NeurIPS 2024 Papers

Deep learning based neural decoding from stereotactic electroencephalography (sEEG) would likely benefit from scaling up both dataset and model size. To achieve this, combining data across multiple subjects is crucial. However, in sEEG cohorts, each subject has a variable number of electrodes placed at distinct locations in their brain, solely based on clinical needs. Such heterogeneity in electrode number/placement poses a significant challenge for data integration, since there is no clear correspondence of the neural activity recorded at distinct sites between individuals. Here we introduce seegnificant: a training framework and architecture that can be used to decode behavior across subjects using sEEG data. We tokenize the neural activity within electrodes using convolutions and extract long-term temporal dependencies between tokens using self-attention in the time dimension. The 3D location of each electrode is then mixed with the tokens, followed by another self-attention in the electrode dimension to extract effective spatiotemporal neural representations. Subject-specific heads are then used for downstream decoding tasks. Using this approach, we construct a multi-subject model trained on the combined data from 21 subjects performing a behavioral task. We demonstrate that our model is able to decode the trial-wise response time of the subjects during the behavioral task solely from neural data. We also show that the neural representations learned by pretraining our model across individuals can be transferred in a few-shot manner to new subjects. This work introduces a scalable approach towards sEEG data integration for multi-subject model training, paving the way for cross-subject generalization for sEEG decoding.

Failures of fairness or robustness in machine learning predictive settings can be due to undesired dependencies between covariates, outcomes and auxiliary factors of variation. A common strategy to mitigate these failures is data balancing, which attempts to remove those undesired dependencies. In this work, we define conditions on the training distribution for data balancing to lead to fair or robust models. Our results display that in many cases, the balanced distribution does not correspond to selectively removing the undesired dependencies in a causal graph of the task, leading to multiple failure modes and even interference with other mitigation techniques such as regularization. Overall, our results highlight the importance of taking the causal graph into account before performing data balancing.

Predicting molecular impact on cellular function is a core challenge in therapeutic design. Phenomic experiments, designed to capture cellular morphology, utilize microscopy based techniques and demonstrate a high throughput solution for uncovering molecular impact on the cell. In this work, we learn a joint latent space between molecular structures and microscopy phenomic experiments, aligning paired samples with contrastive learning. Specifically, we study the problem of Contrastive PhenoMolecular Retrieval, which consists of zero-shot molecular structure identification conditioned on phenomic experiments. We assess challenges in multi-modal learning of phenomics and molecular modalities such as experimental batch effect, inactive molecule perturbations, and encoding perturbation concentration. We demonstrate improved multi-modal learner retrieval through (1) a uni-modal pre-trained phenomics model, (2) a novel inter sample similarity aware loss, and (3) models conditioned on a representation of molecular concentration. Following this recipe, we propose MolPhenix, a molecular phenomics model. MolPhenix leverages a pre-trained phenomics model to demonstrate significant performance gains across perturbation concentrations, molecular scaffolds, and activity thresholds. In particular, we demonstrate an 8.1 times improvement in zero shot molecular retrieval of active molecules over the previous state-of-the-art, reaching 77.33% in top-1% accuracy. These results open the door for machine learning to be applied in virtual phenomics screening, which can significantly benefit drug discovery applications.

We study episodic linear mixture MDPs with the unknown transition and adversarial rewards under full-information feedback, employing *dynamic regret* as the performance measure. We start with in-depth analyses of the strengths and limitations of the two most popular methods: occupancy-measure-based and policy-based methods. We observe that while the occupancy-measure-based method is effective in addressing non-stationary environments, it encounters difficulties with the unknown transition. In contrast, the policy-based method can deal with the unknown transition effectively but faces challenges in handling non-stationary environments. Building on this, we propose a novel algorithm that combines the benefits of both methods. Specifically, it employs (i) an *occupancy-measure-based global optimization* with a two-layer structure to handle non-stationary environments; and (ii) a *policy-based variance-aware value-targeted regression* to tackle the unknown transition. We bridge these two parts by a novel conversion. Our algorithm enjoys an $\widetilde{\mathcal{O}}(d \sqrt{H^3 K} + \sqrt{HK(H + \bar{P}_K)})$ dynamic regret, where $d$ is the feature mapping dimension, $H$ is the episode length, $K$ is the number of episodes, $\bar{P}_K$ is the non-stationarity measure. We show it is minimax optimal up to logarithmic factors by establishing a matching lower bound. To the best of our knowledge, this is the **first** work that achieves **near-optimal** dynamic regret for adversarial linear mixture MDPs with the unknown transition without prior knowledge of the non-stationarity measure.

