Advances in neural information processing systems最新文献

{"title":"Newton Informed Neural Operator for Solving Nonlinear Partial Differential Equations.","authors":"Wenrui Hao, Xinliang Liu, Yahong Yang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Solving nonlinear partial differential equations (PDEs) with multiple solutions is essential in various fields, including physics, biology, and engineering. However, traditional numerical methods, such as finite element and finite difference methods, often face challenges when dealing with nonlinear solvers, particularly in the presence of multiple solutions. These methods can become computationally expensive, especially when relying on solvers like Newton's method, which may struggle with ill-posedness near bifurcation points. In this paper, we propose a novel approach, the Newton Informed Neural Operator, which learns the Newton solver for nonlinear PDEs. Our method integrates traditional numerical techniques with the Newton nonlinear solver, efficiently learning the nonlinear mapping at each iteration. This approach allows us to compute multiple solutions in a single learning process while requiring fewer supervised data points than existing neural network methods.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 ","pages":"120832-120860"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11973962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biomedical Visual Instruction Tuning with Clinician Preference Alignment.","authors":"Hejie Cui, Lingjun Mao, Xin Liang, Jieyu Zhang, Hui Ren, Quanzheng Li, Xiang Li, Carl Yang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Recent advancements in multimodal foundation models have showcased impressive capabilities in understanding and reasoning with visual and textual information. Adapting these foundation models trained for general usage to specialized domains like biomedicine requires large-scale domain-specific instruction datasets. While existing works have explored curating such datasets automatically, the resultant datasets are not explicitly aligned with domain expertise. In this work, we propose a data-centric framework, <b>Biomed</b>ical <b>V</b>isual <b>I</b>nstruction <b>T</b>uning with <b>C</b>linician Preference <b>Al</b>ignment (BioMed-VITAL), that incorporates clinician preferences into both stages of generating and selecting instruction data for tuning biomedical multimodal foundation models. First, during the generation stage, we prompt the GPT-4V generator with a diverse set of clinician-selected demonstrations for preference-aligned data candidate generation. Then, during the selection phase, we train a separate selection model, which explicitly distills clinician and policy-guided model preferences into a rating function to select high-quality data for medical instruction tuning. Results show that the model tuned with the instruction-following data from our method demonstrates a significant improvement in open visual chat (18.5% relatively) and medical VQA (win rate up to 81.73%). Our instruction-following data and models are available at https://BioMed-VITAL.github.io.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 ","pages":"96449-96467"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143525294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cross-Care: Assessing the Healthcare Implications of Pre-training Data on Language Model Bias.","authors":"Shan Chen, Jack Gallifant, Mingye Gao, Pedro Moreira, Nikolaj Munch, Ajay Muthukkumar, Arvind Rajan, Jaya Kolluri, Amelia Fiske, Janna Hastings, Hugo Aerts, Brian Anthony, Leo Anthony Celi, William G La Cava, Danielle S Bitterman","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Large language models (LLMs) are increasingly essential in processing natural languages, yet their application is frequently compromised by biases and inaccuracies originating in their training data. In this study, we introduce <b>Cross-Care</b>, the first benchmark framework dedicated to assessing biases and real world knowledge in LLMs, specifically focusing on the representation of disease prevalence across diverse demographic groups. We systematically evaluate how demographic biases embedded in pre-training corpora like <i>ThePile</i> influence the outputs of LLMs. We expose and quantify discrepancies by juxtaposing these biases against actual disease prevalences in various U.S. demographic groups. Our results highlight substantial misalignment between LLM representation of disease prevalence and real disease prevalence rates across demographic subgroups, indicating a pronounced risk of bias propagation and a lack of real-world grounding for medical applications of LLMs. Furthermore, we observe that various alignment methods minimally resolve inconsistencies in the models' representation of disease prevalence across different languages. For further exploration and analysis, we make all data and a data visualization tool available at: www.crosscare.net.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 D-ampB","pages":"23756-23795"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12045606/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the trade-off between deep-learning and explainable models for brain-machine interfaces.","authors":"Luis H Cubillos, Guy Revach, Matthew J Mender, Joseph T Costello, Hisham Temmar, Aren Hite, Diksha Zutshi, Dylan M Wallace, Xiaoyong Ni, Madison M Kelberman, Matthew S Willsey, Ruud J G van Sloun, Nir Shlezinger, Parag Patil, Anne Draelos, Cynthia A Chestek","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>People with brain or spinal cord-related paralysis often need to rely on others for basic tasks, limiting their independence. A potential solution is brain-machine interfaces (BMIs), which could allow them to voluntarily control external devices (e.g., robotic arm) by decoding brain activity to movement commands. In the past decade, deep-learning decoders have achieved state-of-the-art results in most BMI applications, ranging from speech production to finger control. However, the 'black-box' nature of deep-learning decoders could lead to unexpected behaviors, resulting in major safety concerns in real-world