instance when other instances within the same class are presented. In this paper, we explore text-to-image diffusion models for these tasks. Specifically, we propose a novel approach called PDM for Personalized Diffusion Features Matching, that leverages intermediate features of pre-trained text-to-image models for personalization tasks without any additional training. PDM demonstrates superior performance on popular retrieval and segmentation benchmarks, outperforming even supervised methods. We also highlight notable shortcomings in current instance and segmentation datasets and propose new benchmarks for these tasks.

Optimization · Non-Convex

Hoang Phuc Hau Luu, Hanlin Yu, Bernardo Williams, Petrus Mikkola, Marcelo Hartmann, Kai Puolamäki, Arto Klami

We study a class of optimization problems in the Wasserstein space (the space of probability measures) where the objective function is nonconvex along generalized geodesics. Specifically, the objective exhibits some difference-of-convex structure along these geodesics. The setting also encompasses sampling problems where the logarithm of the target distribution is difference-of-convex. We derive multiple convergence insights for a novel semi Forward-Backward Euler scheme under several nonconvex (and possibly nonsmooth) regimes. Notably, the semi Forward-Backward Euler is just a slight modification of the Forward-Backward Euler whose convergence is---to our knowledge---still unknown in our very general non-geodesically-convex setting.

Reinforcement Learning · Everything Else

Yuwei Fu, Haichao Zhang, Di Wu, Wei Xu, Benoit Boulet

Reward specification is one of the most tricky problems in Reinforcement Learning, which usually requires tedious hand engineering in practice. One promising approach to tackle this challenge is to adopt existing expert video demonstrations for policy learning. Some recent work investigates how to learn robot policies from only a single/few expert video demonstrations. For example, reward labeling via Optimal Transport (OT) has been shown to be an effective strategy to generate a proxy reward by measuring the alignment between the robot trajectory and the expert demonstrations. However, previous work mostly overlooks that the OT reward is invariant to temporal order information, which could bring extra noise to the reward signal. To address this issue, in this paper, we introduce the Temporal Optimal Transport (TemporalOT) reward to incorporate temporal order information for learning a more accurate OT-based proxy reward. Extensive experiments on the Meta-world benchmark tasks validate the efficacy of the proposed method. Our code is available at: https://github.com/fuyw/TemporalOT.

Online Learning

Saeed Masoudian, Julian Zimmert, Yevgeny Seldin

We propose a new best-of-both-worlds algorithm for bandits with variably delayed feedback. In contrast to prior work, which required prior knowledge of the maximal delay $d_{\max}$ and had a linear dependence of the regret on it, our algorithm can tolerate arbitrary excessive delays up to order $T$ (where $T$ is the time horizon). The algorithm is based on three technical innovations, which may all be of independent interest: (1) We introduce the first implicit exploration scheme that works in best-of-both-worlds setting. (2) We introduce the first control of distribution drift that does not rely on boundedness of delays. The control is based on the implicit exploration scheme and adaptive skipping of observations with excessive delays. (3) We introduce a procedure relating standard regret with drifted regret that does not rely on boundedness of delays. At the conceptual level, we demonstrate that complexity of best-of-both-worlds bandits with delayed feedback is characterized by the amount of information missing at the time of decision making (measured by the number of outstanding observations) rather than the time that the information is missing (measured by the delays).

Neuroscience, Cognitive Science

William Qian, Jacob Zavatone-Veth, Ben Ruben, Cengiz Pehlevan

One of the central goals of neuroscience is to gain a mechanistic understanding of how the dynamics of neural circuits give rise to their observed function. A popular approach towards this end is to train recurrent neural networks (RNNs) to reproduce experimental recordings of neural activity. These trained RNNs are then treated as surrogate models of biological neural circuits, whose properties can be dissected via dynamical systems analysis. How reliable are the mechanistic insights derived from this procedure? While recent advances in population-level recording technologies have allowed simultaneous recording of up to tens of thousands of neurons, this represents only a tiny fraction of most cortical circuits. Here we show that observing only a subset of neurons in a circuit can create mechanistic mismatches between a simulated teacher network and a data-constrained student, even when the two networks have matching single-unit dynamics. In particular, we show that partial observation of models of low-dimensional cortical dynamics based on functionally feedforward or low-rank connectivity can lead to surrogate models with spurious attractor structure. In total, our results illustrate the challenges inherent in accurately uncovering neural mechanisms from single-trial data, and suggest the need for new methods of validating data-constrained models for neural dynamics.

