Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In this formulation, each node represents a nucleic acid, protein, or metabolite and edges represent intermolecular interactions (inhibition, regulation, promotion, coexpression, etc.). In this work, a novel algorithm for the discovery of latent graph structures given experimental data is presented.

The Government of Kerala had increased the frequency of supply of free food kits owing to the pandemic, however, these items were static and not indicative of the personal preferences of the consumers. This paper conducts a comparative analysis of various clustering techniques on a scaled-down version of a real-world dataset obtained through a conjoint analysis-based survey. Clustering carried out by centroid-based methods such as k means is analyzed and the results are plotted along with SVD, and finally, a conclusion is reached as to which among the two is better. Once the clusters have been formulated, commodities are also decided upon for each cluster. Also, clustering is further enhanced by reassignment, based on a specific cluster loss threshold. Thus, the most efficacious clustering technique for designing a food kit tailored to the needs of individuals is finally obtained.

Over the past decade, neural networks have been successful at making predictions from biological sequences, especially in the context of regulatory genomics. As in other fields of deep learning, tools have been devised to extract features such as sequence motifs that can explain the predictions made by a trained network. Here we intend to go beyond explainable machine learning and introduce SEISM, a selective inference procedure to test the association between these extracted features and the predicted phenotype. In particular, we discuss how training a one-layer convolutional network is formally equivalent to selecting motifs maximizing some association score. We adapt existing sampling-based selective inference procedures by quantizing this selection over an infinite set to a large but finite grid. Finally, we show that sampling under a specific choice of parameters is sufficient to characterize the composite null hypothesis typically used for selective inference-a result that goes well beyond our particular framework. We illustrate the behavior of our method in terms of calibration, power and speed and discuss its power/speed trade-off with a simpler data-split strategy. SEISM paves the way to an easier analysis of neural networks used in regulatory genomics, and to more powerful methods for genome wide association studies (GWAS).

Prior works on improving speech quality with visual input typically study each type of auditory distortion separately (e.g., separation, inpainting, video-to-speech) and present tailored algorithms. This paper proposes to unify these subjects and study Generalized Speech Enhancement, where the goal is not to reconstruct the exact reference clean signal, but to focus on improving certain aspects of speech. In particular, this paper concerns intelligibility, quality, and video synchronization. We cast the problem as audio-visual speech resynthesis, which is composed of two steps: pseudo audio-visual speech recognition (P-AVSR) and pseudo text-to-speech synthesis (P-TTS). P-AVSR and P-TTS are connected by discrete units derived from a self-supervised speech model. Moreover, we utilize self-supervised audio-visual speech model to initialize P-AVSR. The proposed model is coined ReVISE. ReVISE is the first high-quality model for in-the-wild video-to-speech synthesis and achieves superior performance on all LRS3 audio-visual enhancement tasks with a single model. To demonstrates its applicability in the real world, ReVISE is also evaluated on EasyCom, an audio-visual benchmark collected under challenging acoustic conditions with only 1.6 hours of training data. Similarly, ReVISE greatly suppresses noise and improves quality. Project page: https://wnhsu.github.io/ReVISE.

Due to the high activation sparsity and use of accumulates (AC) instead of expensive multiply-and-accumulates (MAC), neuromorphic spiking neural networks (SNNs) have emerged as a promising low-power alternative to traditional DNNs for several computer vision (CV) applications. However, most existing SNNs require multiple time steps for acceptable inference accuracy, hindering real-time deployment and increasing spiking activity and, consequently, energy consumption. Recent works proposed direct encoding that directly feeds the analog pixel values in the first layer of the SNN in order to significantly reduce the number of time steps. Although the overhead for the first layer MACs with direct encoding is negligible for deep SNNs and the CV processing is efficient using SNNs, the data transfer between the image sensors and the downstream processing costs significant bandwidth and may dominate the total energy. To mitigate this concern, we propose an in-sensor computing hardware-software co-design framework for SNNs targeting image recognition tasks. Our approach reduces the bandwidth between sensing and processing by 12-96x and the resulting total energy by 2.32x compared to traditional CV processing, with a 3.8% reduction in accuracy on ImageNet.

