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Dec 26

Gene Regulatory Network Inference in the Presence of Dropouts: a Causal View

Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by distorting the joint distribution of the measured gene expressions. Existing approaches typically handle dropout error via imputation, which may introduce spurious relations as the true joint distribution is generally unidentifiable. To tackle this issue, we introduce a causal graphical model to characterize the dropout mechanism, namely, Causal Dropout Model. We provide a simple yet effective theoretical result: interestingly, the conditional independence (CI) relations in the data with dropouts, after deleting the samples with zero values (regardless if technical or not) for the conditioned variables, are asymptotically identical to the CI relations in the original data without dropouts. This particular test-wise deletion procedure, in which we perform CI tests on the samples without zeros for the conditioned variables, can be seamlessly integrated with existing structure learning approaches including constraint-based and greedy score-based methods, thus giving rise to a principled framework for GRNI in the presence of dropouts. We further show that the causal dropout model can be validated from data, and many existing statistical models to handle dropouts fit into our model as specific parametric instances. Empirical evaluation on synthetic, curated, and real-world experimental transcriptomic data comprehensively demonstrate the efficacy of our method.

  • 6 authors
·
Mar 21, 2024

Causal Evaluation of Language Models

Causal reasoning is viewed as crucial for achieving human-level machine intelligence. Recent advances in language models have expanded the horizons of artificial intelligence across various domains, sparking inquiries into their potential for causal reasoning. In this work, we introduce Causal evaluation of Language Models (CaLM), which, to the best of our knowledge, is the first comprehensive benchmark for evaluating the causal reasoning capabilities of language models. First, we propose the CaLM framework, which establishes a foundational taxonomy consisting of four modules: causal target (i.e., what to evaluate), adaptation (i.e., how to obtain the results), metric (i.e., how to measure the results), and error (i.e., how to analyze the bad results). This taxonomy defines a broad evaluation design space while systematically selecting criteria and priorities. Second, we compose the CaLM dataset, comprising 126,334 data samples, to provide curated sets of causal targets, adaptations, metrics, and errors, offering extensive coverage for diverse research pursuits. Third, we conduct an extensive evaluation of 28 leading language models on a core set of 92 causal targets, 9 adaptations, 7 metrics, and 12 error types. Fourth, we perform detailed analyses of the evaluation results across various dimensions (e.g., adaptation, scale). Fifth, we present 50 high-level empirical findings across 9 dimensions (e.g., model), providing valuable guidance for future language model development. Finally, we develop a multifaceted platform, including a website, leaderboards, datasets, and toolkits, to support scalable and adaptable assessments. We envision CaLM as an ever-evolving benchmark for the community, systematically updated with new causal targets, adaptations, models, metrics, and error types to reflect ongoing research advancements. Project website is at https://opencausalab.github.io/CaLM.

OpenCausaLab
·
May 1, 2024

Can Loyalty to Creators Dilute Loyalty to Promoted Products? Examining the Heterogeneous Effects of Live-Streamed Content on Video Game Usage

Social media platforms have led to online consumption communities, or fandoms, that involve complex networks of ancillary creators and consumers focused on some core product or intellectual property. For example, video game communities include networks of players and content creators centered around a specific video game. These networks are complex in that video game publishers often sponsor creators, but creators and publishers may have divergent incentives. Specifically, creators can potentially benefit from content that builds their own following at the expense of the core game. Our research investigates the relationship between consuming live-streamed content and engagement with a specific video game. We examine the causal effect of viewing live-streamed content on subsequent gameplay for a specific game, using an unexpected service interruption of the livestreaming platform and time zone differences among users. We find live-streamed content significantly increases gameplay as a 10% increase in live-streamed viewing minutes results in a 3.08% increase in gameplay minutes. We also explore how this effect varies by user loyalty to different types of streamer channels (firm-owned, mega, and micro). The positive effects of live-streamed content are greatest for micro-streamers and smallest for mega-streamers. These findings are salient for firms allocating sponsorship resources.

  • 3 authors
·
Nov 1, 2024

Rethinking the Bias of Foundation Model under Long-tailed Distribution

Long-tailed learning has garnered increasing attention due to its practical significance. Among the various approaches, the fine-tuning paradigm has gained considerable interest with the advent of foundation models. However, most existing methods primarily focus on leveraging knowledge from these models, overlooking the inherent biases introduced by the imbalanced training data they rely on. In this paper, we examine how such imbalances from pre-training affect long-tailed downstream tasks. Specifically, we find the imbalance biases inherited in foundation models on downstream task as parameter imbalance and data imbalance. During fine-tuning, we observe that parameter imbalance plays a more critical role, while data imbalance can be mitigated using existing re-balancing strategies. Moreover, we find that parameter imbalance cannot be effectively addressed by current re-balancing techniques, such as adjusting the logits, during training, unlike data imbalance. To tackle both imbalances simultaneously, we build our method on causal learning and view the incomplete semantic factor as the confounder, which brings spurious correlations between input samples and labels. To resolve the negative effects of this, we propose a novel backdoor adjustment method that learns the true causal effect between input samples and labels, rather than merely fitting the correlations in the data. Notably, we achieve an average performance increase of about 1.67% on each dataset.