Optimization

Rui Pan, Xiang Liu, SHIZHE DIAO, Renjie Pi, Jipeng Zhang, Chi Han, Tong Zhang

The machine learning community has witnessed impressive advancements since large language models (LLMs) first appeared. Yet, their massive memory consumption has become a significant roadblock to large-scale training. For instance, a 7B model typically requires at least 60 GB of GPU memory with full parameter training, which presents challenges for researchers without access to high-resource environments. Parameter Efficient Fine-Tuning techniques such as Low-Rank Adaptation (LoRA) have been proposed to alleviate this problem. However, in most large-scale fine-tuning settings, their performance does not reach the level of full parameter training because they confine the parameter search to a low-rank subspace. Attempting to complement this deficiency, we investigate the layerwise properties of LoRA on fine-tuning tasks and observe an unexpected but consistent skewness of weight norms across different layers. Utilizing this key observation, a surprisingly simple training strategy is discovered, which outperforms both LoRA and full parameter training in a wide range of settings with memory costs as low as LoRA. We name it Layerwise Importance Sampled AdamW (LISA), a promising alternative for LoRA, which applies the idea of importance sampling to different layers in LLMs and randomly freeze most middle layers during optimization. Experimental results show that with similar or less GPU memory consumption, LISA surpasses LoRA or even full parameter tuning in downstream fine-tuning tasks, where LISA consistently outperforms LoRA by over 10%-35% in terms of MT-Bench score while achieving on-par or better performance in MMLU, AGIEval and WinoGrande. On large models, specifically LLaMA-2-70B, LISA surpasses LoRA on MT-Bench, GSM8K, and PubMedQA, demonstrating its effectiveness across different domains.

Interpretability

Deqing Fu, Tian-qi Chen, Robin Jia, Vatsal Sharan

Transformers excel at *in-context learning* (ICL)---learning from demonstrations without parameter updates---but how they do so remains a mystery. Recent work suggests that Transformers may internally run Gradient Descent (GD), a first-order optimization method, to perform ICL. In this paper, we instead demonstrate that Transformers learn to approximate second-order optimization methods for ICL. For in-context linear regression, Transformers share a similar convergence rate as *Iterative Newton's Method*, both *exponentially* faster than GD. Empirically, predictions from successive Transformer layers closely match different iterations of Newton’s Method linearly, with each middle layer roughly computing 3 iterations; thus, Transformers and Newton’s method converge at roughly the same rate. In contrast, Gradient Descent converges exponentially more slowly. We also show that Transformers can learn in-context on ill-conditioned data, a setting where Gradient Descent struggles but Iterative Newton succeeds. Finally, to corroborate our empirical findings, we prove that Transformers can implement $k$ iterations of Newton's method with $k + \mathcal O(1)$ layers.

Causality

Jacob Chen, Rohit Bhattacharya, Katherine Keith

Recent text-based causal methods attempt to mitigate confounding bias by estimating proxies of confounding variables that are partially or imperfectly measured from unstructured text data. These approaches, however, assume analysts have supervised labels of the confounders given text for a subset of instances, a constraint that is sometimes infeasible due to data privacy or annotation costs. In this work, we address settings in which an important confounding variable is completely unobserved. We propose a new causal inference method that uses two instances of pre-treatment text data, infers two proxies using two zero-shot models on the separate instances, and applies these proxies in the proximal g-formula. We prove, under certain assumptions about the instances of text and accuracy of the zero-shot predictions, that our method of inferring text-based proxies satisfies identification conditions of the proximal g-formula while other seemingly reasonable proposals do not. To address untestable assumptions associated with our method and the proximal g-formula, we further propose an odds ratio falsification heuristic that flags when to proceed with downstream effect estimation using the inferred proxies. We evaluate our method in synthetic and semi-synthetic settings---the latter with real-world clinical notes from MIMIC-III and open large language models for zero-shot prediction---and find that our method produces estimates with low bias. We believe that this text-based design of proxies allows for the use of proximal causal inference in a wider range of scenarios, particularly those for which obtaining suitable proxies from structured data is difficult.

