The conference venue Hongo campus of The University of Tokyo is located near Ueno Park, where there are many hotels and restaurants. It will take 20 to 30 minutes walk from Ueno station to the venue (since both Ueno park and Hongo campus are large.) If you are looking for a hotel near the venue, Forest Hongo or Hotel Graphy might be your option. Some of my guests from Europe (they were young post-doc level researchers) said Hotel Graphy was good.
You can also stay at a hotel in your favorite area in Tokyo, such as Ginza, Akihabara, Shibuya, and Shinjuku. Tokyo has a very good train/subway system. It is fast and a system for punctual people. The campus has good access to three subway stations. Todaimae station (N12, Nanboku-line, Tokyo Metro) is a few minutes away from one of the campus gate. Nezu station (C14, Chiyoda Line, Tokyo Metro) and Hongo-sanchome station (M21, Marunouchi Line, Tokyo Metro) are 10 minutes away.
If you have a plan to take a train or subway, we strongly recommend buying a prepaid card named Suica (or Pasmo) at an airport. You can top up it by cache at any train/subway station. The card is also available to pay at a convenience store and a university cafeteria although you would be also able to pay by your credit card. Many vending machines also accept a Suica card. Pasmo is a similar prepaid card issued by a different organization. Suica and Pasmo are interchangeable. You can top up Suica (or Pasmo) by a ticketing machine for Pasmo (or Suica).
Tokyo has two international airports, Narita (NRT) and Haneda (HND). Which airport you arrive at depends on your airline. Although Haneda is much closer to the city center, both airports have good train and bus connections to the city center. For example, a rapid train “Skyliner” connects Ueno and Narita in 40 minutes. If you plan to arrive at Narita, it might be a good idea to stay at a hotel in Ueno.