Motivation: Standard genome-wide association studies in cancer genomics rely on statistical significance with multiple testing correction, but systematically fail in underpowered cohorts. In TCGA breast cancer (n=967, 133 deaths), low event rates (13.8%) create severe power limitations, producing false negatives for known drivers and false positives for large passenger genes. Results: We developed a five-criteria computational framework integrating causal inference (inverse probability weighting, doubly robust estimation) with orthogonal biological validation (expression, mutation patterns, literature evidence). Applied to TCGA-BRCA mortality analysis, standard Cox+FDR detected zero genes at FDR<0.05, confirming complete failure in underpowered settings. Our framework correctly identified RYR2 -- a cardiac gene with no cancer function -- as a false positive despite nominal significance (p=0.024), while identifying KMT2C as a complex candidate requiring validation despite marginal significance (p=0.047, q=0.954). Power analysis revealed median power of 15.1% across genes, with KMT2C achieving only 29.8% power (HR=1.55), explaining borderline statistical significance despite strong biological evidence. The framework distinguished true signals from artifacts through mutation pattern analysis: RYR2 showed 29.8% silent mutations (passenger signature) with no hotspots, while KMT2C showed 6.7% silent mutations with 31.4% truncating variants (driver signature). This multi-evidence approach provides a template for analyzing underpowered cohorts, prioritizing biological interpretability over purely statistical significance. Availability: All code and analysis pipelines available at github.com/akarlaraytu/causal-inference-for-cancer-genomics

Motivation. Understanding the pan-cancer mutational landscape offers critical insights into the molecular mechanisms underlying tumorigenesis. While patient-level machine learning techniques have been widely employed to identify tumor subtypes, cohort-level clustering, where entire cancer types are grouped based on shared molecular features, has largely relied on classical statistical methods. Results. In this study, we introduce a novel unsupervised contrastive learning framework to cluster 43 cancer types based on coding mutation data derived from the COSMIC database. For each cancer type, we construct two complementary mutation signatures: a gene-level profile capturing nucleotide substitution patterns across the most frequently mutated genes, and a chromosome-level profile representing normalized substitution frequencies across chromosomes. These dual views are encoded using TabNet encoders and optimized via a multi-scale contrastive learning objective (NT-Xent loss) to learn unified cancer-type embeddings. We demonstrate that the resulting latent representations yield biologically meaningful clusters of cancer types, aligning with known mutational processes and tissue origins. Our work represents the first application of contrastive learning to cohort-level cancer clustering, offering a scalable and interpretable framework for mutation-driven cancer subtyping.

The growing demand for AI training data has transformed data annotation into a global industry, but traditional approaches relying on human annotators are often time-consuming, labor-intensive, and prone to inconsistent quality. We propose the Model-in-the-Loop (MILO) framework, which integrates AI/ML models into the annotation process. Our research introduces a collaborative paradigm that leverages the strengths of both professional human annotators and large language models (LLMs). By employing LLMs as pre-annotation and real-time assistants, and judges on annotator responses, MILO enables effective interaction patterns between human annotators and LLMs. Three empirical studies on multimodal data annotation demonstrate MILO's efficacy in reducing handling time, improving data quality, and enhancing annotator experiences. We also introduce quality rubrics for flexible evaluation and fine-grained feedback on open-ended annotations. The MILO framework has implications for accelerating AI/ML development, reducing reliance on human annotation alone, and promoting better alignment between human and machine values.

While there are a plethora of methods for link prediction in knowledge graphs, state-of-the-art approaches are often black box, obfuscating model reasoning and thereby limiting the ability of users to make informed decisions about model predictions. Recently, methods have emerged to generate prediction explanations for Knowledge Graph Embedding models, a widely-used class of methods for link prediction. The question then becomes, how well do these explanation systems work? To date this has generally been addressed anecdotally, or through time-consuming user research. In this work, we present an in-depth exploration of a simple link prediction explanation method we call LinkLogic, that surfaces and ranks explanatory information used for the prediction. Importantly, we construct the first-ever link prediction explanation benchmark, based on family structures present in the FB13 dataset. We demonstrate the use of this benchmark as a rich evaluation sandbox, probing LinkLogic quantitatively and qualitatively to assess the fidelity, selectivity and relevance of the generated explanations. We hope our work paves the way for more holistic and empirical assessment of knowledge graph prediction explanation methods in the future.

When we communicate with other humans, we do not simply generate a sequence of words. Rather, we use our cognitive state (beliefs, desires, intentions) and our model of the audience's cognitive state to create utterances that affect the audience's cognitive state in the intended manner. An important part of cognitive state is the common ground, which is the content the speaker believes, and the speaker believes the audience believes, and so on. While much attention has been paid to common ground in cognitive science, there has not been much work in natural language processing. In this paper, we introduce a new annotation and corpus to capture common ground. We then describe some initial experiments extracting propositions from dialog and tracking their status in the common ground from the perspective of each speaker.