Deep Learning · Algorithms

Chia-Hsiang Kao, Bharath Hariharan

Despite its widespread use in neural networks, error backpropagation has faced criticism for its lack of biological plausibility, suffering from issues such as the backward locking problem and the weight transport problem. These limitations have motivated researchers to explore more biologically plausible learning algorithms that could potentially shed light on how biological neural systems adapt and learn. Inspired by the counter-current exchange mechanisms observed in biological systems, we propose counter-current learning (CCL), a biologically plausible framework for credit assignment in deep learning. This framework employs a feedforward network to process input data and a feedback network to process targets, with each network enhancing the other through anti-parallel signal propagation. By leveraging the more informative signals from the bottom layer of the feedback network to guide the updates of the top layer of the feedforward network and vice versa, CCL enables the simultaneous transformation of source inputs to target outputs and the dynamic mutual influence of these transformations.Experimental results on MNIST, FashionMNIST, CIFAR10, CIFAR100, and STL-10 datasets using multi-layer perceptrons and convolutional neural networks demonstrate that CCL achieves comparable performance to other biological plausible algorithms while offering a more biologically realistic learning mechanism. Furthermore, we showcase the applicability of our approach to an autoencoder task, underscoring its potential for unsupervised representation learning.Our work presents a promising direction for biologically inspired and plausible learning algorithms, offering insights into the mechanisms of learning and adaptation in neural networks.

Generative Models

Nikita Gushchin, Daniil Selikhanovych, Sergei Kholkin, Evgeny Burnaev, Aleksandr Korotin

The Schrödinger Bridge (SB) problem offers a powerful framework for combining optimal transport and diffusion models. A promising recent approach to solve the SB problem is the Iterative Markovian Fitting (IMF) procedure, which alternates between Markovian and reciprocal projections of continuous-time stochastic processes. However, the model built by the IMF procedure has a long inference time due to using many steps of numerical solvers for stochastic differential equations. To address this limitation, we propose a novel Discrete-time IMF (D-IMF) procedure in which learning of stochastic processes is replaced by learning just a few transition probabilities in discrete time. Its great advantage is that in practice it can be naturally implemented using the Denoising Diffusion GAN (DD-GAN), an already well-established adversarial generative modeling technique. We show that our D-IMF procedure can provide the same quality of unpaired domain translation as the IMF, using only several generation steps instead of hundreds.

Generative Models · New Approaches

Julien Pourcel, Cédric Colas, Gaia Molinaro, Pierre-Yves Oudeyer, Laetitia Teodorescu

The ability to invent novel and interesting problems is a remarkable feature of human intelligence that drives innovation, art, and science. We propose a method that aims to automate this process by harnessing the power of state-of-the-art generative models to produce a diversity of challenging yet solvable problems, here in the context of Python programming puzzles. Inspired by the intrinsically motivated literature, Autotelic CodE Search (ACES) jointly optimizes for the diversity and difficulty of generated problems. We represent problems in a space of LLM-generated semantic descriptors describing the programming skills required to solve them (e.g. string manipulation, dynamic programming, etc.) and measure their difficulty empirically as a linearly decreasing function of the success rate of \textit{Llama-3-70B}, a state-of-the-art LLM problem solver. ACES iteratively prompts a large language model to generate difficult problems achieving a diversity of target semantic descriptors (goal-directed exploration) using previously generated problems as in-context examples. ACES generates problems that are more diverse and more challenging than problems produced by baseline methods and three times more challenging than problems found in existing Python programming benchmarks on average across 11 state-of-the-art code LLMs.