physical control scenarios. In these applications, explainable but lower-performing decoders, such as the Kalman filter (KF), remain the norm. In this study, we designed a BMI decoder based on KalmanNet, an extension of the KF that augments its operation with recurrent neural networks to compute the Kalman gain. This results in a varying \"trust\" that shifts between inputs and dynamics. We used this algorithm to predict finger movements from the brain activity of two monkeys. We compared KalmanNet results offline (pre-recorded data, <math><mi>n</mi> <mspace></mspace> <mo>=</mo> <mspace></mspace> <mn>13</mn></math> days) and online (real-time predictions, <math><mi>n</mi> <mspace></mspace> <mo>=</mo> <mspace></mspace> <mn>5</mn></math> days) with a simple KF and two recent deep-learning algorithms: tcFNN (non-ReFIT version) and LSTM. KalmanNet achieved comparable or better results than other deep learning models in offline and online modes, relying on the dynamical model for stopping while depending more on neural inputs for initiating movements. We further validated this mechanism by implementing a heteroscedastic KF that used the same strategy, and it also approached state-of-the-art performance while remaining in the explainable domain of standard KFs. However, we also see two downsides to KalmanNet. KalmanNet shares the limited generalization ability of existing deep-learning decoders, and its usage of the KF as an inductive bias limits its performance in the presence of unseen noise distributions. Despite this trade-off, our analysis successfully integrates traditional controls and modern deep-learning approaches to motivate high-performing yet still explainable BMI designs.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 ","pages":"133975-133998"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11996206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Divergences between Language Models and Human Brains.","authors":"Yuchen Zhou, Emmy Liu, Graham Neubig, Michael J Tarr, Leila Wehbe","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Do machines and humans process language in similar ways? Recent research has hinted at the affirmative, showing that human neural activity can be effectively predicted using the internal representations of language models (LMs). Although such results are thought to reflect shared computational principles between LMs and human brains, there are also clear differences in how LMs and humans represent and use language. In this work, we systematically explore the divergences between human and machine language processing by examining the differences between LM representations and human brain responses to language as measured by Magnetoencephalography (MEG) across two datasets in which subjects read and listened to narrative stories. Using an LLM-based data-driven approach, we identify two domains that LMs do not capture well: <b>social/emotional intelligence</b> and <b>physical commonsense</b>. We validate these findings with human behavioral experiments and hypothesize that the gap is due to insufficient representations of social/emotional and physical knowledge in LMs. Our results show that fine-tuning LMs on these domains can improve their alignment with human brain responses.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 ","pages":"137999-138031"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144163893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scale-invariant Optimal Sampling for Rare-events Data and Sparse Models.","authors":"Jing Wang, HaiYing Wang, Hao Helen Zhang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Subsampling is effective in tackling computational challenges for massive data with rare events. Overly aggressive subsampling may adversely affect estimation efficiency, and optimal subsampling is essential to mitigate the information loss. However, existing optimal subsampling probabilities depends on data scales, and some scaling transformations may result in inefficient subsamples. This problem is more significant when there are inactive features, because their influence on the subsampling probabilities can be arbitrarily magnified by inappropriate scaling transformations. We tackle this challenge and introduce a scale-invariant optimal subsampling function in the context of sparse models, where inactive features are commonly assumed. Instead of focusing on estimating model parameters, we define an optimal subsampling function to minimize the prediction error, using adaptive lasso as an example to outline the estimation procedure and study its theoretical guarantee. We first introduce the adaptive lasso estimator for rare-events data and establish its oracle properties, thereby validating the use of subsampling. Then we derive a scale-invariant optimal subsampling function that minimizes the prediction error of the inverse probability weighted (IPW) adaptive lasso. Finally, we present an estimator based on the maximum sampled conditional likelihood (MSCL) to further improve the estimation efficiency. We conduct numerical experiments using both simulated and real-world data sets to demonstrate the performance of the proposed methods.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 ","pages":"98384-98418"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12245189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On Neural Networks as Infinite Tree-Structured Probabilistic Graphical Models.","authors":"Boyao Li, Alexander J Thomson, Houssam Nassif, Matthew M Engelhard, David Page","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Deep neural networks (DNNs) lack the precise semantics and definitive probabilistic interpretation of probabilistic graphical models (PGMs). In this paper, we propose an innovative solution by constructing infinite tree-structured PGMs that correspond exactly to neural networks. Our research reveals that DNNs, during forward propagation, indeed perform approximations of PGM inference that are precise in this alternative PGM structure. Not only does our research complement existing studies that describe neural networks as kernel machines or infinite-sized Gaussian processes, it also elucidates a more direct approximation that DNNs make to exact inference in PGMs. Potential benefits include improved pedagogy and interpretation of DNNs, and algorithms that can merge the strengths of PGMs and DNNs.