  • 5 authors
·
Jan 27

Causal Inference by String Diagram Surgery

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

  • 3 authors
·
Nov 20, 2018

Multimodal Causal Reasoning Benchmark: Challenging Vision Large Language Models to Infer Causal Links Between Siamese Images

Large Language Models (LLMs) have showcased exceptional ability in causal reasoning from textual information. However, will these causalities remain straightforward for Vision Large Language Models (VLLMs) when only visual hints are provided? Motivated by this, we propose a novel Multimodal Causal Reasoning benchmark, namely MuCR, to challenge VLLMs to infer semantic cause-and-effect relationship when solely relying on visual cues such as action, appearance, clothing, and environment. Specifically, we introduce a prompt-driven image synthesis approach to create siamese images with embedded semantic causality and visual cues, which can effectively evaluate VLLMs' causal reasoning capabilities. Additionally, we develop tailored metrics from multiple perspectives, including image-level match, phrase-level understanding, and sentence-level explanation, to comprehensively assess VLLMs' comprehension abilities. Our extensive experiments reveal that the current state-of-the-art VLLMs are not as skilled at multimodal causal reasoning as we might have hoped. Furthermore, we perform a comprehensive analysis to understand these models' shortcomings from different views and suggest directions for future research. We hope MuCR can serve as a valuable resource and foundational benchmark in multimodal causal reasoning research. The project is available at: https://github.com/Zhiyuan-Li-John/MuCR

  • 7 authors
·
Aug 15, 2024

Monarch Mixer: A Simple Sub-Quadratic GEMM-Based Architecture

Machine learning models are increasingly being scaled in both sequence length and model dimension to reach longer contexts and better performance. However, existing architectures such as Transformers scale quadratically along both these axes. We ask: are there performant architectures that can scale sub-quadratically along sequence length and model dimension? We introduce Monarch Mixer (M2), a new architecture that uses the same sub-quadratic primitive along both sequence length and model dimension: Monarch matrices, a simple class of expressive structured matrices that captures many linear transforms, achieves high hardware efficiency on GPUs, and scales sub-quadratically. As a proof of concept, we explore the performance of M2 in three domains: non-causal BERT-style language modeling, ViT-style image classification, and causal GPT-style language modeling. For non-causal BERT-style modeling, M2 matches BERT-base and BERT-large in downstream GLUE quality with up to 27% fewer parameters, and achieves up to 9.1times higher throughput at sequence length 4K. On ImageNet, M2 outperforms ViT-b by 1% in accuracy, with only half the parameters. Causal GPT-style models introduce a technical challenge: enforcing causality via masking introduces a quadratic bottleneck. To alleviate this bottleneck, we develop a novel theoretical view of Monarch matrices based on multivariate polynomial evaluation and interpolation, which lets us parameterize M2 to be causal while remaining sub-quadratic. Using this parameterization, M2 matches GPT-style Transformers at 360M parameters in pretraining perplexity on The PILE--showing for the first time that it may be possible to match Transformer quality without attention or MLPs.

  • 10 authors
·
Oct 18, 2023

Efficient Parallel Samplers for Recurrent-Depth Models and Their Connection to Diffusion Language Models

Language models with recurrent depth, also referred to as universal or looped when considering transformers, are defined by the capacity to increase their computation through the repetition of layers. Recent efforts in pretraining have demonstrated that these architectures can scale to modern language modeling tasks while exhibiting advantages in reasoning tasks. In this work, we examine the relationship between recurrent-depth models and diffusion language models. Building on their similarities, we develop a new diffusion forcing sampler for these models to accelerate generation. The sampler advances by decoding new tokens at every forward pass of the model, while the latent states of these tokens can be further refined in parallel through recurrence. Theoretically, generation with our sampler is strictly more expressive than the baseline autoregressive generation using the same time budget on modern hardware. Moreover, this sampler, based on principles from diffusion literature, can be directly applied to existing 3.5B recurrent-depth transformers without any tuning, leading to up to a 5x speedup. Consequently, our findings not only provide an efficient mechanism for parallelizing the extra computation in recurrent-depth models at inference, but also suggest that such models can be naturally viewed as strong continuous, though causal, diffusion language models.

ImplicitQA: Going beyond frames towards Implicit Video Reasoning

Video QA has made significant strides by leveraging multimodal learning to align visual and textual modalities. However, current benchmarks overwhelmingly focus on questions answerable through explicit visual content - actions, objects & events directly observable within individual frames or short clips. In contrast, creative and cinematic videos - such as movies, TV shows, and narrative-driven content - employ storytelling techniques that deliberately omit certain depictions, requiring viewers to infer motives, causality, and relationships across discontinuous frames. Humans naturally excel at such implicit reasoning, seamlessly integrating information across time and context to construct coherent narratives. Current VideoQA systems and benchmarks fail to capture this essential dimension of human-like understanding. To bridge this gap, we present ImplicitQA, a novel benchmark specifically designed to test models on implicit reasoning. It comprises 1K meticulously annotated QA pairs derived from 320+ high-quality creative video clips, systematically categorized into key reasoning dimensions: lateral and vertical spatial reasoning, depth and proximity, viewpoint and visibility, motion and trajectory, causal and motivational reasoning, social interactions, physical context, and inferred counting. These annotations are deliberately challenging, crafted by authors ensuring high-quality. Our extensive evaluations on leading VideoQA models reveals performance degradation, underscoring their reliance on surface-level visual cues and highlighting the difficulty of implicit reasoning. Performance variations across models further illustrate the complexity and diversity of the challenges presented by ImplicitQA. By releasing both the dataset and our data collection framework, we aim to stimulate further research and development in the community. https://huggingface.co/datasets/ucf-crcv/ImplicitQA.

  • 8 authors
·
Jun 26