Deep Learning · Algorithms

Jianrong Ding, Zhanyu Liu, Guanjie Zheng, Haiming Jin, Linghe Kong

\textit{Dataset condensation} is a newborn technique that generates a small dataset that can be used in training deep neural networks (DNNs) to lower storage and training costs. The objective of dataset condensation is to ensure that the model trained with the synthetic dataset can perform comparably to the model trained with full datasets. However, existing methods predominantly concentrate on classification tasks, posing challenges in their adaptation to time series forecasting (TS-forecasting). This challenge arises from disparities in the evaluation of synthetic data. In classification, the synthetic data is considered well-distilled if the model trained with the full dataset and the model trained with the synthetic dataset yield identical labels for the same input, regardless of variations in output logits distribution. Conversely, in TS-forecasting, the effectiveness of synthetic data distillation is determined by the distance between predictions of the two models. The synthetic data is deemed well-distilled only when all data points within the predictions are similar. Consequently, TS-forecasting has a more rigorous evaluation methodology compared to classification. To mitigate this gap, we theoretically analyze the optimization objective of dataset condensation for TS-forecasting and propose a new one-line plugin of dataset condensation for TS-forecasting designated as Dataset \textbf{Cond}ensation for \textbf{T}ime \textbf{S}eries \textbf{F}orecasting (CondTSF) based on our analysis. Plugging CondTSF into previous dataset condensation methods facilitates a reduction in the distance between the predictions of the model trained with the full dataset and the model trained with the synthetic dataset, thereby enhancing performance. We conduct extensive experiments on eight commonly used time series datasets. CondTSF consistently improves the performance of all previous dataset condensation methods across all datasets, particularly at low condensing ratios.

Alkis Kalavasis, Amin Karbasi, Argyris Oikonomou, Katerina Sotiraki, Grigoris Velegkas, Manolis Zampetakis

As ML models become increasingly complex and integral to high-stakes domains such as finance and healthcare, they also become more susceptible to sophisticated adversarial attacks. We investigate the threat posed by undetectable backdoors, as defined in Goldwasser et al. [2022], in models developed by insidious external expert firms. When such backdoors exist, they allow the designer of the model to sell information on how to slightly perturb their input to change the outcome of the model. We develop a general strategy to plant backdoors to obfuscated neural networks, that satisfy the security properties of the celebrated notion of indistinguishability obfuscation. Applying obfuscation before releasing neural networks is a strategy that is well motivated to protect sensitive information of the external expert firm. Our method to plant backdoors ensures that even if the weights and architecture of the obfuscated model are accessible, the existence ofthe backdoor is still undetectable. Finally, we introduce the notion of undetectable backdoors to language models and extend our neural network backdoor attacks to such models based on the existence of steganographic functions.

Miscellaneous Aspects of Machine Learning · Kernel methods

Florian Kalinke, Zoltan Szabo

Kernel techniques are among the most influential approaches in data science and statistics. Under mild conditions, the reproducing kernel Hilbert space associated to a kernel is capable of encoding the independence of $M\ge2$ random variables. Probably the most widespread independence measure relying on kernels is the so-called Hilbert-Schmidt independence criterion (HSIC; also referred to as distance covariance in the statistics literature). Despite various existing HSIC estimators designed since its introduction close to two decades ago, the fundamental question of the rate at which HSIC can be estimated is still open. In this work, we prove that the minimax optimal rate of HSIC estimation on $\mathbb{R}^d$ for Borel measures containing the Gaussians with continuous bounded translation-invariant characteristic kernels is $\mathcal{O}\left(n^{-1/2}\right)$. Specifically, our result implies the optimality in the minimax sense of many of the most-frequently used estimators (including the U-statistic, the V-statistic, and the Nyström-based one) on $\mathbb{R}^d$.

Optimization · Zero-order and Black-box Optimization

Huidong Liang, Xingchen Wan, Xiaowen Dong

We address the problem of optimizing over functions defined on node subsets in a graph. The optimization of such functions is often a non-trivial task given their combinatorial, black-box and expensive-to-evaluate nature. Although various algorithms have been introduced in the literature, most are either task-specific or computationally inefficient and only utilize information about the graph structure without considering the characteristics of the function. To address these limitations, we utilize Bayesian Optimization (BO), a sample-efficient black-box solver, and propose a novel framework for combinatorial optimization on graphs. More specifically, we map each $k$-node subset in the original graph to a node in a new combinatorial graph and adopt a local modeling approach to efficiently traverse the latter graph by progressively sampling its subgraphs using a recursive algorithm. Extensive experiments under both synthetic and real-world setups demonstrate the effectiveness of the proposed BO framework on various types of graphs and optimization tasks, where its behavior is analyzed in detail with ablation studies.