During natural evolution, the primary visual cortex (V1) of lower mammals typically forms salt-and-pepper organizations, while higher mammals and primates develop pinwheel structures with distinct topological properties. Despite the general belief that V1 neurons primarily serve as edge detectors, the functional advantages of pinwheel structures over salt-and-peppers are not well recognized. To this end, we propose a two-dimensional self-evolving spiking neural network that integrates Hebbian-like plasticity and empirical morphological data. Through extensive exposure to image data, our network evolves from salt-and-peppers to pinwheel structures, with neurons becoming localized bandpass filters responsive to various orientations. This transformation is accompanied by an increase in visual field overlap. Our findings indicate that neurons in pinwheel centers (PCs) respond more effectively to complex spatial textures in natural images, exhibiting quicker responses than those in salt-and-pepper organizations. PCs act as first-order stage processors with heightened sensitivity and reduced latency to intricate contours, while adjacent iso-orientation domains serve as second-order stage processors that refine edge representations for clearer perception. This study presents the first theoretical evidence that pinwheel structures function as crucial detectors of spatial contour saliency in the visual cortex.

Algorithms with predictions are gaining traction across various domains, as a way to surpass traditional worst-case bounds through (machine-learned) advice. We study the canonical problem of $k$-facility location mechanism design, where the $n$ agents are strategic and might misreport their locations. We receive a prediction for each agent's location, and these predictions are crucially allowed to be only "mostly" and "approximately" correct (MAC for short): a $\delta$-fraction of the predicted locations are allowed to be arbitrarily incorrect, and the remainder of the predictions are required to be correct up to an $\varepsilon$-error. Moreover, we make no assumption on the independence of the errors. Can such "flawed" predictions allow us to beat the current best bounds for strategyproof facility location? We show how natural robustness of the $1$-median (also known as the geometric median) of a set of points leads to an algorithm for single-facility location with MAC predictions. We extend our results to a natural "balanced" variant of the $k$-facility case, and show that without balancedness, robustness completely breaks down even for $k=2$ facilities on a line. As our main result, for this "unbalanced" setting we devise a truthful random mechanism, which outperforms the best known mechanism (with no predictions) by Lu et al.~[2010]. En route, we introduce the problem of "second" facility location, in which the first facility location is already fixed. Our robustness findings may be of independent interest, as quantitative versions of classic breakdown-point results in robust statistics.

Binary analysis is a core component of many critical security tasks, including reverse engineering, malware analysis, and vulnerability detection. Manual analysis is often time-consuming, but identifying commonly-used or previously-seen functions can reduce the time it takes to understand a new file. However, given the complexity of assembly, and the NP-hard nature of determining function equivalence, this task is extremely difficult. Common approaches often use sophisticated disassembly and decompilation tools, graph analysis, and other expensive pre-processing steps to perform function similarity searches over some corpus. In this work, we identify a number of discrepancies between the current research environment and the underlying application need. To remedy this, we build a new benchmark, REFuSe-Bench, for binary function similarity detection consisting of high-quality datasets and tests that better reflect real-world use cases. In doing so, we address issues like data duplication and accurate labeling, experiment with real malware, and perform the first serious evaluation of ML binary function similarity models on Windows data. Our benchmark reveals that a new, simple baseline — one which looks at only the raw bytes of a function, and requires no disassembly or other pre-processing --- is able to achieve state-of-the-art performance in multiple settings. Our findings challenge conventional assumptions that complex models with highly-engineered features are being used to their full potential, and demonstrate that simpler approaches can provide significant value.