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 ","pages":"4598-4628"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974605/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Text to Blind Motion.","authors":"Hee Jae Kim, Kathakoli Sengupta, Masaki Kuribayashi, Hernisa Kacorri, Eshed Ohn-Bar","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>People who are blind perceive the world differently than those who are sighted, which can result in distinct motion characteristics. For instance, when crossing at an intersection, blind individuals may have different patterns of movement, such as veering more from a straight path or using touch-based exploration around curbs and obstacles. These behaviors may appear less predictable to motion models embedded in technologies such as autonomous vehicles. Yet, the ability of 3D motion models to capture such behavior has not been previously studied, as existing datasets for 3D human motion currently lack diversity and are biased toward people who are sighted. In this work, we introduce BlindWays, the first multimodal motion benchmark for pedestrians who are blind. We collect 3D motion data using wearable sensors with 11 blind participants navigating eight different routes in a real-world urban setting. Additionally, we provide rich textual descriptions that capture the distinctive movement characteristics of blind pedestrians and their interactions with both the navigation aid (<i>e.g</i>., a white cane or a guide dog) and the environment. We benchmark state-of-the-art 3D human prediction models, finding poor performance with off-the-shelf and pre-training-based methods for our novel task. To contribute toward safer and more reliable systems that can seamlessly reason over diverse human movements in their environments, our text-and-motion benchmark is available at https://blindways.github.io/.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 ","pages":"16272-16285"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12013345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144065352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ultrafast classical phylogenetic method beats large protein language models on variant effect prediction.","authors":"Sebastian Prillo, Wilson Wu, Yun S Song","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Amino acid substitution rate matrices are fundamental to statistical phylogenetics and evolutionary biology. Estimating them typically requires reconstructed trees for massive amounts of aligned proteins, which poses a major computational bottleneck. In this paper, we develop a near-linear time method to estimate these rate matrices from multiple sequence alignments (MSAs) alone, thereby speeding up computation by orders of magnitude. Our method relies on a near-linear time cherry reconstruction algorithm which we call <i>FastCherries</i> and it can be easily applied to MSAs with millions of sequences. On both simulated and real data, we demonstrate the speed and accuracy of our method as applied to the classical model of protein evolution. By leveraging the unprecedented scalability of our method, we develop a new, rich phylogenetic model called <i>SiteRM</i>, which can estimate a general <i>site-specific</i> rate matrix for each column of an MSA. Remarkably, in variant effect prediction for both clinical and deep mutational scanning data in ProteinGym, we show that despite being an independent-sites model, our SiteRM model outperforms large protein language models that learn complex residue-residue interactions between different sites. We attribute our increased performance to conceptual advances in our probabilistic treatment of evolutionary data and our ability to handle extremely large MSAs. We anticipate that our work will have a lasting impact across both statistical phylogenetics and computational variant effect prediction. FastCherries and SiteRM are implemented in the CherryML package https://github.com/songlab-cal/CherryML.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 ","pages":"130265-130290"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144251069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Binding in hippocampal-entorhinal circuits enables compositionality in cognitive maps.","authors":"Christopher J Kymn, Sonia Mazelet, Anthony Thomas, Denis Kleyko, E Paxon Frady, Friedrich T Sommer, Bruno A Olshausen","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We propose a normative model for spatial representation in the hippocampal formation that combines optimality principles, such as maximizing coding range and spatial information per neuron, with an algebraic framework for computing in distributed representation. Spatial position is encoded in a residue number system, with individual residues represented by high-dimensional, complex-valued vectors. These are composed into a single vector representing position by a similarity-preserving, conjunctive vector-binding operation. Self-consistency between the representations of the overall position and of the individual residues is enforced by a modular attractor network whose modules correspond to the grid cell modules in entorhinal cortex. The vector binding operation can also associate different contexts to spatial representations, yielding a model for entorhinal cortex and hippocampus. We show that the model achieves normative desiderata including superlinear scaling of patterns with dimension, robust error correction, and hexagonal, carry-free encoding of spatial position. These properties in turn enable robust path integration and association with sensory inputs. More generally, the model formalizes how compositional computations could occur in the hippocampal formation and leads to testable experimental predictions.</p>","PeriodicalId":72099,"journal":{"name":"Advances in neural information processing systems","volume":"37 ","pages":"39128-39157"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12183976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}