Conventional deep learning methods typically employ supervised learning for drug response prediction (DRP). This entails dependence on labeled response data from drugs for model training. However, practical applications in the preclinical drug screening phase demand that DRP models predict responses for novel compounds, often with unknown drug responses. This presents a challenge, rendering supervised deep learning methods unsuitable for such scenarios. In this paper, we propose a zero-shot learning solution for the DRP task in preclinical drug screening. Specifically, we propose a Multi-branch Multi-Source Domain Adaptation Test Enhancement Plug-in, called MSDA. MSDA can be seamlessly integrated with conventional DRP methods, learning invariant features from the prior response data of similar drugs to enhance real-time predictions of unlabeled compounds. We conducted experiments using the GDSCv2 and CellMiner datasets. The results demonstrate that MSDA efficiently predicts drug responses for novel compounds, leading to a general performance improvement of 5-10\% in the preclinical drug screening phase. The significance of this solution resides in its potential to accelerate the drug discovery process, improve drug candidate assessment, and facilitate the success of drug discovery.

Recent advances in zero-shot image recognition suggest that vision-language models learn generic visual representations with a high degree of semantic information that may be arbitrarily probed with natural language phrases. Understanding an image, however, is not just about understanding what content resides within an image, but importantly, where that content resides. In this work we examine how well vision-language models are able to understand where objects reside within an image and group together visually related parts of the imagery. We demonstrate how contemporary vision and language representation learning models based on contrastive losses and large web-based data capture limited object localization information. We propose a minimal set of modifications that results in models that uniquely learn both semantic and spatial information. We measure this performance in terms of zero-shot image recognition, unsupervised bottom-up and top-down semantic segmentations, as well as robustness analyses. We find that the resulting model achieves state-of-the-art results in terms of unsupervised segmentation, and demonstrate that the learned representations are uniquely robust to spurious correlations in datasets designed to probe the causal behavior of vision models.

In this paper, we present our solutions for the Multimodal Sentiment Analysis Challenge (MuSe) 2022, which includes MuSe-Humor, MuSe-Reaction and MuSe-Stress Sub-challenges. The MuSe 2022 focuses on humor detection, emotional reactions and multimodal emotional stress utilizing different modalities and data sets. In our work, different kinds of multimodal features are extracted, including acoustic, visual, text and biological features. These features are fused by TEMMA and GRU with self-attention mechanism frameworks. In this paper, 1) several new audio features, facial expression features and paragraph-level text embeddings are extracted for accuracy improvement. 2) we substantially improve the accuracy and reliability of multimodal sentiment prediction by mining and blending the multimodal features. 3) effective data augmentation strategies are applied in model training to alleviate the problem of sample imbalance and prevent the model from learning biased subject characters. For the MuSe-Humor sub-challenge, our model obtains the AUC score of 0.8932. For the MuSe-Reaction sub-challenge, the Pearson's Correlations Coefficient of our approach on the test set is 0.3879, which outperforms all other participants. For the MuSe-Stress sub-challenge, our approach outperforms the baseline in both arousal and valence on the test dataset, reaching a final combined result of 0.5151.

The treatment of malaria is a global health challenge that stands to benefit from the widespread introduction of a vaccine for the disease. A method has been developed to create a live organism vaccine using the sporozoites (SPZ) of the parasite Plasmodium falciparum (Pf), which are concentrated in the salivary glands of infected mosquitoes. Current manual dissection methods to obtain these PfSPZ are not optimally efficient for large-scale vaccine production. We propose an improved dissection procedure and a mechanical fixture that increases the rate of mosquito dissection and helps to deskill this stage of the production process. We further demonstrate the automation of a key step in this production process, the picking and placing of mosquitoes from a staging apparatus into a dissection assembly. This unit test of a robotic mosquito pick-and-place system is performed using a custom-designed micro-gripper attached to a four degree of freedom (4-DOF) robot under the guidance of a computer vision system. Mosquitoes are autonomously grasped and pulled to a pair of notched dissection blades to remove the head of the mosquito, allowing access to the salivary glands. Placement into these blades is adapted based on output from computer vision to accommodate for the unique anatomy and orientation of each grasped mosquito. In this pilot test of the system on 50 mosquitoes, we demonstrate a 100% grasping accuracy and a 90% accuracy in placing the mosquito with its neck within the blade notches such that the head can be removed. This is a promising result for this difficult and non-standard pick-and-place task.

The challenge we face today is not a "world without work" but a world with rapidly changing work. This article is part of an MIT SMR initiative exploring how technology is reshaping the practice of management. The pace of progress in AI and machine learning is accelerating rapidly. In the past month alone, these are just a few of the news items I've seen: Deep learning and neural networks have dramatically improved in effectiveness and impact, leading to human-level performance in many aspects of vision, conversational speech, and problem-solving. As a result, industries are in the midst of a major transformation and more is on the way.