In recent years, there has been significant research focusing on addressing security concerns in single-modal person re-identification (ReID) systems that are based on RGB images. However, the safety of cross-modality scenarios, which are more commonly encountered in practical applications involving images captured by infrared cameras, has not received adequate attention. The main challenge in cross-modality ReID lies in effectively dealing with visual differences between different modalities. For instance, infrared images are typically grayscale, unlike visible images that contain color information. Existing attack methods have primarily focused on the characteristics of the visible image modality, overlooking the features of other modalities and the variations in data distribution among different modalities. This oversight can potentially undermine the effectiveness of these methods in image retrieval across diverse modalities. This study represents the first exploration into the security of cross-modality ReID models and proposes a universal perturbation attack specifically designed for cross-modality ReID. This attack optimizes perturbations by leveraging gradients from diverse modality data, thereby disrupting the discriminator and reinforcing the differences between modalities. We conducted experiments on three widely used cross-modality datasets, namely RegDB, SYSU, and LLCM. The results not only demonstrate the effectiveness of our method but also provide insights for future improvements in the robustness of cross-modality ReID systems.

With the widespread application of Large Language Models (LLMs) to various domains, concerns regarding the trustworthiness of LLMs in safety-critical scenarios have been raised, due to their unpredictable tendency to hallucinate and generate misinformation. Existing LLMs do not have an inherent functionality to provide the users with an uncertainty/confidence metric for each response it generates, making it difficult to evaluate trustworthiness. Although several studies aim to develop uncertainty quantification methods for LLMs, they have fundamental limitations, such as being restricted to classification tasks, requiring additional training and data, considering only lexical instead of semantic information, and being prompt-wise but not response-wise. A new framework is proposed in this paper to address these issues. Semantic density extracts uncertainty/confidence information for each response from a probability distribution perspective in semantic space. It has no restriction on task types and is "off-the-shelf" for new models and tasks. Experiments on seven state-of-the-art LLMs, including the latest Llama 3 and Mixtral-8x22B models, on four free-form question-answering benchmarks demonstrate the superior performance and robustness of semantic density compared to prior approaches.

Self-supervised large language models have demonstrated the ability to perform various tasks via in-context learning, but little is known about where the model locates the task with respect to prompt instructions and demonstration examples. In this work, we attempt to characterize the region where large language models transition from recognizing the task to performing the task. Through a series of layer-wise context-masking experiments on GPTNeo2.7B, Bloom3B, Starcoder2-7B, Llama3.1-8B, Llama3.1-8B-Instruct, on Machine Translation and Code generation, we demonstrate evidence of a "task recognition" point where the task is encoded into the input representations and attention to context is no longer necessary. Taking advantage of this redundancy results in 45% computational savings when prompting with 5 examples, and task recognition achieved at layer 14 / 32 using an example with Machine Translation. Our findings also have implications for resource and parameter efficient fine-tuning; we observe a correspondence between strong fine-tuning performance of individual LoRA layers and the task recognition layers.

We present NeuralFluid, a novel framework to explore neural control and design of complex fluidic systems with dynamic solid boundaries. Our system features a fast differentiable Navier-Stokes solver with solid-fluid interface handling, a low-dimensional differentiable parametric geometry representation, a control-shape co-design algorithm, and gym-like simulation environments to facilitate various fluidic control design applications. Additionally, we present a benchmark of design, control, and learning tasks on high-fidelity, high-resolution dynamic fluid environments that pose challenges for existing differentiable fluid simulators. These tasks include designing the control of artificial hearts, identifying robotic end-effector shapes, and controlling a fluid gate. By seamlessly incorporating our differentiable fluid simulator into a learning framework, we demonstrate successful design, control, and learning results that surpass gradient-free solutions in these benchmark tasks.