Language models (LMs) often generate incoherent outputs: they refer to events and entity states that are incompatible with the state of the world described in their inputs. We introduce SituationSupervision, a family of approaches for improving coherence in LMs by training them to construct and condition on explicit representations of entities and their states. SituationSupervision has two components: an auxiliary situation modeling task that trains models to predict state representations in context, and a latent state inference procedure that imputes these states from partially annotated training data. SituationSupervision can be applied to both fine-tuning (by supervising LMs to encode state variables in their hidden representations) and prompting (by inducing LMs to interleave textual descriptions of entity states with output text). In both cases, SituationSupervision requires only a small number of state annotations to produce major coherence improvements (between 4-11%), showing that standard LMs can be sample-efficiently trained to model not just language but the situations it describes.

We describe PromptBoosting, a query-efficient procedure for building a text classifier from a neural language model (LM) without access to the LM's parameters, gradients, or hidden representations. This form of "black-box" classifier training has become increasingly important as the cost of training and inference in large-scale LMs grows. But existing black-box LM classifier learning approaches are themselves computationally inefficient, typically specializing LMs to the target task by searching in a large space of (discrete or continuous) prompts using zeroth-order optimization methods. Instead of directly optimizing in prompt space, PromptBoosting obtains a small pool of prompts via a gradient-free approach and then constructs a large pool of weak learners by pairing these prompts with different elements of the LM's output distribution. These weak learners are then ensembled using the AdaBoost algorithm. The entire learning process requires only a small number of forward passes and no backward pass. Experiments show that PromptBoosting achieves state-of-the-art performance in multiple black-box few-shot classification tasks, and matches or outperforms full fine-tuning in both few-shot and standard learning paradigms, while training 10x faster than existing black-box methods.

Large language models (LLMs) have shown impressive results across a variety of tasks while requiring little or no direct supervision. Further, there is mounting evidence that LLMs may have potential in information-seeking scenarios. We believe the ability of an LLM to attribute the text that it generates is likely to be crucial for both system developers and users in this setting. We propose and study Attributed QA as a key first step in the development of attributed LLMs. We develop a reproducable evaluation framework for the task, using human annotations as a gold standard and a correlated automatic metric that we show is suitable for development settings. We describe and benchmark a broad set of architectures for the task. Our contributions give some concrete answers to two key questions (How to measure attribution?, and How well do current state-of-the-art methods perform on attribution?), and give some hints as to how to address a third key question (How to build LLMs with attribution?).

Existing techniques for training language models can be misaligned with the truth: if we train models with imitation learning, they may reproduce errors that humans make; if we train them to generate text that humans rate highly, they may output errors that human evaluators can't detect. We propose circumventing this issue by directly finding latent knowledge inside the internal activations of a language model in a purely unsupervised way. Specifically, we introduce a method for accurately answering yes-no questions given only unlabeled model activations. It works by finding a direction in activation space that satisfies logical consistency properties, such as that a statement and its negation have opposite truth values. We show that despite using no supervision and no model outputs, our method can recover diverse knowledge represented in large language models: across 6 models and 10 question-answering datasets, it outperforms zero-shot accuracy by 4\% on average. We also find that it cuts prompt sensitivity in half and continues to maintain high accuracy even when models are prompted to generate incorrect answers. Our results provide an initial step toward discovering what language models know, distinct from what they say, even when we don't have access to explicit ground truth labels.

Sampling-based Model Predictive Control (MPC) is a flexible control framework that can reason about non-smooth dynamics and cost functions. Recently, significant work has focused on the use of machine learning to improve the performance of MPC, often through learning or fine-tuning the dynamics or cost function. In contrast, we focus on learning to optimize more effectively. In other words, to improve the update rule within MPC. We show that this can be particularly useful in sampling-based MPC, where we often wish to minimize the number of samples for computational reasons. Unfortunately, the cost of computational efficiency is a reduction in performance; fewer samples results in noisier updates. We show that we can contend with this noise by learning how to update the control distribution more effectively and make better use of the few samples that we have. Our learned controllers are trained via imitation learning to mimic an expert which has access to substantially more samples. We test the efficacy of our approach on multiple simulated robotics tasks in sample-constrained regimes and demonstrate that our approach can outperform a MPC controller with the same number of samples.