We prove that single-parameter natural exponential families with subexponential tails are self-concordant with polynomial-sized parameters. For subgaussian natural exponential families we establish an exact characterization of the growth rate of the self-concordance parameter. Applying these findings to bandits allows us to fill gaps in the literature: We show that optimistic algorithms for generalized linear bandits enjoy regret bounds that are both second-order (scale with the variance of the optimal arm's reward distribution) and free of an exponential dependence on the bound of the problem parameter in the leading term. To the best of our knowledge, ours is the first regret bound for generalized linear bandits with subexponential tails, broadening the class of problems to include Poisson, exponential and gamma bandits.

Point Cloud Interpolation confronts challenges from point sparsity, complex spatiotemporal dynamics, and the difficulty of deriving complete 3D point clouds from sparse temporal information. This paper presents NeuroGauss4D-PCI, which excels at modeling complex non-rigid deformations across varied dynamic scenes. The method begins with an iterative Gaussian cloud soft clustering module, offering structured temporal point cloud representations. The proposed temporal radial basis function Gaussian residual utilizes Gaussian parameter interpolation over time, enabling smooth parameter transitions and capturing temporal residuals of Gaussian distributions. Additionally, a 4D Gaussian deformation field tracks the evolution of these parameters, creating continuous spatiotemporal deformation fields. A 4D neural field transforms low-dimensional spatiotemporal coordinates ($x,y,z,t$) into a high-dimensional latent space. Finally, we adaptively and efficiently fuse the latent features from neural fields and the geometric features from Gaussian deformation fields. NeuroGauss4D-PCI outperforms existing methods in point cloud frame interpolation, delivering leading performance on both object-level (DHB) and large-scale autonomous driving datasets (NL-Drive), with scalability to auto-labeling and point cloud densification tasks.

We study the evaluation of a policy under best- and worst-case perturbations to a Markov decision process (MDP), using transition observations from the original MDP, whether they are generated under the same or a different policy. This is an important problem when there is the possibility of a shift between historical and future environments, \emph{e.g.} due to unmeasured confounding, distributional shift, or an adversarial environment. We propose a perturbation model that allows changes in the transition kernel densities up to a given multiplicative factor or its reciprocal, extending the classic marginal sensitivity model (MSM) for single time-step decision-making to infinite-horizon RL. We characterize the sharp bounds on policy value under this model -- \emph{i.e.}, the tightest possible bounds based on transition observations from the original MDP -- and we study the estimation of these bounds from such transition observations. We develop an estimator with several important guarantees: it is semiparametrically efficient, and remains so even when certain necessary nuisance functions, such as worst-case Q-functions, are estimated at slow, nonparametric rates. Our estimator is also asymptotically normal, enabling straightforward statistical inference using Wald confidence intervals. Moreover, when certain nuisances are estimated inconsistently, the estimator still provides valid, albeit possibly not sharp, bounds on the policy value. We validate these properties in numerical simulations. The combination of accounting for environment shifts from train to test (robustness), being insensitive to nuisance-function estimation (orthogonality), and addressing the challenge of learning from finite samples (inference) together leads to credible and reliable policy evaluation.

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.

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.

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.

Using image models naively for solving inverse video problems often suffers from flickering, texture-sticking, and temporal inconsistency in generated videos. To tackle these problems, in this paper, we view frames as continuous functions in the 2D space, and videos as a sequence of continuous warping transformations between different frames. This perspective allows us to train function space diffusion models only on **images** and utilize them to solve temporally correlated inverse problems. The function space diffusion models need to be equivariant with respect to the underlying spatial transformations. To ensure temporal consistency, we introduce a simple post-hoc test-time guidance towards (self)-equivariant solutions. Our method allows us to deploy state-of-the-art latent diffusion models such as Stable Diffusion XL to solve video inverse problems. We demonstrate the effectiveness of our method for video inpainting and $8\times$ video super-resolution, outperforming existing techniques based on noise transformations. We provide generated video results in the following URL: https://giannisdaras.github.io/warped_diffusion.github.io/.

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.